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  • High Resolution LC/MS Analysis of Therapeutic Oligonucleotides on a New Porous Polymer-Based Reversed Phase Column Julia Baek, Jim Thayer, Shanhua Lin, Hongxia Wang, Ilze Birznieks and Xiaodong LiuThermo Fisher Scientific,Sunnyvale, CA

    Po

    ster No

    te 21515

    Conclusions ON product and n-1 failure sequence, were separated

    on the DNAPac RP column. High resolution orbitrapmass spectrometer revealed loss of each of the four bases.

    RNAi ONs harboring diastereomers of phosphorothioate with our without 2’-O-methyl modifications were separated using high pH mobile phases.

    CpG methylation was successfully identified using DNAPac RP and high resolution mass spectrometer.

    References1. Dias, N. et al. Molecular Cancer Therapeutics (2002) 1,

    347-355.2. Resnier, P. et al. Biomaterials (2013) 34, 6429-6443.3. Jones, P.A. et al. Nature Reviews Genetics (2002) 3,

    415-428.

    Overview Purpose: Demonstrate fast analysis of oligonucleotides (ONs), impurities and structurally modified ONs using ion-pair reversed phase chromatography and ESI-MS.

    Methods: Reverse phase separation of ONs were acheived using Thermo Scientific™ DNAPac™ RP column coupled with Thermo Scientific™ Q Exactive™ Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer. TEA/HFIP mobile phases at two different pH values were used for separation of ONs.

    Results: ON product, n-1 failure sequence, phosphorothioate, 2’-O-methyl modified siRNA strands and CpG methylated ON were successfully separated and identified by LC-MS using short 3 or 5 minute gradients.

    Introduction Synthetic ONs with different functionalities including antisense ONs, small interfering RNAs (siRNAs), aptamers and immunostimulatory RNAs (isRNAs) are candidate therapeutic agents due to their specificity, and well-established synthesis and modification technologies. Still characterization is required to satisfy regulatory agencies that efficacy and safety of these therapeutic ONs are established. Such analyses include characterization of modifications to the base, sugar and backbone linkages, as these are commonly employed to decrease in vivo degradation and increase therapeutic efficacy. High performance LC and LC/MS are the preferred tools for these analyses, and are often used for more common ON purity assessments. Ion-pair reversed phase LC, with volatile mobile phase components, can be directly coupled to MS. Here we introduce a new polymeric reversed phase column and ion-pair methods for LC/MS ON analysis.

    MethodsSamples21mer DNA: GATTGTAGGTTCTCTAACGCT

    21mer siRNA sense strand 1: AGCUGACCCUGAAGSUUCAUdCdT

    21mer siRNA sense strand 2: A-MeOG-C-MeOU-G-MeOA-s-C-MeOC-C-MeOU-G-MeOA-A-MeOG-s-U-MeOU-C-MeOA-U-dCdT15mer DNA: CGGCATCCTTATTGG CpG methylated 15mer DNA: iMe-dC/GGCATCCTTATTGG Liquid ChromatographyHPLC experiments were carried out using a Thermo Scientific™ Dionex™ UltiMate™ 3000 BioRS systemequipped with:

    SR-3000 Solvent Rack (P/N 5035.9200)LPG-3400RS Biocompatible Quaternary Rapid Separation Pump (P/N 5040.0036)WPS-3000TBRS Biocompatible Rapid Separation Thermostatted Autosampler (P/N 5841.0020)TCC-3000RS Rapid Separation Thermostatted Column Compartment (P/N 5730.0000)VWD-3400RS Rapid Separation Variable Wavelength Detector (VWD) equipped with micro flow cell (P/N 5074.0010)Chromatography was controlled by Thermo Scientific™ Dionex™ Chromeleon™ Chromatography Data System .

    Mass SpectrometryThe Q Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer was used for this study. All data were acquired in negative ion mode.

    ResultsAnalysis of failure sequencesSynthetic ONs molecules are used as PCR primers,aptamers, as library adaptors for genomic studies and as therapeutic agents.1,2 High purity ONs in these applications are required. Therefore separation and identification of failure sequences and other impurities is critical for the production of ON drugs.

    In Figure 1a, a 21mer ON was analyzed using mass spec compatible mobile phases (TEA, HFIP). A small peak infront of the target peak was observed. The MS data confirmed the desired target product. Monoisotopic m/z value at charge state -4 for the 21 mer DNA was 1605.016with mass accuracy of 1.87 ppm (Figure 1b). The highresolution mass spectrometer revealed loss of each of the four bases in the n-1 peak. The masses of failure sequences with missing Guanine or Adenine or Cytosine or Thymine were detected (Figure 1c).

    Analysis of phosphorothioate and 2’-O-methyl modified siRNAsSynthetic siRNAs are important tools for gene function studies and as potential therapeutic agents.2 Nucleic acids are often modified to increase in vivo stability. A common modification in DNA and RNA is incorporation of phosphorothioate (PS) linkages. Another common, but RNA-specific modification is 2’-O-methylation on ribose. The PS linkage introduces a chiral center at phosphorus inaddition to the chiral centers in D-ribose of the nucleic acid. Therefore PS modified linkages produce diastereoisomer pairs at each PS linkage.

    Figure 2 shows the separation of a sense strand that has one phosphorothioate linkage incorporated at base 14 inthe sequence. The two possible diastereoisomers were baseline separated on the DNAPac RP column using high pH mobile phases. At -4 charge state, m/z value of first andthe second peaks were 1655.964 and 1655.971 respectively, indicating these molecules to be diastereoisomers rather than failure sequences other impurities.

    © 2016 Thermo Scientific Inc. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries.This information is not intended to encourage use of these products in any manners that might infringe the intellectual property rights of others.

    FIGURE 1. LC-MS analysis of failure sequences. a) UV and ion current traces. b) Mass spectrum of 21mer at -4 charge state. c) Mass spectrum of n-1 failure sequence at -4 charge state.

    FIGURE 2. LC/MS analysis of phosphorothioate modified siRNA

    High Resolution LC/MS Analysis of Therapeutic Oligonucleotides on a new Porous Polymer-Based Reversed Phase ColumnJulia Baek, Jim Thayer, Shanhua Lin, Hongxia Wang, Ilze Birznieks and Xiaodong LiuThermo Fisher Scientific, Sunnyvale, CA

    FIGURE 4. LC/MS analysis of CpG methylation. a) UV and ion current traces. b) Mass spectra of peaks at -3 charge state.

    Analysis of phosphorothioate and 2’-O-methyl modified siRNAsMethylation of CpG sequences in the promoter regions suppresses the expression of the gene and aberrant methylation has been implicated in the development andprogression of cancer.3 Therefore detection of CpG methylation is important for epigenetics studies and cancer research. In Figure 4, an unmodified ON and the CpG methylated ON are well resolved on the DNAPac RPcolumn. Figure 4b shows the -3 charge state of unmodified CpG ON at m/z 1517.919 and the -3 charge state of methylated CpG ON at m/z 1522.593.The mass difference between the methylated and unmodified peaks corresponds to one methyl group.

    FIGURE 3. LC/MS analysis of phosphorothioate and 2’-O-methyl modified siRNA. a) UV and ion current traces. b) Mass spectra of peaks at -4 charge state.

    In Figure 3, sense strand of the siRNA was 2’-O-methylated on alternate bases and contains phosphorothioate linkages at the 6th and 14th bases. TheUV trace and the ion current traces show the separation of all four possible phosphorothioate diastereoisomers. Thehigh resolution MS data reveal identical masses for all four peaks confirming these molecules to be isomers.

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    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 15 mM TEA, 400 mM HFIP, pH 7.9Mobile phase B: 15 mM TEA, 400 mM HFIP in

    Water / Methanol (50:50 v/v)

    Gradient:Time (min) %A %B0.0 70 303.0 48 533.1 10 905.0 10 905.1 70 30

    11.0 70 30

    Temperature: 60 ºCFlow rate: 0.25 mL/minInj. volume: 4 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer DNA

    GATTGTAGGTTCTCTAACGCT

    100

    Mi=1605.0160

    [M+Na+K-6H]4-

    [M-4H]4-

    [M+Na-5H]4-[M+K-5H]4-

    [M+2Na-6H]4-

    1600 1605 1610 1615 1620 1625 1630m/z

    0

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    1615.2522z=4

    1611.0105z=4

    1620.4968z=4 1624.7399

    z=4 1629.9860z=4

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    1520 1522 1524 1526 1528 1530 1532 1534 1536 1538 1540 1542 1544 1546 1548 1550m/z

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    1529.5098z=4

    1527.2569z=4

    z=4

    z=4

    1523.2571z=4

    Mi=1526.7534

    Mi=1522.7602

    Mi=1529.0094

    Mi=1532.2514

    1533.2577z=4

    1535.0061

    1538.9978z=4

    1542.7451z=4

    1536.7438

    1548.4852z=4

    1544.4927z=4 1546.4824

    z=4

    -G

    -A-C

    2 3 4 5 6 7 8Time (min)

    0

    0

    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 35 mM TEA, 40 mM HFIP, pH 9.9Mobile phase B: 35 mM TEA, 40 mM HFIP in Water

    / Methanol (75:25 v/v)

    Gradient:Time (min) %A %B0.0 67 335.0 42 585.1 10 907.0 10 907.1 67 33

    13.0 67 33

    Temperature: 30 ºCFlow rate: 0.25 mL/minInj. volume: 3 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer siRNA

    A-MeOG-C-MeOU-G-MeOA-s-C-MeOC-C-MeOU-G-MeOA-A-MeOG-s-U-MeOU-C-MeOA-U-dCdT

    100

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    Peak 1: RT 5.93 min

    Peak 3: RT 6.23 min[M-4H]4-

    Peak 2: RT 6.13 min

    Peak 4: RT 6.43 min[M-4H]4-

    [M-4H]4-

    1688 1689 1690 1691 1692 1693 1694 1695 1696m/z

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    100

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    1001692.2498

    z=41692.5007z=4

    1691.7489z=4

    1692.9972z=41691.5004

    z=4 1693.5048z=4

    1692.2515z=4

    1692.4994z=41691.7504z=4

    1692.9998z=41691.4985z=4 1693.7490

    z=4

    1692.2498z=41691.7498

    z=4 1692.7501z=4

    1693.0035z=41691.5001z=4 1693.7549

    z=4

    1692.5012z=4

    1692.2517z=4 1692.7518

    z=41691.7488z=4 1693.0029z=41691.5002z=4

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    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 35 mM TEA, 40 mM HFIP, pH 9.9Mobile phase B: 35 mM TEA, 40 mM HFIP in Water /

    Methanol (75:25 v/v)

    Gradient:Time (min) %A %B0.0 93 75.0 52 485.1 10 907.0 10 907.1 93 7

    13.0 93 7

    Temperature: 30 ºCFlow rate: 0.25 mL/minInj. volume: 3 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer siRNA

    AGCUGACCCUGAAGSUUCAUdCdT

    1 2 3 4 5 6 70

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    2Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 15 mM TEA, 400 mM HFIP, pH 7.6Mobile phase B: 15 mM TEA, 400 mM HFIP in

    Water / Methanol (50:50 v/v)

    Gradient:Time (min) %A %B0.0 75 254.0 56 444.1 10 906.0 10 906.1 75 25

    11.0 75 25

    Temperature: 60 ºCFlow rate: 0.25Inj. volume: 3 µL Detection: UV (260 nm)Sample: 1) CGGCATCCTTATTGG

    2) /iMe-dC/GGCATCCTTATTGG

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    1001518.5880

    z=3

    1525.9135z=3 1531.2359z=3

    1532.9063z=3

    1538.5626z=3

    1523.2603z=3

    1530.5860z=3 1535.9079

    z=3

    1524.2618z=3

    1537.5784z=3

    1543.2351z=3

    1529.2527z=3

    z=3

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    1517.9194z=3

    Peak 1

    Peak 2

    [M-3H]3-

    a

    b

    PO21515-EN 0316S

    Conclusions ON product and n-1 failure sequence, were separated

    on the DNAPac RP column. High resolution orbitrapmass spectrometer revealed loss of each of the four bases.

