Enzymes for manipulating DNA
*** Buffers and solution conditions***
I. DNA polymerasesIII. Kinase and alkaline phosphataseIV. NucleasesV. Topoisomerase
Course Readings: 19 and 20
Buffers are crucial for activity of enzymes!
Ideal biochemical buffers:
•pKa between 6 and 8•Chemically inert•Polar (soluble and not membrane permeable)•Non-toxic•Inexpensive•Salt and temperature indifferent
Tris: pKa is 8.0
Tris(hydroxymethyl)aminomethane (THAM): the free base for (pH 7.5-8.5)Tris-HCl: the acidic form (for pH 7-8)
Tris is widely used, but it isn’t perfect:
•Buffering is weak below pH 7.5 and above pH 9.0•pH must be measured using a special pH meter electrode•Toxic to many types of mammalian cell cultures•Tris solution pH changes with temperature! Drops 0.03 pH units for each degree C increase•Tris solution pH changes with concentration! Example: 10mM Tris pH 7.9, 100mM Tris pH 8.0
•Below pH 7.5, use a “Good” buffer: HEPES, Tricine, BES, MOPS, MES
Enzyme “reaction buffers”:
•Buffer: Tris, HEPES, etc.•Salt: NaCl, KCl, PO4
-, etc.--stabilizes protein structure, facilitates protein-DNA interactions•Divalent metal ions: Mg2+, Ca2+, Zn2+, etc.--often required for enzyme activity•Glycerol: (for storage)--stabilizes protein structure•EDTA: chelates (removes) divalent cations--important especially for storage, if your enzyme is especially sensitive to metal ion-dependent proteases•Beta mercaptoethanol or dithiothreitol: reducing agents that prevent illegitimate disulfide bond formation•Non-specific protein: Bovine serum albumin (BSA)•Other cofactors, eg. ATP, NADH
DNA polymerases--making copies, adding labels, or fixing
DNA
E. coli DNA polymerase I --the classic DNA polymerase– Moderately processive polymerase– 3'->5' proof-reading exonuclease– 5'->3' strand-displacing (nick-
translating) exonuclease– Used mostly for labelling DNA
molecules by nick translation. For other purposes, the Klenow fragment is usually preferred
• Klenow fragment --the C-terminal 70% of E. coli DNA polymerase I; originally prepared as a proteolytic fragment (discovered by Klenow); now cloned– Lacks the 5'->3' exonuclease activity– Uses include:
• Labeling DNA termini by filling in the cohesive ends generated by certain restriction enzymes
•generation of blunt ends•DNA sequencing
DNA polymerases
A way of making blunt ended DNA (repair after mechanical fragmentation)
A way of radiolabeling DNA
DNA polymerases
• Native T7 DNA polymerase --highly processive, with highly active 3'->5' exonuclease– Useful for extensive DNA synthesis on long,
single-stranded (e.g. M13) templates– Useful for labeling DNA termini and for
converting protruding ends to blunt ends• Modified T7 polymerase (Sequenase) --lack of
both 3'->5' exonuclease and 5'->3' exonuclease– Ideal for sequencing, due to high processivity– Efficiently incorporates dNTPs at low
concentrations, making it ideal for labeling DNA
DNA polymerases
• Reverse transcriptase– RNA-dependent DNA polymerase– Essential for making cDNA copies of
RNA transcripts
– Cloning intron-less genes– Quantitation of RNA
Reverse transcriptase:
The Km for dNTPs is very high (relatively non-processive)
Makes a DNA copy of RNA or DNA
-- but --
The self-primed second strand synthesis is inefficient
“Second-strand” cDNA synthesis is usually done with DNA polymerase and a primer
How RT works
cDNA library construction
using reverse
transcriptase cDNA Library
Construction Kit (Clontech)
Priming reverse transcriptase:
1) General RNA amplification:• Oligo(dT)12-18
• Random sequence oligonucleotides
2) Specific mRNA• Single oligonucleotide sequence
complementary to your mRNA
NOTE: Reverse transcriptase is error-prone (about 1/500 bp is mutated)
Terminal transferase
• template-independent DNA polymerase• Incorporates dNTPs onto the 3' ends of
DNA chains
• Useful for adding homopolymeric tails or single nucleotides (can be labelled) to the 3' ends of DNA strands (make DNA fragments more easily clonable)