    RNAi ONs harboring diastereomers of phosphorothioate with our without 2’-O-methyl modifications were separated using high pH mobile phases.

    CpG methylation was successfully identified using DNAPac RP and high resolution mass spectrometer.

    References1. Dias, N. et al. Molecular Cancer Therapeutics (2002) 1,

    347-355.2. Resnier, P. et al. Biomaterials (2013) 34, 6429-6443.3. Jones, P.A. et al. Nature Reviews Genetics (2002) 3,

    415-428.

    OverviewPurpose: Demonstrate fast analysis of oligonucleotides(ONs), impurities and structurally modified ONs using ion-pair reversed phase chromatography and ESI-MS.

    Methods: Reverse phase separation of ONs were acheived using Thermo Scientific™ DNAPac™ RP column coupled with Thermo Scientific™ Q Exactive™ Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer. TEA/HFIP mobile phases at two different pH values were used for separation of ONs.

    Results: ON product, n-1 failure sequence, phosphorothioate, 2’-O-methyl modified siRNA strands and CpG methylated ON were successfully separated andidentified by LC-MS using short 3 or 5 minute gradients.

    IntroductionSynthetic ONs with different functionalities including antisense ONs, small interfering RNAs (siRNAs), aptamers and immunostimulatory RNAs (isRNAs) are candidate therapeutic agents due to their specificity, andwell-established synthesis and modification technologies. Still characterization is required to satisfy regulatory agencies that efficacy and safety of these therapeutic ONs are established. Such analyses include characterization of modifications to the base, sugar and backbone linkages, as these are commonly employed to decrease in vivodegradation and increase therapeutic efficacy. High performance LC and LC/MS are the preferred tools for these analyses, and are often used for more common ON purity assessments. Ion-pair reversed phase LC, with volatile mobile phase components, can be directly coupled to MS. Here we introduce a new polymeric reversed phase column and ion-pair methods for LC/MS ON analysis.

    Methods Samples 21mer DNA: GATTGTAGGTTCTCTAACGCT

    21mer siRNA sense strand 1: AGCUGACCCUGAAGSUUCAUdCdT

    21mer siRNA sense strand 2: A-MeOG-C-MeOU-G-MeOA-s-C-MeOC-C-MeOU-G-MeOA-A-MeOG-s-U-MeOU-C-MeOA-U-dCdT 15mer DNA: CGGCATCCTTATTGG CpG methylated 15mer DNA: iMe-dC/GGCATCCTTATTGG Liquid Chromatography HPLC experiments were carried out using a Thermo Scientific™ Dionex™ UltiMate™ 3000 BioRS system equipped with:

    SR-3000 Solvent Rack (P/N 5035.9200)LPG-3400RS Biocompatible Quaternary RapidSeparation Pump (P/N 5040.0036) WPS-3000TBRS Biocompatible Rapid SeparationThermostatted Autosampler (P/N 5841.0020) TCC-3000RS Rapid Separation Thermostatted ColumnCompartment (P/N 5730.0000) VWD-3400RS Rapid Separation Variable WavelengthDetector (VWD) equipped with micro flow cell (P/N 5074.0010) Chromatography was controlled by Thermo Scientific™Dionex™ Chromeleon™ Chromatography Data System .

    Mass Spectrometry The Q Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer was used for this study. All data were acquired in negative ion mode.

    ResultsAnalysis of failure sequencesSynthetic ONs molecules are used as PCR primers,aptamers, as library adaptors for genomic studies and as therapeutic agents.1,2 High purity ONs in these applications are required. Therefore separation and identification of failure sequences and other impurities is critical for the production of ON drugs.

    In Figure 1a, a 21mer ON was analyzed using mass spec compatible mobile phases (TEA, HFIP). A small peak infront of the target peak was observed. The MS data confirmed the desired target product. Monoisotopic m/z value at charge state -4 for the 21 mer DNA was 1605.016with mass accuracy of 1.87 ppm (Figure 1b). The highresolution mass spectrometer revealed loss of each of the four bases in the n-1 peak. The masses of failure sequences with missing Guanine or Adenine or Cytosine or Thymine were detected (Figure 1c).

    Analysis of phosphorothioate and 2’-O-methyl modified siRNAsSynthetic siRNAs are important tools for gene function studies and as potential therapeutic agents.2 Nucleic acids are often modified to increase in vivo stability. A common modification in DNA and RNA is incorporation of phosphorothioate (PS) linkages. Another common, but RNA-specific modification is 2’-O-methylation on ribose. The PS linkage introduces a chiral center at phosphorus inaddition to the chiral centers in D-ribose of the nucleic acid. Therefore PS modified linkages produce diastereoisomer pairs at each PS linkage.

    Figure 2 shows the separation of a sense strand that has one phosphorothioate linkage incorporated at base 14 inthe sequence. The two possible diastereoisomers were baseline separated on the DNAPac RP column using high pH mobile phases. At -4 charge state, m/z value of first andthe second peaks were 1655.964 and 1655.971 respectively, indicating these molecules to be diastereoisomers rather than failure sequences other impurities.

    © 2016 Thermo Scientific Inc. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries.This information is not intended to encourage use of these products in any manners that might infringe the intellectual property rights of others.

    FIGURE 1. LC-MS analysis of failure sequences. a) UV and ion current traces. b) Mass spectrum of 21mer at -4 charge state. c) Mass spectrum of n-1 failure sequence at -4 charge state.

    FIGURE 2. LC/MS analysis of phosphorothioate modified siRNA

    High Resolution LC/MS Analysis of Therapeutic Oligonucleotides on a new Porous Polymer-Based Reversed Phase ColumnJulia Baek, Jim Thayer, Shanhua Lin, Hongxia Wang, Ilze Birznieks and Xiaodong LiuThermo Fisher Scientific, Sunnyvale, CA

    FIGURE 4. LC/MS analysis of CpG methylation. a) UV and ion current traces. b) Mass spectra of peaks at -3 charge state.

    Analysis of phosphorothioate and 2’-O-methyl modified siRNAsMethylation of CpG sequences in the promoter regions suppresses the expression of the gene and aberrant methylation has been implicated in the development andprogression of cancer.3 Therefore detection of CpG methylation is important for epigenetics studies and cancer research. In Figure 4, an unmodified ON and the CpG methylated ON are well resolved on the DNAPac RPcolumn. Figure 4b shows the -3 charge state of unmodified CpG ON at m/z 1517.919 and the -3 charge state of methylated CpG ON at m/z 1522.593.The mass difference between the methylated and unmodified peaks corresponds to one methyl group.

    FIGURE 3. LC/MS analysis of phosphorothioate and 2’-O-methyl modified siRNA. a) UV and ion current traces. b) Mass spectra of peaks at -4 charge state.

    In Figure 3, sense strand of the siRNA was 2’-O-methylated on alternate bases and contains phosphorothioate linkages at the 6th and 14th bases. TheUV trace and the ion current traces show the separation of all four possible phosphorothioate diastereoisomers. Thehigh resolution MS data reveal identical masses for all four peaks confirming these molecules to be isomers.

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    Water / Methanol (50:50 v/v)

    Gradient:Time (min) %A %B0.0 70 303.0 48 533.1 10 905.0 10 905.1 70 30

    11.0 70 30

    Temperature: 60 ºCFlow rate: 0.25 mL/minInj. volume: 4 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer DNA

    GATTGTAGGTTCTCTAACGCT

    100

    Mi=1605.0160

    [M+Na+K-6H]4-

    [M-4H]4-

    [M+Na-5H]4-[M+K-5H]4-

    [M+2Na-6H]4-

    1600 1605 1610 1615 1620 1625 1630m/z

    0

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    1615.2522z=4

    1611.0105z=4

    1620.4968z=4 1624.7399

    z=4 1629.9860z=4

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    RT: 4.10-4.16

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    1527.2569z=4

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    z=4

    1523.2571z=4

    Mi=1526.7534

    Mi=1522.7602

    Mi=1529.0094

    Mi=1532.2514

    1533.2577z=4

    1535.0061

    1538.9978z=4

    1542.7451z=4

    1536.7438

    1548.4852z=4

    1544.4927z=4 1546.4824

    z=4

    -G

    -A-C

    2 3 4 5 6 7 8Time (min)

    0

    0

    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 35 mM TEA, 40 mM HFIP, pH 9.9Mobile phase B: 35 mM TEA, 40 mM HFIP in Water

    / Methanol (75:25 v/v)

    Gradient:Time (min) %A %B0.0 67 335.0 42 585.1 10 907.0 10 907.1 67 33

    13.0 67 33

    Temperature: 30 ºCFlow rate: 0.25 mL/minInj. volume: 3 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer siRNA

    A-MeOG-C-MeOU-G-MeOA-s-C-MeOC-C-MeOU-G-MeOA-A-MeOG-s-U-MeOU-C-MeOA-U-dCdT

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    Peak 1: RT 5.93 min

    Peak 3: RT 6.23 min[M-4H]4-

    Peak 2: RT 6.13 min

    Peak 4: RT 6.43 min[M-4H]4-

    [M-4H]4-

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    1001692.2498

    z=41692.5007z=4

    1691.7489z=4

    1692.9972z=41691.5004

    z=4 1693.5048z=4

    1692.2515z=4

    1692.4994z=41691.7504z=4

    1692.9998z=41691.4985z=4 1693.7490

    z=4

    1692.2498z=41691.7498

    z=4 1692.7501z=4

    1693.0035z=41691.5001z=4 1693.7549

    z=4

    1692.5012z=4

    1692.2517z=4 1692.7518

    z=41691.7488z=4 1693.0029z=41691.5002z=4

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    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 35 mM TEA, 40 mM HFIP, pH 9.9Mobile phase B: 35 mM TEA, 40 mM HFIP in Water /

    Methanol (75:25 v/v)