T4 polynucleotide kinase
• Transfers gamma phosphate of ATP to the 5’ end of polynucleotides
• Useful for preparing DNA fragments for ligation (if they lack 5’ phosphates)
• Useful for radiolabelling DNA fragments using gamma 32P ATP as a phosphate donor
alkaline phosphatase
• Catalyzes removal of 5’ (and 3’) phosphates from polynucleotides
• Useful for treating restricted vector DNA sequences prior to ligation reactions, prevents religation of vector in the absence of insert DNA
• Lack of vector 5’ phosphates may inhibit transformation efficiency? Use only when absolutely necessary…
Nucleases
• Exonucleases– Remove nucleotides one at a time from a
DNA molecule
• Endonucleases– Break phosphodiester bonds within a DNA
molecule– Include restriction enzymes
Exonucleases
• Bal 31– Double-stranded exonuclease,
operates in a time-dependent manner– Degrades both 5’ and 3’ ends of DNA
– Useful for generating deletion sets, get bigger deletions with longer incubations
Exonucleases
• Exonuclease III--double-stranded DNA– 3’-5’ exonuclease activity– 3’ overhangs resistant to activity, can
use this property to generate “nested” deletions from one end of a piece of DNA (use S1 nuclease to degrade other strand of DNA)
Exonucleases
• Exonuclease I– 3’-5’ exonuclease– Works only on single-stranded DNA– Useful for removing unextended
primers from PCR reactions or other primer extension reactions
Endonucleases
• Dnase I– Cleaves double-stranded DNA
randomly (also cleaves single-stranded DNA)
– Mn++: both strands of DNA cut– Mg++: single strands nicked– Very useful for defining binding sites
for DNA binding proteins
DNAse I footprinting
Calibrate the nicking: 1 hit per DNA molecule
0DNAse I
footprinting:
Gel following
footprinting reaction
Drosophila heat-shockfactor
Sites for interaction of HSF with DNA
Topoisomerase
Function:A restriction enzyme and ligase--all in one
altering the “linking number” in coiled, constrained (supercoiled) DNA--relaxing DNA twisting during replication
Model for function: http://mcb.berkeley.edu/labs/berger/structures.html#modeling
Cloning with topoisomerase
•Topoisomerase catalyzed ligation is EXTREMELY efficient (>85% of resulting plasmids are recombinant)--excellent for library constructions
•Can be used to clone blunt ended DNA (PCR products, restriction digests), T-overhang PCR products (from Taq polymerase), and directional clones
•You have to use their plasmid vectors (ie. forget about using your favorite lab plasmid unless you know how to covalently attach topoisomerase)
Topoisomerase
Enzymes for manipulating DNA
*** Buffers and solution conditions***
I. DNA polymerasesIII. Kinase and alkaline phosphataseIV. NucleasesV. Topoisomerase
Course Readings: 19 and 20
Cutting and pasting DNA
I. Restriction and modification systems
II. Recognition and cleavage of DNA by restriction endonucleases (REases)
III. Joining (ligating) DNA moleculesIV. Cloning techniques
Discovery of restriction/modification
EOP = efficiency of plating (a measure of phage virulence)
= bacteriophage
E. coli K has R/M systemE. coli C has no M system
Cautions for cloning in E.coli
• Strains with methylases (dam or dcm) produce methylated DNA--difficult to cleave with certain enzymes, hard to transform some strains
• Strains with restriction systems intact will restrict DNA coming from a host lacking methylases, or from a host with specific types of methylations
• Best bet is to delete the restriction systems, but not all cloning strains have this deletion
Types of endonucleases• Type I: multisubunit proteins that function as a single protein
complex, usually contain two R subunits,two M subunits and one S subunit
• Type II: recognize specific DNA sequences and cleave at constant positions at or close to that sequence to produce 5’-phosphates and 3’-hydroxyls. Most useful in cloning!!