    Gradient:Time (min) %A %B0.0 93 75.0 52 485.1 10 907.0 10 907.1 93 7

    13.0 93 7

    Temperature: 30 ºCFlow rate: 0.25 mL/minInj. volume: 3 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer siRNA

    AGCUGACCCUGAAGSUUCAUdCdT

    1 2 3 4 5 6 70

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    2Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 15 mM TEA, 400 mM HFIP, pH 7.6Mobile phase B: 15 mM TEA, 400 mM HFIP in

    Water / Methanol (50:50 v/v)

    Gradient:Time (min) %A %B0.0 75 254.0 56 444.1 10 906.0 10 906.1 75 25

    11.0 75 25

    Temperature: 60 ºCFlow rate: 0.25Inj. volume: 3 µL Detection: UV (260 nm)Sample: 1) CGGCATCCTTATTGG

    2) /iMe-dC/GGCATCCTTATTGG

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    1525.9135z=3 1531.2359z=3

    1532.9063z=3

    1538.5626z=3

    1523.2603z=3

    1530.5860z=3 1535.9079

    z=3

    1524.2618z=3

    1537.5784z=3

    1543.2351z=3

    1529.2527z=3

    z=3

    Rel

    ativ

    e Ab

    unda

    nce

    Rel

    ativ

    e Ab

    unda

    nce

    1517.9194z=3

    Peak 1

    Peak 2

    [M-3H]3-

    a

    b

    PO21515-EN 0316S

  • 2 High Resolution LC/MS Analysis of Therapeutic Oligonucleotides on a New Porous Polymer-Based Reversed Phase Column

    Conclusions ON product and n-1 failure sequence, were separated

    on the DNAPac RP column. High resolution orbitrapmass spectrometer revealed loss of each of the four bases.

    RNAi ONs harboring diastereomers of phosphorothioate with our without 2’-O-methyl modifications were separated using high pH mobile phases.

    CpG methylation was successfully identified using DNAPac RP and high resolution mass spectrometer.

    References1. Dias, N. et al. Molecular Cancer Therapeutics (2002) 1,

    347-355.2. Resnier, P. et al. Biomaterials (2013) 34, 6429-6443.3. Jones, P.A. et al. Nature Reviews Genetics (2002) 3,

    415-428.

    OverviewPurpose: Demonstrate fast analysis of oligonucleotides(ONs), impurities and structurally modified ONs using ion-pair reversed phase chromatography and ESI-MS.

    Methods: Reverse phase separation of ONs were acheived using Thermo Scientific™ DNAPac™ RP column coupled with Thermo Scientific™ Q Exactive™ Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer. TEA/HFIP mobile phases at two different pH values were used for separation of ONs.

    Results: ON product, n-1 failure sequence, phosphorothioate, 2’-O-methyl modified siRNA strands and CpG methylated ON were successfully separated andidentified by LC-MS using short 3 or 5 minute gradients.

    IntroductionSynthetic ONs with different functionalities including antisense ONs, small interfering RNAs (siRNAs), aptamers and immunostimulatory RNAs (isRNAs) are candidate therapeutic agents due to their specificity, andwell-established synthesis and modification technologies. Still characterization is required to satisfy regulatory agencies that efficacy and safety of these therapeutic ONs are established. Such analyses include characterization of modifications to the base, sugar and backbone linkages, as these are commonly employed to decrease in vivodegradation and increase therapeutic efficacy. High performance LC and LC/MS are the preferred tools for these analyses, and are often used for more common ON purity assessments. Ion-pair reversed phase LC, with volatile mobile phase components, can be directly coupled to MS. Here we introduce a new polymeric reversed phase column and ion-pair methods for LC/MS ON analysis.

    MethodsSamples21mer DNA: GATTGTAGGTTCTCTAACGCT

    21mer siRNA sense strand 1: AGCUGACCCUGAAGSUUCAUdCdT

    21mer siRNA sense strand 2: A-MeOG-C-MeOU-G-MeOA-s-C-MeOC-C-MeOU-G-MeOA-A-MeOG-s-U-MeOU-C-MeOA-U-dCdT15mer DNA: CGGCATCCTTATTGG CpG methylated 15mer DNA: iMe-dC/GGCATCCTTATTGG Liquid ChromatographyHPLC experiments were carried out using a Thermo Scientific™ Dionex™ UltiMate™ 3000 BioRS systemequipped with:

    SR-3000 Solvent Rack (P/N 5035.9200)LPG-3400RS Biocompatible Quaternary Rapid Separation Pump (P/N 5040.0036)WPS-3000TBRS Biocompatible Rapid Separation Thermostatted Autosampler (P/N 5841.0020)TCC-3000RS Rapid Separation Thermostatted Column Compartment (P/N 5730.0000)VWD-3400RS Rapid Separation Variable Wavelength Detector (VWD) equipped with micro flow cell (P/N 5074.0010)Chromatography was controlled by Thermo Scientific™ Dionex™ Chromeleon™ Chromatography Data System .

    Mass SpectrometryThe Q Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer was used for this study. All data were acquired in negative ion mode.

    Results Analysis of failure sequences Synthetic ONs molecules are used as PCR primers, aptamers, as library adaptors for genomic studies and as therapeutic agents.1,2 High purity ONs in these applications are required. Therefore separation and identification of failure sequences and other impurities is critical for the production of ON drugs.

    In Figure 1a, a 21mer ON was analyzed using mass spec compatible mobile phases (TEA, HFIP). A small peak in front of the target peak was observed. The MS data confirmed the desired target product. Monoisotopic m/z value at charge state -4 for the 21 mer DNA was 1605.016 with mass accuracy of 1.87 ppm (Figure 1b). The high resolution mass spectrometer revealed loss of each of the four bases in the n-1 peak. The masses of failure sequences with missing Guanine or Adenine or Cytosine or Thymine were detected (Figure 1c).

    Analysis of phosphorothioate and 2’-O-methyl modified siRNAsSynthetic siRNAs are important tools for gene function studies and as potential therapeutic agents.2 Nucleic acids are often modified to increase in vivo stability. A common modification in DNA and RNA is incorporation of phosphorothioate (PS) linkages. Another common, but RNA-specific modification is 2’-O-methylation on ribose. The PS linkage introduces a chiral center at phosphorus inaddition to the chiral centers in D-ribose of the nucleic acid. Therefore PS modified linkages produce diastereoisomer pairs at each PS linkage.

    Figure 2 shows the separation of a sense strand that has one phosphorothioate linkage incorporated at base 14 inthe sequence. The two possible diastereoisomers were baseline separated on the DNAPac RP column using high pH mobile phases. At -4 charge state, m/z value of first andthe second peaks were 1655.964 and 1655.971 respectively, indicating these molecules to be diastereoisomers rather than failure sequences other impurities.

    © 2016 Thermo Scientific Inc. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries.This information is not intended to encourage use of these products in any manners that might infringe the intellectual property rights of others.

    FIGURE 1. LC-MS analysis of failure sequences. a) UV and ion current traces. b) Mass spectrum of 21mer at -4 charge state. c) Mass spectrum of n-1 failure sequence at -4 charge state.

    FIGURE 2. LC/MS analysis of phosphorothioate modified siRNA

    High Resolution LC/MS Analysis of Therapeutic Oligonucleotides on a new Porous Polymer-Based Reversed Phase ColumnJulia Baek, Jim Thayer, Shanhua Lin, Hongxia Wang, Ilze Birznieks and Xiaodong LiuThermo Fisher Scientific, Sunnyvale, CA

    FIGURE 4. LC/MS analysis of CpG methylation. a) UV and ion current traces. b) Mass spectra of peaks at -3 charge state.

    Analysis of phosphorothioate and 2’-O-methyl modified siRNAsMethylation of CpG sequences in the promoter regions suppresses the expression of the gene and aberrant methylation has been implicated in the development andprogression of cancer.3 Therefore detection of CpG methylation is important for epigenetics studies and cancer research. In Figure 4, an unmodified ON and the CpG methylated ON are well resolved on the DNAPac RPcolumn. Figure 4b shows the -3 charge state of unmodified CpG ON at m/z 1517.919 and the -3 charge state of methylated CpG ON at m/z 1522.593.The mass difference between the methylated and unmodified peaks corresponds to one methyl group.

    FIGURE 3. LC/MS analysis of phosphorothioate and 2’-O-methyl modified siRNA. a) UV and ion current traces. b) Mass spectra of peaks at -4 charge state.

    In Figure 3, sense strand of the siRNA was 2’-O-methylated on alternate bases and contains phosphorothioate linkages at the 6th and 14th bases. TheUV trace and the ion current traces show the separation of all four possible phosphorothioate diastereoisomers. Thehigh resolution MS data reveal identical masses for all four peaks confirming these molecules to be isomers.

    1 2 3 4 5Time (min)

    0

    240

    100

    Rel

    ativ

    e Ab

    unda

    nce

    Abso

    rban

    ce (m

    AU)

    Ion current

    UV

    n

    n-1

    n

    n-1

    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 15 mM TEA, 400 mM HFIP, pH 7.9Mobile phase B: 15 mM TEA, 400 mM HFIP in

    Water / Methanol (50:50 v/v)

    Gradient:Time (min) %A %B0.0 70 303.0 48 533.1 10 905.0 10 905.1 70 30

    11.0 70 30

    Temperature: 60 ºCFlow rate: 0.25 mL/minInj. volume: 4 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer DNA

    GATTGTAGGTTCTCTAACGCT

    100

    Mi=1605.0160

    [M+Na+K-6H]4-

    [M-4H]4-

    [M+Na-5H]4-[M+K-5H]4-

    [M+2Na-6H]4-

    1600 1605 1610 1615 1620 1625 1630m/z

    0

    20

    40

    60

    80

    1615.2522z=4

    1611.0105z=4

    1620.4968z=4 1624.7399

    z=4 1629.9860z=4

    Rel

    ativ

    e Ab

    unda

    nce

    RT: 4.10-4.16

    a

    b

    c -T

    1520 1522 1524 1526 1528 1530 1532 1534 1536 1538 1540 1542 1544 1546 1548 1550m/z

    0

    20

    40

    60

    80

    100

    Rel

    ativ

    e Abu

    ndan

    ce

    1529.5098z=4

    1527.2569z=4

    z=4

    z=4

    1523.2571z=4

    Mi=1526.7534

    Mi=1522.7602

    Mi=1529.0094

    Mi=1532.2514

    1533.2577z=4

    1535.0061

    1538.9978z=4

    1542.7451z=4

    1536.7438

    1548.4852z=4

    1544.4927z=4 1546.4824

    z=4

    -G

    -A-C

    2 3 4 5 6 7 8Time (min)

    0

    0

    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 35 mM TEA, 40 mM HFIP, pH 9.9Mobile phase B: 35 mM TEA, 40 mM HFIP in Water

    / Methanol (75:25 v/v)

    Gradient:Time (min) %A %B0.0 67 335.0 42 585.1 10 907.0 10 907.1 67 33

    13.0 67 33

    Temperature: 30 ºCFlow rate: 0.25 mL/minInj. volume: 3 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer siRNA

    A-MeOG-C-MeOU-G-MeOA-s-C-MeOC-C-MeOU-G-MeOA-A-MeOG-s-U-MeOU-C-MeOA-U-dCdT

    100

    16

    Ion current

    UV

    Rel

    ativ

    e Ab

    unda

    nce

    Abso

    rban

    ce (m

    AU)

    1

    23

    4

    1

    2 3

    4

    a

    [M-4H]4-

    Peak 1: RT 5.93 min

    Peak 3: RT 6.23 min[M-4H]4-

    Peak 2: RT 6.13 min

    Peak 4: RT 6.43 min[M-4H]4-

    [M-4H]4-

    1688 1689 1690 1691 1692 1693 1694 1695 1696m/z

    0

    100

    0

    100

    0

    100

    0

    1001692.2498

    z=41692.5007z=4

    1691.7489z=4

    1692.9972z=41691.5004

    z=4 1693.5048z=4

    1692.2515z=4

    1692.4994z=41691.7504z=4

    1692.9998z=41691.4985z=4 1693.7490

    z=4

    1692.2498z=41691.7498

    z=4 1692.7501z=4

    1693.0035z=41691.5001z=4 1693.7549

    z=4

    1692.5012z=4

    1692.2517z=4 1692.7518

    z=41691.7488z=4 1693.0029z=41691.5002z=4

    Rel

    ativ

    e Ab

    unda

    nce

    b

    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 35 mM TEA, 40 mM HFIP, pH 9.9Mobile phase B: 35 mM TEA, 40 mM HFIP in Water /

    Methanol (75:25 v/v)

    Gradient:Time (min) %A %B0.0 93 75.0 52 485.1 10 907.0 10 907.1 93 7

    13.0 93 7

    Temperature: 30 ºCFlow rate: 0.25 mL/minInj. volume: 3 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer siRNA

    AGCUGACCCUGAAGSUUCAUdCdT

    1 2 3 4 5 6 70

    0

    100

    Rel

    ativ

    e Ab

    unda

    nce

    Abso

    rban

    ce (m

    AU)

    Ion current

    UV40

    1

    2

    12

    Time (min)

    2Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 15 mM TEA, 400 mM HFIP, pH 7.6Mobile phase B: 15 mM TEA, 400 mM HFIP in

    Water / Methanol (50:50 v/v)

    Gradient:Time (min) %A %B0.0 75 254.0 56 444.1 10 906.0 10 906.1 75 25

    11.0 75 25

    Temperature: 60 ºCFlow rate: 0.25Inj. volume: 3 µL Detection: UV (260 nm)Sample: 1) CGGCATCCTTATTGG

    2) /iMe-dC/GGCATCCTTATTGG

    1 2 3 4 5 6 7Time (min)

    0

    0

    100

    40

    Rel

    ativ

    e Ab

    unda

    nce

    Abso

    rban

    ce (m

    AU)

    1

    12

    1522.5926

    1510 1515 1520 1525 1530 1535 1540 1545 1550m/z

    0

    20

    40

    60

    80

    100

    0

    20

    40

    60

    80

    1001518.5880

    z=3

    1525.9135z=3 1531.2359z=3

    1532.9063z=3

    1538.5626z=3

    1523.2603z=3

    1530.5860z=3 1535.9079

    z=3

    1524.2618z=3

    1537.5784z=3

    1543.2351z=3

    1529.2527z=3

    z=3

    Rel

    ativ

    e Ab

    unda

    nce

    Rel

    ativ

    e Ab

    unda

    nce

    1517.9194z=3

    Peak 1

    Peak 2

    [M-3H]3-

    a

    b

    PO21515-EN 0316S

    Conclusions ON product and n-1 failure sequence, were separated

    on the DNAPac RP column. High resolution orbitrapmass spectrometer revealed loss of each of the four bases.

    RNAi ONs harboring diastereomers of phosphorothioate with our without 2’-O-methyl modifications were separated using high pH mobile phases.

    CpG methylation was successfully identified using DNAPac RP and high resolution mass spectrometer.

    References1. Dias, N. et al. Molecular Cancer Therapeutics (2002) 1,

    347-355.2. Resnier, P. et al. Biomaterials (2013) 34, 6429-6443.3. Jones, P.A. et al. Nature Reviews Genetics (2002) 3,

    415-428.

    OverviewPurpose: Demonstrate fast analysis of oligonucleotides(ONs), impurities and structurally modified ONs using ion-pair reversed phase chromatography and ESI-MS.

    Methods: Reverse phase separation of ONs were acheived using Thermo Scientific™ DNAPac™ RP column coupled with Thermo Scientific™ Q Exactive™ Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer. TEA/HFIP mobile phases at two different pH values were used for separation of ONs.

    Results: ON product, n-1 failure sequence, phosphorothioate, 2’-O-methyl modified siRNA strands and CpG methylated ON were successfully separated andidentified by LC-MS using short 3 or 5 minute gradients.

    IntroductionSynthetic ONs with different functionalities including antisense ONs, small interfering RNAs (siRNAs), aptamers and immunostimulatory RNAs (isRNAs) are candidate therapeutic agents due to their specificity, andwell-established synthesis and modification technologies. Still characterization is required to satisfy regulatory agencies that efficacy and safety of these therapeutic ONs are established. Such analyses include characterization of modifications to the base, sugar and backbone linkages, as these are commonly employed to decrease in vivodegradation and increase therapeutic efficacy. High performance LC and LC/MS are the preferred tools for these analyses, and are often used for more common ON purity assessments. Ion-pair reversed phase LC, with volatile mobile phase components, can be directly coupled to MS. Here we introduce a new polymeric reversed phase column and ion-pair methods for LC/MS ON analysis.

    MethodsSamples21mer DNA: GATTGTAGGTTCTCTAACGCT

    21mer siRNA sense strand 1: AGCUGACCCUGAAGSUUCAUdCdT

    21mer siRNA sense strand 2: A-MeOG-C-MeOU-G-MeOA-s-C-MeOC-C-MeOU-G-MeOA-A-MeOG-s-U-MeOU-C-MeOA-U-dCdT15mer DNA: CGGCATCCTTATTGG CpG methylated 15mer DNA: iMe-dC/GGCATCCTTATTGG Liquid ChromatographyHPLC experiments were carried out using a Thermo Scientific™ Dionex™ UltiMate™ 3000 BioRS systemequipped with:

    SR-3000 Solvent Rack (P/N 5035.9200)LPG-3400RS Biocompatible Quaternary Rapid Separation Pump (P/N 5040.0036)WPS-3000TBRS Biocompatible Rapid Separation Thermostatted Autosampler (P/N 5841.0020)TCC-3000RS Rapid Separation Thermostatted Column Compartment (P/N 5730.0000)VWD-3400RS Rapid Separation Variable Wavelength Detector (VWD) equipped with micro flow cell (P/N 5074.0010)Chromatography was controlled by Thermo Scientific™ Dionex™ Chromeleon™ Chromatography Data System .

    Mass SpectrometryThe Q Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer was used for this study. All data were acquired in negative ion mode.

    ResultsAnalysis of failure sequencesSynthetic ONs molecules are used as PCR primers,aptamers, as library adaptors for genomic studies and as therapeutic agents.1,2 High purity ONs in these applications are required. Therefore separation and identification of failure sequences and other impurities is critical for the production of ON drugs.

    In Figure 1a, a 21mer ON was analyzed using mass spec compatible mobile phases (TEA, HFIP). A small peak infront of the target peak was observed. The MS data confirmed the desired target product. Monoisotopic m/z value at charge state -4 for the 21 mer DNA was 1605.016with mass accuracy of 1.87 ppm (Figure 1b). The highresolution mass spectrometer revealed loss of each of the four bases in the n-1 peak. The masses of failure sequences with missing Guanine or Adenine or Cytosine or Thymine were detected (Figure 1c).

    Analysis of phosphorothioate and 2’-O-methyl modified siRNAsSynthetic siRNAs are important tools for gene function studies and as potential therapeutic agents.2 Nucleic acids are often modified to increase in vivo stability. A common modification in DNA and RNA is incorporation of phosphorothioate (PS) linkages. Another common, but RNA-specific modification is 2’-O-methylation on ribose. The PS linkage introduces a chiral center at phosphorus inaddition to the chiral centers in D-ribose of the nucleic acid. Therefore PS modified linkages produce diastereoisomer pairs at each PS linkage.

    Figure 2 shows the separation of a sense strand that has one phosphorothioate linkage incorporated at base 14 inthe sequence. The two possible diastereoisomers were baseline separated on the DNAPac RP column using high pH mobile phases. At -4 charge state, m/z value of first andthe second peaks were 1655.964 and 1655.971 respectively, indicating these molecules to be diastereoisomers rather than failure sequences other impurities.

    © 2016 Thermo Scientific Inc. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries.This information is not intended to encourage use of these products in any manners that might infringe the intellectual property rights of others.

    FIGURE 1. LC-MS analysis of failure sequences. a) UV and ion current traces. b) Mass spectrum of 21mer at -4 charge state. c) Mass spectrum of n-1 failure sequence at -4 charge state.

    FIGURE 2. LC/MS analysis of phosphorothioate modified siRNA

    High Resolution LC/MS Analysis of Therapeutic Oligonucleotides on a new Porous Polymer-Based Reversed Phase ColumnJulia Baek, Jim Thayer, Shanhua Lin, Hongxia Wang, Ilze Birznieks and Xiaodong LiuThermo Fisher Scientific, Sunnyvale, CA

    FIGURE 4. LC/MS analysis of CpG methylation. a) UV and ion current traces. b) Mass spectra of peaks at -3 charge state.

    Analysis of phosphorothioate and 2’-O-methyl modified siRNAsMethylation of CpG sequences in the promoter regions suppresses the expression of the gene and aberrant methylation has been implicated in the development andprogression of cancer.3 Therefore detection of CpG methylation is important for epigenetics studies and cancer research. In Figure 4, an unmodified ON and the CpG methylated ON are well resolved on the DNAPac RPcolumn. Figure 4b shows the -3 charge state of unmodified CpG ON at m/z 1517.919 and the -3 charge state of methylated CpG ON at m/z 1522.593.The mass difference between the methylated and unmodified peaks corresponds to one methyl group.

    FIGURE 3. LC/MS analysis of phosphorothioate and 2’-O-methyl modified siRNA. a) UV and ion current traces. b) Mass spectra of peaks at -4 charge state.

    In Figure 3, sense strand of the siRNA was 2’-O-methylated on alternate bases and contains phosphorothioate linkages at the 6th and 14th bases. TheUV trace and the ion current traces show the separation of all four possible phosphorothioate diastereoisomers. Thehigh resolution MS data reveal identical masses for all four peaks confirming these molecules to be isomers.