• Type III: composed of two genes (mod and res) encoding protein subunits that function either in DNA recognition and modification (Mod) or restriction (Res)
• Type IV: one or two genes encoding proteins that cleave only modified DNA, including methylated, hydroxymethylated and glucosyl-hydroxymethylated bases
Mode of action of type II REases
5´ ... G^A A T T C ... 3´3´ ... C T T A A^G ... 5´
5´ ... G^ 3’ 5’ A A T T C ... 3´3´ ... C T T A A 5’ 3’ ^G ... 5´
EcoRI
EcoRI
Example recognition sequences for REases
4-cutters:
AluI 5´ ... AG^CT ... 3´ blunt ends
MspI 5´ ... C^CGG ... 3´ 5’ overhang (2 bp)
6-cutters
PvuII 5´ ... CAG^CTG ... 3´ blunt ends
KpnI 5´ ... GGTAC^C ... 3´ 3’ overhang (4 bp)
8-cutters
NotI 5´ ... GC^GGCCGC ... 3´ 5’ overhang (4 bp)
Unusual sites
MwoI 5´ ... GCNNNNN^NNGC ... 3´ 3’ overhang
3´ ... CGNN^NNNNNCG ... 5´ (3 bp)
How often does REase cut my sequence?
1) Known sequence: scan for sites by computer (eg. at www.rebase.neb.com)
2) Unknown sequence: hypothetical calculations4 cutter: site occurs randomly every 44 (256) base
pairs6 cutter: every 46 (4096) bp8 cutter: every 48 (65536) bpBut sequences are not distributed randomly (table
3.4)3) Sequence context effects
Some sites are preferred over others by enzyme
Biological function of ligases:•Lagging strand DNA synthesis•genetic recombination•DNA repair
The ligation reaction
Behavior of cohesive ends (overhangs)
Cloning techniques
A) Modify the ends of the DNAs to make foreign DNA sequences more ligate-able
B) Directional cloning (generate easily cloned PCR fragments)
C) Treat the vector DNA with alkaline phosphatase to improve the efficiency of ligation of foreign DNA versus vector recircularization
Creating a recombinant DNA molecule
Plasmid vector:a cloning vehicle
it can replicate itself in a bacterial host and contains a means for selection (eg. antibiotic resistance)
Ligation efficiency depends on the DNA ends in the reaction
Complementary “sticky” ends• Ligation is efficient• annealing of complementary overhangs brings 5’P and 3’OH into close proximity
“Blunt” ends• Ligation is inefficient• need high concentrations of ligase and DNA• molecular crowding reagents (like PEG 8000) improve intermolecular ligation, then dilute to promote intramolecular ligation
Follow the manufacturer’s instructions…
Cloning foreign DNA by adding linkers
(your DNA molecule should not have EcoRI sites in this case)
Cloning foreign DNA by adding adaptors
The advantage of this is you do not need to treat the adaptor-modified DNA with restriction enzyme
Terminal transferase to add polynucleotide tails to foreign DNA and
vector DNA
dTTP
Foreign DNA
Vector DNA
Cloning Taq PCR products
•Taq PCR products have a 3’ “A” overhang•Prepare vector to have a 3’ “T” overhang
HphI leaves T overhangs
Directional cloning
Directional cloning
This guarantees the orientation of your DNA fragment
Easy cloning: PCR products
Ready for directional cloning
Design PCR primers with built in restriction sites (check amplified sequence for those sites first!)