    1 2 3 4 5Time (min)

    0

    240

    100

    Rel

    ativ

    e Ab

    unda

    nce

    Abso

    rban

    ce (m

    AU)

    Ion current

    UV

    n

    n-1

    n

    n-1

    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 15 mM TEA, 400 mM HFIP, pH 7.9Mobile phase B: 15 mM TEA, 400 mM HFIP in

    Water / Methanol (50:50 v/v)

    Gradient:Time (min) %A %B0.0 70 303.0 48 533.1 10 905.0 10 905.1 70 30

    11.0 70 30

    Temperature: 60 ºCFlow rate: 0.25 mL/minInj. volume: 4 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer DNA

    GATTGTAGGTTCTCTAACGCT

    100

    Mi=1605.0160

    [M+Na+K-6H]4-

    [M-4H]4-

    [M+Na-5H]4-[M+K-5H]4-

    [M+2Na-6H]4-

    1600 1605 1610 1615 1620 1625 1630m/z

    0

    20

    40

    60

    80

    1615.2522z=4

    1611.0105z=4

    1620.4968z=4 1624.7399

    z=4 1629.9860z=4

    Rel

    ativ

    e Ab

    unda

    nce

    RT: 4.10-4.16

    a

    b

    c -T

    1520 1522 1524 1526 1528 1530 1532 1534 1536 1538 1540 1542 1544 1546 1548 1550m/z

    0

    20

    40

    60

    80

    100

    Rel

    ativ

    e Abu

    ndan

    ce

    1529.5098z=4

    1527.2569z=4

    z=4

    z=4

    1523.2571z=4

    Mi=1526.7534

    Mi=1522.7602

    Mi=1529.0094

    Mi=1532.2514

    1533.2577z=4

    1535.0061

    1538.9978z=4

    1542.7451z=4

    1536.7438

    1548.4852z=4

    1544.4927z=4 1546.4824

    z=4

    -G

    -A-C

    2 3 4 5 6 7 8Time (min)

    0

    0

    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 35 mM TEA, 40 mM HFIP, pH 9.9Mobile phase B: 35 mM TEA, 40 mM HFIP in Water

    / Methanol (75:25 v/v)

    Gradient:Time (min) %A %B0.0 67 335.0 42 585.1 10 907.0 10 907.1 67 33

    13.0 67 33

    Temperature: 30 ºCFlow rate: 0.25 mL/minInj. volume: 3 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer siRNA

    A-MeOG-C-MeOU-G-MeOA-s-C-MeOC-C-MeOU-G-MeOA-A-MeOG-s-U-MeOU-C-MeOA-U-dCdT

    100

    16

    Ion current

    UV

    Rel

    ativ

    e Ab

    unda

    nce

    Abso

    rban

    ce (m

    AU)

    1

    23

    4

    1

    2 3

    4

    a

    [M-4H]4-

    Peak 1: RT 5.93 min

    Peak 3: RT 6.23 min[M-4H]4-

    Peak 2: RT 6.13 min

    Peak 4: RT 6.43 min[M-4H]4-

    [M-4H]4-

    1688 1689 1690 1691 1692 1693 1694 1695 1696m/z

    0

    100

    0

    100

    0

    100

    0

    1001692.2498

    z=41692.5007z=4

    1691.7489z=4

    1692.9972z=41691.5004

    z=4 1693.5048z=4

    1692.2515z=4

    1692.4994z=41691.7504z=4

    1692.9998z=41691.4985z=4 1693.7490

    z=4

    1692.2498z=41691.7498

    z=4 1692.7501z=4

    1693.0035z=41691.5001z=4 1693.7549

    z=4

    1692.5012z=4

    1692.2517z=4 1692.7518

    z=41691.7488z=4 1693.0029z=41691.5002z=4

    Rel

    ativ

    e Ab

    unda

    nce

    b

    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 35 mM TEA, 40 mM HFIP, pH 9.9Mobile phase B: 35 mM TEA, 40 mM HFIP in Water /

    Methanol (75:25 v/v)

    Gradient:Time (min) %A %B0.0 93 75.0 52 485.1 10 907.0 10 907.1 93 7

    13.0 93 7

    Temperature: 30 ºCFlow rate: 0.25 mL/minInj. volume: 3 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer siRNA

    AGCUGACCCUGAAGSUUCAUdCdT

    1 2 3 4 5 6 70

    0

    100

    Rel

    ativ

    e Ab

    unda

    nce

    Abso

    rban

    ce (m

    AU)

    Ion current

    UV40

    1

    2

    12

    Time (min)

    2Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 15 mM TEA, 400 mM HFIP, pH 7.6Mobile phase B: 15 mM TEA, 400 mM HFIP in

    Water / Methanol (50:50 v/v)

    Gradient:Time (min) %A %B0.0 75 254.0 56 444.1 10 906.0 10 906.1 75 25

    11.0 75 25

    Temperature: 60 ºCFlow rate: 0.25Inj. volume: 3 µL Detection: UV (260 nm)Sample: 1) CGGCATCCTTATTGG

    2) /iMe-dC/GGCATCCTTATTGG

    1 2 3 4 5 6 7Time (min)

    0

    0

    100

    40

    Rel

    ativ

    e Ab

    unda

    nce

    Abso

    rban

    ce (m

    AU)

    1

    12

    1522.5926

    1510 1515 1520 1525 1530 1535 1540 1545 1550m/z

    0

    20

    40

    60

    80

    100

    0

    20

    40

    60

    80

    1001518.5880

    z=3

    1525.9135z=3 1531.2359z=3

    1532.9063z=3

    1538.5626z=3

    1523.2603z=3

    1530.5860z=3 1535.9079

    z=3

    1524.2618z=3

    1537.5784z=3

    1543.2351z=3

    1529.2527z=3

    z=3

    Rel

    ativ

    e Ab

    unda

    nce

    Rel

    ativ

    e Ab

    unda

    nce

    1517.9194z=3

    Peak 1

    Peak 2

    [M-3H]3-

    a

    b

    PO21515-EN 0316S

    Conclusions ON product and n-1 failure sequence, were separated

    on the DNAPac RP column. High resolution orbitrapmass spectrometer revealed loss of each of the four bases.

    RNAi ONs harboring diastereomers of phosphorothioate with our without 2’-O-methyl modifications were separated using high pH mobile phases.

    CpG methylation was successfully identified using DNAPac RP and high resolution mass spectrometer.

    References1. Dias, N. et al. Molecular Cancer Therapeutics (2002) 1,

    347-355.2. Resnier, P. et al. Biomaterials (2013) 34, 6429-6443.3. Jones, P.A. et al. Nature Reviews Genetics (2002) 3,

    415-428.

    OverviewPurpose: Demonstrate fast analysis of oligonucleotides(ONs), impurities and structurally modified ONs using ion-pair reversed phase chromatography and ESI-MS.

    Methods: Reverse phase separation of ONs were acheived using Thermo Scientific™ DNAPac™ RP column coupled with Thermo Scientific™ Q Exactive™ Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer. TEA/HFIP mobile phases at two different pH values were used for separation of ONs.

    Results: ON product, n-1 failure sequence, phosphorothioate, 2’-O-methyl modified siRNA strands and CpG methylated ON were successfully separated andidentified by LC-MS using short 3 or 5 minute gradients.

    IntroductionSynthetic ONs with different functionalities including antisense ONs, small interfering RNAs (siRNAs), aptamers and immunostimulatory RNAs (isRNAs) are candidate therapeutic agents due to their specificity, andwell-established synthesis and modification technologies. Still characterization is required to satisfy regulatory agencies that efficacy and safety of these therapeutic ONs are established. Such analyses include characterization of modifications to the base, sugar and backbone linkages, as these are commonly employed to decrease in vivodegradation and increase therapeutic efficacy. High performance LC and LC/MS are the preferred tools for these analyses, and are often used for more common ON purity assessments. Ion-pair reversed phase LC, with volatile mobile phase components, can be directly coupled to MS. Here we introduce a new polymeric reversed phase column and ion-pair methods for LC/MS ON analysis.

    MethodsSamples21mer DNA: GATTGTAGGTTCTCTAACGCT

    21mer siRNA sense strand 1: AGCUGACCCUGAAGSUUCAUdCdT

    21mer siRNA sense strand 2: A-MeOG-C-MeOU-G-MeOA-s-C-MeOC-C-MeOU-G-MeOA-A-MeOG-s-U-MeOU-C-MeOA-U-dCdT15mer DNA: CGGCATCCTTATTGG CpG methylated 15mer DNA: iMe-dC/GGCATCCTTATTGG Liquid ChromatographyHPLC experiments were carried out using a Thermo Scientific™ Dionex™ UltiMate™ 3000 BioRS systemequipped with:

    SR-3000 Solvent Rack (P/N 5035.9200)LPG-3400RS Biocompatible Quaternary Rapid Separation Pump (P/N 5040.0036)WPS-3000TBRS Biocompatible Rapid Separation Thermostatted Autosampler (P/N 5841.0020)TCC-3000RS Rapid Separation Thermostatted Column Compartment (P/N 5730.0000)VWD-3400RS Rapid Separation Variable Wavelength Detector (VWD) equipped with micro flow cell (P/N 5074.0010)Chromatography was controlled by Thermo Scientific™ Dionex™ Chromeleon™ Chromatography Data System .

    Mass SpectrometryThe Q Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer was used for this study. All data were acquired in negative ion mode.

    ResultsAnalysis of failure sequencesSynthetic ONs molecules are used as PCR primers,aptamers, as library adaptors for genomic studies and as therapeutic agents.1,2 High purity ONs in these applications are required. Therefore separation and identification of failure sequences and other impurities is critical for the production of ON drugs.

    In Figure 1a, a 21mer ON was analyzed using mass spec compatible mobile phases (TEA, HFIP). A small peak infront of the target peak was observed. The MS data confirmed the desired target product. Monoisotopic m/z value at charge state -4 for the 21 mer DNA was 1605.016with mass accuracy of 1.87 ppm (Figure 1b). The highresolution mass spectrometer revealed loss of each of the four bases in the n-1 peak. The masses of failure sequences with missing Guanine or Adenine or Cytosine or Thymine were detected (Figure 1c).

    Analysis of phosphorothioate and 2’-O-methyl modified siRNAs Synthetic siRNAs are important tools for gene function studies and as potential therapeutic agents.2 Nucleic acids are often modified to increase in vivo stability. A common modification in DNA and RNA is incorporation of phosphorothioate (PS) linkages. Another common, but RNA-specific modification is 2’-O-methylation on ribose. The PS linkage introduces a chiral center at phosphorus in addition to the chiral centers in D-ribose of the nucleic acid. Therefore PS modified linkages produce diastereoisomer pairs at each PS linkage.

    Figure 2 shows the separation of a sense strand that has one phosphorothioate linkage incorporated at base 14 in the sequence. The two possible diastereoisomers were baseline separated on the DNAPac RP column using high pH mobile phases. At -4 charge state, m/z value of first and the second peaks were 1655.964 and 1655.971 respectively, indicating these molecules to be diastereoisomers rather than failure sequences other impurities.

    © 2016 Thermo Scientific Inc. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries.This information is not intended to encourage use of these products in any manners that might infringe the intellectual property rights of others.

    FIGURE 1. LC-MS analysis of failure sequences. a) UV and ion current traces. b) Mass spectrum of 21mer at -4 charge state. c) Mass spectrum of n-1 failure sequence at -4 charge state.

    FIGURE 2. LC/MS analysis of phosphorothioate modified siRNA

    High Resolution LC/MS Analysis of Therapeutic Oligonucleotides on a new Porous Polymer-Based Reversed Phase ColumnJulia Baek, Jim Thayer, Shanhua Lin, Hongxia Wang, Ilze Birznieks and Xiaodong LiuThermo Fisher Scientific, Sunnyvale, CA

    FIGURE 4. LC/MS analysis of CpG methylation. a) UV and ion current traces. b) Mass spectra of peaks at -3 charge state.

    Analysis of phosphorothioate and 2’-O-methyl modified siRNAsMethylation of CpG sequences in the promoter regions suppresses the expression of the gene and aberrant methylation has been implicated in the development andprogression of cancer.3 Therefore detection of CpG methylation is important for epigenetics studies and cancer research. In Figure 4, an unmodified ON and the CpG methylated ON are well resolved on the DNAPac RPcolumn. Figure 4b shows the -3 charge state of unmodified CpG ON at m/z 1517.919 and the -3 charge state of methylated CpG ON at m/z 1522.593.The mass difference between the methylated and unmodified peaks corresponds to one methyl group.

    FIGURE 3. LC/MS analysis of phosphorothioate and 2’-O-methyl modified siRNA. a) UV and ion current traces. b) Mass spectra of peaks at -4 charge state.

    In Figure 3, sense strand of the siRNA was 2’-O-methylated on alternate bases and contains phosphorothioate linkages at the 6th and 14th bases. TheUV trace and the ion current traces show the separation of all four possible phosphorothioate diastereoisomers. Thehigh resolution MS data reveal identical masses for all four peaks confirming these molecules to be isomers.

    1 2 3 4 5Time (min)

    0

    240

    100

    Rel

    ativ

    e Ab

    unda

    nce

    Abso

    rban

    ce (m

    AU)

    Ion current

    UV

    n

    n-1

    n

    n-1

    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 15 mM TEA, 400 mM HFIP, pH 7.9Mobile phase B: 15 mM TEA, 400 mM HFIP in

    Water / Methanol (50:50 v/v)

    Gradient:Time (min) %A %B0.0 70 303.0 48 533.1 10 905.0 10 905.1 70 30

    11.0 70 30

    Temperature: 60 ºCFlow rate: 0.25 mL/minInj. volume: 4 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer DNA

    GATTGTAGGTTCTCTAACGCT

    100

    Mi=1605.0160

    [M+Na+K-6H]4-

    [M-4H]4-

    [M+Na-5H]4-[M+K-5H]4-

    [M+2Na-6H]4-

    1600 1605 1610 1615 1620 1625 1630m/z

    0

    20

    40

    60

    80

    1615.2522z=4

    1611.0105z=4

    1620.4968z=4 1624.7399

    z=4 1629.9860z=4

    Rel

    ativ

    e Ab

    unda

    nce

    RT: 4.10-4.16

    a

    b

    c -T

    1520 1522 1524 1526 1528 1530 1532 1534 1536 1538 1540 1542 1544 1546 1548 1550m/z

    0

    20

    40

    60

    80

    100

    Rel

    ativ

    e Abu

    ndan

    ce

    1529.5098z=4

    1527.2569z=4

    z=4

    z=4

    1523.2571z=4

    Mi=1526.7534

    Mi=1522.7602

    Mi=1529.0094

    Mi=1532.2514

    1533.2577z=4

    1535.0061

    1538.9978z=4

    1542.7451z=4

    1536.7438

    1548.4852z=4

    1544.4927z=4 1546.4824

    z=4

    -G

    -A-C

    2 3 4 5 6 7 8Time (min)

    0

    0

    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 35 mM TEA, 40 mM HFIP, pH 9.9Mobile phase B: 35 mM TEA, 40 mM HFIP in Water

    / Methanol (75:25 v/v)

    Gradient:Time (min) %A %B0.0 67 335.0 42 585.1 10 907.0 10 907.1 67 33

    13.0 67 33

    Temperature: 30 ºCFlow rate: 0.25 mL/minInj. volume: 3 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer siRNA

    A-MeOG-C-MeOU-G-MeOA-s-C-MeOC-C-MeOU-G-MeOA-A-MeOG-s-U-MeOU-C-MeOA-U-dCdT

    100

    16

    Ion current

    UV

    Rel

    ativ

    e Ab

    unda

    nce

    Abso

    rban

    ce (m

    AU)

    1

    23

    4

    1

    2 3

    4

    a

    [M-4H]4-

    Peak 1: RT 5.93 min

    Peak 3: RT 6.23 min[M-4H]4-

    Peak 2: RT 6.13 min

    Peak 4: RT 6.43 min[M-4H]4-

    [M-4H]4-

    1688 1689 1690 1691 1692 1693 1694 1695 1696m/z

    0

    100

    0

    100

    0

    100

    0

    1001692.2498

    z=41692.5007z=4

    1691.7489z=4

    1692.9972z=41691.5004

    z=4 1693.5048z=4

    1692.2515z=4

    1692.4994z=41691.7504z=4

    1692.9998z=41691.4985z=4 1693.7490

    z=4

    1692.2498z=41691.7498

    z=4 1692.7501z=4

    1693.0035z=41691.5001z=4 1693.7549

    z=4

    1692.5012z=4

    1692.2517z=4 1692.7518

    z=41691.7488z=4 1693.0029z=41691.5002z=4

    Rel

    ativ

    e Ab

    unda

    nce

    b

    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 35 mM TEA, 40 mM HFIP, pH 9.9Mobile phase B: 35 mM TEA, 40 mM HFIP in Water /

    Methanol (75:25 v/v)

    Gradient:Time (min) %A %B0.0 93 75.0 52 485.1 10 907.0 10 907.1 93 7

    13.0 93 7

    Temperature: 30 ºCFlow rate: 0.25 mL/minInj. volume: 3 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer siRNA

    AGCUGACCCUGAAGSUUCAUdCdT

    1 2 3 4 5 6 70

    0

    100R

    elat

    ive

    Abun

    danc

    eAb

    sorb

    ance

    (mAU

    )Ion current

    UV40

    1

    2

    12

    Time (min)

    2Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 15 mM TEA, 400 mM HFIP, pH 7.6Mobile phase B: 15 mM TEA, 400 mM HFIP in

    Water / Methanol (50:50 v/v)

    Gradient:Time (min) %A %B0.0 75 254.0 56 444.1 10 906.0 10 906.1 75 25

    11.0 75 25

    Temperature: 60 ºCFlow rate: 0.25Inj. volume: 3 µL Detection: UV (260 nm)Sample: 1) CGGCATCCTTATTGG

    2) /iMe-dC/GGCATCCTTATTGG

    1 2 3 4 5 6 7Time (min)

    0

    0

    100

    40

    Rel

    ativ

    e Ab

    unda

    nce

    Abso

    rban

    ce (m

    AU)

    1

    12

    1522.5926

    1510 1515 1520 1525 1530 1535 1540 1545 1550m/z

    0

    20

    40

    60

    80

    100

    0

    20

    40

    60

    80

    1001518.5880

    z=3

    1525.9135z=3 1531.2359z=3

    1532.9063z=3

    1538.5626z=3

    1523.2603z=3

    1530.5860z=3 1535.9079

    z=3

    1524.2618z=3

    1537.5784z=3

    1543.2351z=3

    1529.2527z=3

    z=3

    Rel

    ativ

    e Ab

    unda

    nce

    Rel

    ativ

    e Ab

    unda

    nce

    1517.9194z=3

    Peak 1

    Peak 2

    [M-3H]3-

    a

    b

    PO21515-EN 0316S

  • Conclusions ON product and n-1 failure sequence, were separated

    on the DNAPac RP column. High resolution orbitrapmass spectrometer revealed loss of each of the four bases.

    RNAi ONs harboring diastereomers of phosphorothioate with our without 2’-O-methyl modifications were separated using high pH mobile phases.

    CpG methylation was successfully identified using DNAPac RP and high resolution mass spectrometer.

    References1. Dias, N. et al. Molecular Cancer Therapeutics (2002) 1,

    347-355.2. Resnier, P. et al. Biomaterials (2013) 34, 6429-6443.3. Jones, P.A. et al. Nature Reviews Genetics (2002) 3,

    415-428.

    OverviewPurpose: Demonstrate fast analysis of oligonucleotides(ONs), impurities and structurally modified ONs using ion-pair reversed phase chromatography and ESI-MS.

    Methods: Reverse phase separation of ONs were acheived using Thermo Scientific™ DNAPac™ RP column coupled with Thermo Scientific™ Q Exactive™ Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer. TEA/HFIP mobile phases at two different pH values were used for separation of ONs.

    Results: ON product, n-1 failure sequence, phosphorothioate, 2’-O-methyl modified siRNA strands and CpG methylated ON were successfully separated andidentified by LC-MS using short 3 or 5 minute gradients.

    IntroductionSynthetic ONs with different functionalities including antisense ONs, small interfering RNAs (siRNAs), aptamers and immunostimulatory RNAs (isRNAs) are candidate therapeutic agents due to their specificity, andwell-established synthesis and modification technologies. Still characterization is required to satisfy regulatory agencies that efficacy and safety of these therapeutic ONs are established. Such analyses include characterization of modifications to the base, sugar and backbone linkages, as these are commonly employed to decrease in vivodegradation and increase therapeutic efficacy. High performance LC and LC/MS are the preferred tools for these analyses, and are often used for more common ON purity assessments. Ion-pair reversed phase LC, with volatile mobile phase components, can be directly coupled to MS. Here we introduce a new polymeric reversed phase column and ion-pair methods for LC/MS ON analysis.

    MethodsSamples21mer DNA: GATTGTAGGTTCTCTAACGCT

    21mer siRNA sense strand 1: AGCUGACCCUGAAGSUUCAUdCdT

    21mer siRNA sense strand 2: A-MeOG-C-MeOU-G-MeOA-s-C-MeOC-C-MeOU-G-MeOA-A-MeOG-s-U-MeOU-C-MeOA-U-dCdT15mer DNA: CGGCATCCTTATTGG CpG methylated 15mer DNA: iMe-dC/GGCATCCTTATTGG Liquid ChromatographyHPLC experiments were carried out using a Thermo Scientific™ Dionex™ UltiMate™ 3000 BioRS systemequipped with:

    SR-3000 Solvent Rack (P/N 5035.9200)LPG-3400RS Biocompatible Quaternary Rapid Separation Pump (P/N 5040.0036)WPS-3000TBRS Biocompatible Rapid Separation Thermostatted Autosampler (P/N 5841.0020)TCC-3000RS Rapid Separation Thermostatted Column Compartment (P/N 5730.0000)VWD-3400RS Rapid Separation Variable Wavelength Detector (VWD) equipped with micro flow cell (P/N 5074.0010)Chromatography was controlled by Thermo Scientific™ Dionex™ Chromeleon™ Chromatography Data System .