Utility of alkaline
phosphatase in ligation
Chances of getting recombinant product are improved
Cutting and pasting DNA
I. Restriction and modification systems
II. Recognition and cleavage of DNA by restriction endonucleases (REases)
III. Joining (ligating) DNA moleculesIV. Cloning techniques
Mobilizing DNA: vectors for propagation in E. coli
•Plasmids•Bacteriophage
M13 Lambda
•Cosmids and BACs
Plasmids and transformation
I. Properties of plasmidsII. Plasmids as cloning vehicles
(‘vectors’)III. Ligation and transformation, and
identification of recombinant plasmids
Course Readings: #21 (plasmids) and #22 (antibiotic selection)
Plasmids• Extrachromosomal, double-stranded, usually
circular, supercoiled DNA molecules• Found in many bacterial species• Replicate and are inherited independently of
the bacterial chromosome• Maintain copy number in cell through an
origin of replication (replicon)• Usually have genes coding for enzymes that
provide benefits for the host bacterium, eg. antibiotic resistance
a generic, minimal plasmid
origin of replication
antibiotic resistance
restriction site for cloning
pBi430/5301500 base pairs
(a manageable size
Replicon -- how the plasmid replicates
• Governs replication of plasmid and number of plasmid copies per cell (“copy number”)
• A replicon includes:– origin of replication (ori: a site on the DNA)– associated factors
• > 30 different replicons known, but most plasmids used today have pMB1 (or the close relative colE1) replicon
1
2
3
4
pMB1/colE1 replication mechanism
Deletion of Rop or mutation of RNA II cause increases in replication and copy number
PLASMID REPLICON COPY #
pBR322 pMB1 15-20
pUC Modified form of pMB1 (RNAII mutation)
500-700
pACYC p15A 18-22
pSC101 pSC101 about 5
Common plasmids and their stats
Plasmid copy number
• High copy number plasmids– Workhorses of molecular cloning– Used for almost all routine manipulation of
small (<15 kb) recombinant DNAs
• Low copy number plasmids– For genes that are lethal or unstable in high
copy number plasmids– For constructing Bacterial Artificial
Chromosomes (BACs) that can propagate large (>100 kb) recombinant DNAs
Plasmid maintenance
• Plasmids contain selectable markers: genes carried by the plasmid that confer functions required for host survival
• Selection: only those cells with the plasmid will survive – Allows transformation (a rare event) to be
feasible– A way to keep cells from losing plasmids
that may otherwise confer a selective disadvantage
Antibiotic resistance genes
• Beta lactamase (bla): breaks down ampicillin and carbenicillin (inhibitors of cell wall synthesis). Cells carrying this gene are often termed ampr
• CAUTION: Over time beta-lactamase is secreted into the medium where it breaks down the antibiotic and depletes it. Eventually this allows the growth of ampicillin/ carbenicillin sensitive cells, defeating the selection
Antibiotic resistance genes
• Chloramphenicol acetyl transferase (CAT): inactivates chloramphenicol (cm), which normally inhibits peptidyl transferase activity of the ribosome (no protein synthesis = dead cell)
• Another use for cm:– replication of plasmids with pMB1/colE1
replicons is not inhibited by cm– Cm-treated cells stop growing but continue
making these plasmids, this is a way to amplify plasmid copy numbers prior to a plasmid prep
Antibiotic resistance genes
• Tet A (C ) protein: confers resistance to tetracycline (an inhibitor of protein synthesis) by pumping this antibiotic out of the cell
• Bacterial aminophosphotransferases: confer resistant to kanamycins (aminoglycoside antibiotics that inhibit protein synthesis) by transferring the gamma phosphate of ATP to a 3’ hydroxyl group of the kanamycin
The ideal plasmid
1. Confers a readily selectable phenotypic trait
2. Has single sites for many restriction enzymes
3. Low molecular weight -- Gives higher copy #, stability, and
transforming efficiency-- Can accept larger pieces of DNA-- Easier to handle (less susceptible to
breakage)
pBR322
• The first widely useful cloning vehicle
Created using transposition and restriction/ligation reactions
pBR322
Utility of pBR322:
Clone into sites in the Tcr gene, which allows identification of recombinants--these will be amp resistant but tet sensitive (initially plate on ampicillin, then replica plate on tetracycline plates).
But: pBR322 has low copy number, large size, and too few options for cloning sites
Boldface indicates the restriction site is present in only one site within the plasmid
pUC plasmidssecond generation cloning vectors
• Reduced size (about 2000 bp)• Multiple cloning site (MCS, also called “poly-
linker”): unique sites for lots of different restriction enzymes
• Very high copy number (mutation in RNA II)• New “blue-white” screening tool for
recombinants (“alpha complementation” is disrupted by foreign DNA in the MCS)
Alpha complementation• Plasmid encodes N-terminus of beta galactosidase (alpha fragment)
• Host strain encodes the C-terminus of beta galactosidase (omega fragment)
• Beta galactosidase function is only seen in the presence of both the N- and C-terminal fragments
• Beta gal function can be monitored by the cleavage of X-gal which yields a bright blue product (blue colonies on a plate)
Bright blue
X-gal
pUC 19
An alpha complementing plasmid vector
DNA in the MCS interrupts the lacZ gene (no Beta galactosidase)
(MCS)
Alpha complementation• Plasmid encodes N-terminus of beta galactosidase (alpha fragment), with an MCS
• Foreign DNA in the MCS, no alpha fragment
• No alpha fragment, no B-gal
• No B-gal, no blue color (white colonies)
pUC19 transformation plate
Colony without foreign DNA in MCS
Colony with foreign DNA in MCS
Third generation cloning vectors: specialized plasmids
• Vectors containing bacteriophage RNA polymerase promoters: for production of a specific RNA (probe synthesis, in vitro translation, etc.)