    Mass SpectrometryThe Q Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer was used for this study. All data were acquired in negative ion mode.

    ResultsAnalysis of failure sequencesSynthetic ONs molecules are used as PCR primers,aptamers, as library adaptors for genomic studies and as therapeutic agents.1,2 High purity ONs in these applications are required. Therefore separation and identification of failure sequences and other impurities is critical for the production of ON drugs.

    In Figure 1a, a 21mer ON was analyzed using mass spec compatible mobile phases (TEA, HFIP). A small peak infront of the target peak was observed. The MS data confirmed the desired target product. Monoisotopic m/z value at charge state -4 for the 21 mer DNA was 1605.016with mass accuracy of 1.87 ppm (Figure 1b). The highresolution mass spectrometer revealed loss of each of the four bases in the n-1 peak. The masses of failure sequences with missing Guanine or Adenine or Cytosine or Thymine were detected (Figure 1c).

    Analysis of phosphorothioate and 2’-O-methyl modified siRNAsSynthetic siRNAs are important tools for gene function studies and as potential therapeutic agents.2 Nucleic acids are often modified to increase in vivo stability. A common modification in DNA and RNA is incorporation of phosphorothioate (PS) linkages. Another common, but RNA-specific modification is 2’-O-methylation on ribose. The PS linkage introduces a chiral center at phosphorus inaddition to the chiral centers in D-ribose of the nucleic acid. Therefore PS modified linkages produce diastereoisomer pairs at each PS linkage.

    Figure 2 shows the separation of a sense strand that has one phosphorothioate linkage incorporated at base 14 inthe sequence. The two possible diastereoisomers were baseline separated on the DNAPac RP column using high pH mobile phases. At -4 charge state, m/z value of first andthe second peaks were 1655.964 and 1655.971 respectively, indicating these molecules to be diastereoisomers rather than failure sequences other impurities.

    © 2016 Thermo Scientific Inc. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries.This information is not intended to encourage use of these products in any manners that might infringe the intellectual property rights of others.

    FIGURE 1. LC-MS analysis of failure sequences. a) UV and ion current traces. b) Mass spectrum of 21mer at -4 charge state. c) Mass spectrum of n-1 failure sequence at -4 charge state.

    FIGURE 2. LC/MS analysis of phosphorothioate modified siRNA

    High Resolution LC/MS Analysis of Therapeutic Oligonucleotides on a new Porous Polymer-Based Reversed Phase ColumnJulia Baek, Jim Thayer, Shanhua Lin, Hongxia Wang, Ilze Birznieks and Xiaodong LiuThermo Fisher Scientific, Sunnyvale, CA

    FIGURE 4. LC/MS analysis of CpG methylation. a) UV and ion current traces. b) Mass spectra of peaks at -3 charge state.

    Analysis of phosphorothioate and 2’-O-methyl modified siRNAs Methylation of CpG sequences in the promoter regions suppresses the expression of the gene and aberrant methylation has been implicated in the development and progression of cancer.3 Therefore detection of CpG methylation is important for epigenetics studies and cancer research. In Figure 4, an unmodified ON and the CpG methylated ON are well resolved on the DNAPac RP column. Figure 4b shows the -3 charge state of unmodified CpG ON at m/z 1517.919 and the -3 charge state of methylated CpG ON at m/z 1522.593.The mass difference between the methylated and unmodified peaks corresponds to one methyl group.

    FIGURE 3. LC/MS analysis of phosphorothioate and 2’-O-methyl modified siRNA. a) UV and ion current traces. b) Mass spectra of peaks at -4 charge state.

    In Figure 3, sense strand of the siRNA was 2’-O-methylated on alternate bases and contains phosphorothioate linkages at the 6th and 14th bases. The UV trace and the ion current traces show the separation of all four possible phosphorothioate diastereoisomers. The high resolution MS data reveal identical masses for all four peaks confirming these molecules to be isomers.

    1 2 3 4 5Time (min)

    0

    240

    100

    Rel

    ativ

    e Ab

    unda

    nce

    Abso

    rban

    ce (m

    AU)

    Ion current

    UV

    n

    n-1

    n

    n-1

    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 15 mM TEA, 400 mM HFIP, pH 7.9Mobile phase B: 15 mM TEA, 400 mM HFIP in

    Water / Methanol (50:50 v/v)

    Gradient:Time (min) %A %B0.0 70 303.0 48 533.1 10 905.0 10 905.1 70 30

    11.0 70 30

    Temperature: 60 ºCFlow rate: 0.25 mL/minInj. volume: 4 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer DNA

    GATTGTAGGTTCTCTAACGCT

    100

    Mi=1605.0160

    [M+Na+K-6H]4-

    [M-4H]4-

    [M+Na-5H]4-[M+K-5H]4-

    [M+2Na-6H]4-

    1600 1605 1610 1615 1620 1625 1630m/z

    0

    20

    40

    60

    80

    1615.2522z=4

    1611.0105z=4

    1620.4968z=4 1624.7399

    z=4 1629.9860z=4

    Rel

    ativ

    e Ab

    unda

    nce

    RT: 4.10-4.16

    a

    b

    c -T

    1520 1522 1524 1526 1528 1530 1532 1534 1536 1538 1540 1542 1544 1546 1548 1550m/z

    0

    20

    40

    60

    80

    100

    Rel

    ativ

    e Abu

    ndan

    ce

    1529.5098z=4

    1527.2569z=4

    z=4

    z=4

    1523.2571z=4

    Mi=1526.7534

    Mi=1522.7602

    Mi=1529.0094

    Mi=1532.2514

    1533.2577z=4

    1535.0061

    1538.9978z=4

    1542.7451z=4

    1536.7438

    1548.4852z=4

    1544.4927z=4 1546.4824

    z=4

    -G

    -A-C

    2 3 4 5 6 7 8Time (min)

    0

    0

    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 35 mM TEA, 40 mM HFIP, pH 9.9Mobile phase B: 35 mM TEA, 40 mM HFIP in Water

    / Methanol (75:25 v/v)

    Gradient:Time (min) %A %B0.0 67 335.0 42 585.1 10 907.0 10 907.1 67 33

    13.0 67 33

    Temperature: 30 ºCFlow rate: 0.25 mL/minInj. volume: 3 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer siRNA

    A-MeOG-C-MeOU-G-MeOA-s-C-MeOC-C-MeOU-G-MeOA-A-MeOG-s-U-MeOU-C-MeOA-U-dCdT

    100

    16

    Ion current

    UV

    Rel

    ativ

    e Ab

    unda

    nce

    Abso

    rban

    ce (m

    AU)

    1

    23

    4

    1

    2 3

    4

    a

    [M-4H]4-

    Peak 1: RT 5.93 min

    Peak 3: RT 6.23 min[M-4H]4-

    Peak 2: RT 6.13 min

    Peak 4: RT 6.43 min[M-4H]4-

    [M-4H]4-

    1688 1689 1690 1691 1692 1693 1694 1695 1696m/z

    0

    100

    0

    100

    0

    100

    0

    1001692.2498

    z=41692.5007z=4

    1691.7489z=4

    1692.9972z=41691.5004

    z=4 1693.5048z=4

    1692.2515z=4

    1692.4994z=41691.7504z=4

    1692.9998z=41691.4985z=4 1693.7490

    z=4

    1692.2498z=41691.7498

    z=4 1692.7501z=4

    1693.0035z=41691.5001z=4 1693.7549

    z=4

    1692.5012z=4

    1692.2517z=4 1692.7518

    z=41691.7488z=4 1693.0029z=41691.5002z=4

    Rel

    ativ

    e Ab

    unda

    nce

    b

    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 35 mM TEA, 40 mM HFIP, pH 9.9Mobile phase B: 35 mM TEA, 40 mM HFIP in Water /

    Methanol (75:25 v/v)

    Gradient:Time (min) %A %B0.0 93 75.0 52 485.1 10 907.0 10 907.1 93 7

    13.0 93 7

    Temperature: 30 ºCFlow rate: 0.25 mL/minInj. volume: 3 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer siRNA

    AGCUGACCCUGAAGSUUCAUdCdT

    1 2 3 4 5 6 70

    0

    100

    Rel

    ativ

    e Ab

    unda

    nce

    Abso

    rban

    ce (m

    AU)

    Ion current

    UV40

    1

    2

    12

    Time (min)

    2Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 15 mM TEA, 400 mM HFIP, pH 7.6Mobile phase B: 15 mM TEA, 400 mM HFIP in

    Water / Methanol (50:50 v/v)

    Gradient:Time (min) %A %B0.0 75 254.0 56 444.1 10 906.0 10 906.1 75 25

    11.0 75 25

    Temperature: 60 ºCFlow rate: 0.25Inj. volume: 3 µL Detection: UV (260 nm)Sample: 1) CGGCATCCTTATTGG

    2) /iMe-dC/GGCATCCTTATTGG

    1 2 3 4 5 6 7Time (min)

    0

    0

    100

    40

    Rel

    ativ

    e Ab

    unda

    nce

    Abso

    rban

    ce (m

    AU)

    1

    12

    1522.5926

    1510 1515 1520 1525 1530 1535 1540 1545 1550m/z

    0

    20

    40

    60

    80

    100

    0

    20

    40

    60

    80

    1001518.5880

    z=3

    1525.9135z=3 1531.2359z=3

    1532.9063z=3

    1538.5626z=3

    1523.2603z=3

    1530.5860z=3 1535.9079

    z=3

    1524.2618z=3

    1537.5784z=3

    1543.2351z=3

    1529.2527z=3

    z=3

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    1517.9194z=3

    Peak 1

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    a

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    PO21515-EN 0316S

    Conclusions ON product and n-1 failure sequence, were separated

    on the DNAPac RP column. High resolution orbitrapmass spectrometer revealed loss of each of the fourbases.

    RNAi ONs harboring diastereomers ofphosphorothioate with our without 2’-O-methylmodifications were separated using high pH mobilephases.

    CpG methylation was successfully identified usingDNAPac RP and high resolution mass spectrometer.

    References 1. Dias, N. et al. Molecular Cancer Therapeutics (2002) 1,

    347-355.2. Resnier, P. et al. Biomaterials (2013) 34, 6429-6443.3. Jones, P.A. et al. Nature Reviews Genetics (2002) 3,

    415-428.

    OverviewPurpose: Demonstrate fast analysis of oligonucleotides(ONs), impurities and structurally modified ONs using ion-pair reversed phase chromatography and ESI-MS.

    Methods: Reverse phase separation of ONs were acheived using Thermo Scientific™ DNAPac™ RP column coupled with Thermo Scientific™ Q Exactive™ Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer. TEA/HFIP mobile phases at two different pH values were used for separation of ONs.

    Results: ON product, n-1 failure sequence, phosphorothioate, 2’-O-methyl modified siRNA strands and CpG methylated ON were successfully separated andidentified by LC-MS using short 3 or 5 minute gradients.

    IntroductionSynthetic ONs with different functionalities including antisense ONs, small interfering RNAs (siRNAs), aptamers and immunostimulatory RNAs (isRNAs) are candidate therapeutic agents due to their specificity, andwell-established synthesis and modification technologies. Still characterization is required to satisfy regulatory agencies that efficacy and safety of these therapeutic ONs are established. Such analyses include characterization of modifications to the base, sugar and backbone linkages, as these are commonly employed to decrease in vivodegradation and increase therapeutic efficacy. High performance LC and LC/MS are the preferred tools for these analyses, and are often used for more common ON purity assessments. Ion-pair reversed phase LC, with volatile mobile phase components, can be directly coupled to MS. Here we introduce a new polymeric reversed phase column and ion-pair methods for LC/MS ON analysis.

    MethodsSamples21mer DNA: GATTGTAGGTTCTCTAACGCT

    21mer siRNA sense strand 1: AGCUGACCCUGAAGSUUCAUdCdT

    21mer siRNA sense strand 2: A-MeOG-C-MeOU-G-MeOA-s-C-MeOC-C-MeOU-G-MeOA-A-MeOG-s-U-MeOU-C-MeOA-U-dCdT15mer DNA: CGGCATCCTTATTGG CpG methylated 15mer DNA: iMe-dC/GGCATCCTTATTGG Liquid ChromatographyHPLC experiments were carried out using a Thermo Scientific™ Dionex™ UltiMate™ 3000 BioRS systemequipped with:

    SR-3000 Solvent Rack (P/N 5035.9200)LPG-3400RS Biocompatible Quaternary Rapid Separation Pump (P/N 5040.0036)WPS-3000TBRS Biocompatible Rapid Separation Thermostatted Autosampler (P/N 5841.0020)TCC-3000RS Rapid Separation Thermostatted Column Compartment (P/N 5730.0000)VWD-3400RS Rapid Separation Variable Wavelength Detector (VWD) equipped with micro flow cell (P/N 5074.0010)Chromatography was controlled by Thermo Scientific™ Dionex™ Chromeleon™ Chromatography Data System .

    Mass SpectrometryThe Q Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer was used for this study. All data were acquired in negative ion mode.

    ResultsAnalysis of failure sequencesSynthetic ONs molecules are used as PCR primers,aptamers, as library adaptors for genomic studies and as therapeutic agents.1,2 High purity ONs in these applications are required. Therefore separation and identification of failure sequences and other impurities is critical for the production of ON drugs.

    In Figure 1a, a 21mer ON was analyzed using mass spec compatible mobile phases (TEA, HFIP). A small peak infront of the target peak was observed. The MS data confirmed the desired target product. Monoisotopic m/z value at charge state -4 for the 21 mer DNA was 1605.016with mass accuracy of 1.87 ppm (Figure 1b). The highresolution mass spectrometer revealed loss of each of the four bases in the n-1 peak. The masses of failure sequences with missing Guanine or Adenine or Cytosine or Thymine were detected (Figure 1c).

    Analysis of phosphorothioate and 2’-O-methyl modified siRNAsSynthetic siRNAs are important tools for gene function studies and as potential therapeutic agents.2 Nucleic acids are often modified to increase in vivo stability. A common modification in DNA and RNA is incorporation of phosphorothioate (PS) linkages. Another common, but RNA-specific modification is 2’-O-methylation on ribose. The PS linkage introduces a chiral center at phosphorus inaddition to the chiral centers in D-ribose of the nucleic acid. Therefore PS modified linkages produce diastereoisomer pairs at each PS linkage.

    Figure 2 shows the separation of a sense strand that has one phosphorothioate linkage incorporated at base 14 inthe sequence. The two possible diastereoisomers were baseline separated on the DNAPac RP column using high pH mobile phases. At -4 charge state, m/z value of first andthe second peaks were 1655.964 and 1655.971 respectively, indicating these molecules to be diastereoisomers rather than failure sequences other impurities.

    © 2016 Thermo Scientific Inc. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries.This information is not intended to encourage use of these products in any manners that might infringe the intellectual property rights of others.

    FIGURE 1. LC-MS analysis of failure sequences. a) UV and ion current traces. b) Mass spectrum of 21mer at -4 charge state. c) Mass spectrum of n-1 failure sequence at -4 charge state.

    FIGURE 2. LC/MS analysis of phosphorothioate modified siRNA

    High Resolution LC/MS Analysis of Therapeutic Oligonucleotides on a new Porous Polymer-Based Reversed Phase ColumnJulia Baek, Jim Thayer, Shanhua Lin, Hongxia Wang, Ilze Birznieks and Xiaodong LiuThermo Fisher Scientific, Sunnyvale, CA

    FIGURE 4. LC/MS analysis of CpG methylation. a) UV and ion current traces. b) Mass spectra of peaks at -3 charge state.

    Analysis of phosphorothioate and 2’-O-methyl modified siRNAsMethylation of CpG sequences in the promoter regions suppresses the expression of the gene and aberrant methylation has been implicated in the development andprogression of cancer.3 Therefore detection of CpG methylation is important for epigenetics studies and cancer research. In Figure 4, an unmodified ON and the CpG methylated ON are well resolved on the DNAPac RPcolumn. Figure 4b shows the -3 charge state of unmodified CpG ON at m/z 1517.919 and the -3 charge state of methylated CpG ON at m/z 1522.593.The mass difference between the methylated and unmodified peaks corresponds to one methyl group.

    FIGURE 3. LC/MS analysis of phosphorothioate and 2’-O-methyl modified siRNA. a) UV and ion current traces. b) Mass spectra of peaks at -4 charge state.

    In Figure 3, sense strand of the siRNA was 2’-O-methylated on alternate bases and contains phosphorothioate linkages at the 6th and 14th bases. TheUV trace and the ion current traces show the separation of all four possible phosphorothioate diastereoisomers. Thehigh resolution MS data reveal identical masses for all four peaks confirming these molecules to be isomers.

    1 2 3 4 5Time (min)

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    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 15 mM TEA, 400 mM HFIP, pH 7.9Mobile phase B: 15 mM TEA, 400 mM HFIP in

    Water / Methanol (50:50 v/v)

    Gradient:Time (min) %A %B0.0 70 303.0 48 533.1 10 905.0 10 905.1 70 30

    11.0 70 30

    Temperature: 60 ºCFlow rate: 0.25 mL/minInj. volume: 4 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer DNA

    GATTGTAGGTTCTCTAACGCT

    100

    Mi=1605.0160

    [M+Na+K-6H]4-

    [M-4H]4-

    [M+Na-5H]4-[M+K-5H]4-

    [M+2Na-6H]4-

    1600 1605 1610 1615 1620 1625 1630m/z

    0

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    60

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    1615.2522z=4

    1611.0105z=4

    1620.4968z=4 1624.7399

    z=4 1629.9860z=4

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    RT: 4.10-4.16

    a

    b

    c -T

    1520 1522 1524 1526 1528 1530 1532 1534 1536 1538 1540 1542 1544 1546 1548 1550m/z

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    1529.5098z=4

    1527.2569z=4

    z=4

    z=4

    1523.2571z=4

    Mi=1526.7534

    Mi=1522.7602

    Mi=1529.0094

    Mi=1532.2514

    1533.2577z=4

    1535.0061

    1538.9978z=4

    1542.7451z=4

    1536.7438

    1548.4852z=4

    1544.4927z=4 1546.4824

    z=4

    -G

    -A-C

    2 3 4 5 6 7 8Time (min)

    0

    0

    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 35 mM TEA, 40 mM HFIP, pH 9.9Mobile phase B: 35 mM TEA, 40 mM HFIP in Water

    / Methanol (75:25 v/v)

    Gradient:Time (min) %A %B0.0 67 335.0 42 585.1 10 907.0 10 907.1 67 33

    13.0 67 33

    Temperature: 30 ºCFlow rate: 0.25 mL/minInj. volume: 3 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer siRNA

    A-MeOG-C-MeOU-G-MeOA-s-C-MeOC-C-MeOU-G-MeOA-A-MeOG-s-U-MeOU-C-MeOA-U-dCdT

    100

    16

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    Peak 1: RT 5.93 min

    Peak 3: RT 6.23 min[M-4H]4-

    Peak 2: RT 6.13 min

    Peak 4: RT 6.43 min[M-4H]4-

    [M-4H]4-

    1688 1689 1690 1691 1692 1693 1694 1695 1696m/z

    0

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    1001692.2498

    z=41692.5007z=4

    1691.7489z=4

    1692.9972z=41691.5004

    z=4 1693.5048z=4

    1692.2515z=4

    1692.4994z=41691.7504z=4

    1692.9998z=41691.4985z=4 1693.7490

    z=4

    1692.2498z=41691.7498

    z=4 1692.7501z=4

    1693.0035z=41691.5001z=4 1693.7549

    z=4

    1692.5012z=4

    1692.2517z=4 1692.7518

    z=41691.7488z=4 1693.0029z=41691.5002z=4

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    Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 35 mM TEA, 40 mM HFIP, pH 9.9Mobile phase B: 35 mM TEA, 40 mM HFIP in Water /

    Methanol (75:25 v/v)

    Gradient:Time (min) %A %B0.0 93 75.0 52 485.1 10 907.0 10 907.1 93 7

    13.0 93 7

    Temperature: 30 ºCFlow rate: 0.25 mL/minInj. volume: 3 µL Detection: UV (260 nm)

    MS (Negative-ion mode)Mass Spec: Q Exactive PlusSample: 21mer siRNA

    AGCUGACCCUGAAGSUUCAUdCdT

    1 2 3 4 5 6 70

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    Time (min)

    2Column: DNAPac RP, 4 µmFormat: 2.1 50 mmMobile phase A: 15 mM TEA, 400 mM HFIP, pH 7.6Mobile phase B: 15 mM TEA, 400 mM HFIP in

    Water / Methanol (50:50 v/v)

    Gradient:Time (min) %A %B0.0 75 254.0 56 444.1 10 906.0 10 906.1 75 25

    11.0 75 25

    Temperature: 60 ºCFlow rate: 0.25Inj. volume: 3 µL Detection: UV (260 nm)Sample: 1) CGGCATCCTTATTGG

    2) /iMe-dC/GGCATCCTTATTGG

    1 2 3 4 5 6 7Time (min)

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    1510 1515 1520 1525 1530 1535 1540 1545 1550m/z

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    1001518.5880

    z=3

    1525.9135z=3 1531.2359z=3

    1532.9063z=3

    1538.5626z=3

    1523.2603z=3

    1530.5860z=3 1535.9079

    z=3

    1524.2618z=3

    1537.5784z=3

    1543.2351z=3

    1529.2527z=3

    z=3R

    elat

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    1517.9194z=3

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    PO21515-EN 0316S

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