• Low copy number vectors: for cloning of unstable or toxic genes
• Vectors designed for expression of specific proteins (for further purification and biochemical characterization). Proteins may be synthesized with “tags” to assist in purification
Transformation of E.coli with plasmid DNA
• E.coli strain: must be antibiotic sensitive, best if it lacks restriction-modification systems
• Make cells take up DNA by– Chemical competence– Electroporation– (natural competence--not E.coli though)
Chemically competent cells-basic method
• Grow cells to A600 of 0.4, spin to get cell pellet
• Resuspend cells in CaCl2 (100 mM), pellet again
• Resuspend in small volume of CaCl2/glycerol
• Freeze cells (-80°C) or go straight to transformation protocol
Transformation of chemically competent cells
• Mix DNA and competent cells, on ice for 30 min.
• Heat shock (42°C) for 1.5 minutes
• Add growth media, 37°C for 1 hour
• Plate on growth medium plus selection (antibiotic) for the plasmid
Efficiency ~ 106 - 107 cells/microgram plasmid DNA
DNA binds to cells
DNA uptake by cells
Cells recover
Selection occurs
If cells are good:
Ultra competent cells (chemical)
• 5 x 108 transformants/microgram plasmid• See protocol 23 of Molecular Cloning ch. 1• Treat with
– MnCl2– CaCl2– KCl
– Hexammine CoCl2– Store in DMSO
• (protocol rather difficult, inconsistent)• These can be bought
Transformation by electroporation
• > 109 transformants/microgram DNA (ideally)
• Grow cells to A600 of 0.4
• Centrifuge and resuspend in water + 10% glycerol (do this 4 times to reduce conductivity)
• Place cells with DNA in electrode-containing cuvette, deliver electrical pulse
• If there is arcing (sparks) transformation efficiency will be poor (uneven transfer of charge). To avoid this make sure the ion concentration is very low (less than 10 mM salt)
When cloning a piece of DNA consider:
1) Choice of vector: what kind of plasmid vector to use (which restriction sites can be used in the vector)?
2) Ligating DNA to vector: how will the ligation reaction be set up to facilitate getting what you want?
3) Moving DNA by transformation: what strain of E. coli will you transform into? Which method for transformation?
4) Screening for successful ligation products (recombinant plasmid DNA): how will the recombinant plasmids be identified?
Setting up a transformation--how will the competent cells be
treated?1. No plasmid (negative control, nothing
should grow on this plate)2. Supercoiled plasmid of a known
concentration (to determine efficiency of competent cells)
3. Vector DNA (dephosphorylated?) ligated without insert DNA (background transformants)
4. Vector DNA ligated with insert DNA (desired products)
Example outcome of a successful transformation: chemically competent
cells
1) No DNA--No colonies2) 2 nanograms (10-9 g, 10-3 micrograms)
supercoiled plasmid DNA--500 colonies (efficiency of cells: 2.5 x 105 transformants per microgram DNA)
3) Vector alone--small number of colonies4) Vector plus insert--larger number of colonies
than for #3
Identifying recombinant plasmid-containing cells
• Alpha complementation: most white colonies represent presence of insert DNA blocking functional beta galactosidase
• Increase in number of transformants in presence of insert vs. absence of insert– Insert treated with alkaline phosphatase– Directional cloning--preventing religation of
vector– Must screen colonies/plasmids for inserts,
usually by PCR
Confirm clones by sequencing
Mobilizing DNA: vectors for propagation in E. coli
•Plasmids•Bacteriophage
M13 Lambda
•Cosmids and BACs
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