RNA Self-assembly · 2006-03-30 · 3/29/06 LaBean COMPSCI 296.5 Ellington & Szostak Nature. 1990...
Transcript of RNA Self-assembly · 2006-03-30 · 3/29/06 LaBean COMPSCI 296.5 Ellington & Szostak Nature. 1990...
![Page 1: RNA Self-assembly · 2006-03-30 · 3/29/06 LaBean COMPSCI 296.5 Ellington & Szostak Nature. 1990 Aug 30;346(6287):818-22. In vitro selection of RNA molecules that bind specific ligands.](https://reader034.fdocuments.us/reader034/viewer/2022042021/5e78f44dd33b707cc65eb059/html5/thumbnails/1.jpg)
3/29/06 LaBean COMPSCI 296.5
RNA Self-assembly
(2004) Science 306, 2068-2072
![Page 2: RNA Self-assembly · 2006-03-30 · 3/29/06 LaBean COMPSCI 296.5 Ellington & Szostak Nature. 1990 Aug 30;346(6287):818-22. In vitro selection of RNA molecules that bind specific ligands.](https://reader034.fdocuments.us/reader034/viewer/2022042021/5e78f44dd33b707cc65eb059/html5/thumbnails/2.jpg)
3/29/06 LaBean COMPSCI 296.5
RNA Self-assembly(2004) Science 306, 2068-2072
![Page 3: RNA Self-assembly · 2006-03-30 · 3/29/06 LaBean COMPSCI 296.5 Ellington & Szostak Nature. 1990 Aug 30;346(6287):818-22. In vitro selection of RNA molecules that bind specific ligands.](https://reader034.fdocuments.us/reader034/viewer/2022042021/5e78f44dd33b707cc65eb059/html5/thumbnails/3.jpg)
3/29/06 LaBean COMPSCI 296.5
RNA Self-assembly (2004) Science 306, 2068-2072
![Page 4: RNA Self-assembly · 2006-03-30 · 3/29/06 LaBean COMPSCI 296.5 Ellington & Szostak Nature. 1990 Aug 30;346(6287):818-22. In vitro selection of RNA molecules that bind specific ligands.](https://reader034.fdocuments.us/reader034/viewer/2022042021/5e78f44dd33b707cc65eb059/html5/thumbnails/4.jpg)
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stemmer
2003
Rational designDirectedevolution
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RNA Physical Catalyst
(2004) Science 304, 850-852
*UTP is 5-(4-pyridylmethyl)-uridine 5’ triphosphatePd2(DBA)3 is dibenzylide-acetone palladium (0)
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*UTP is 5-(4-pyridylmethyl)-uridine 5’ triphosphatePd2(DBA)3 is dibenzylide-acetone palladium (0)
RNA Physical Catalyst
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Ellington & Szostak
Nature. 1990 Aug 30;346(6287):818-22.
In vitro selection of RNA molecules that bind specificligands.
Ellington AD, Szostak JW.Department of Molecular Biology, Massachusetts General Hospital, Boston 02114.
Subpopulations of RNA molecules that bind specifically to a variety oforganic dyes have been isolated from a population of random sequenceRNA molecules. Roughly one in 1010 random sequence RNA moleculesfolds in such a way as to create a specific binding site for small ligands.
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Ellington & Szostak Nature. 1990 Aug 30;346(6287):818-22.
Random DNA
Random RNA
Transcription
Column fractionation
Unbound (discard)[flow-through high salt]Bound RNA
[high salt wash, water elute]
T7 Promoter cDNA Priming
ReverseTranscription Dye column
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Ellington & Szostak Nature. 1990 Aug 30;346(6287):818-22.
100 random nucleotides (+ constant regions) Complexity of initial pool ~1015 (1060 possible) Poor transcription; PCR amp; ~1013 diversity ~4x1014 RNA molecules applied to column <0.1% of initial RNA library bound then after 4 to 5
cycles of bind, RT, PCR, Transcribe, rebind ~50% ofRNA molecules bound.
Binding is specific for dye selected. For 1 column 20 clones were sequenced ~16-20
nucleotides were invariant over the set of clones. APTAMER from Latin ‘aptus’, to fit.
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Ellington & Szostak Nature. 1990 Aug 30;346(6287):818-22.
AC A C G C A C U C A GAAAA GUAC A C C UCACA A-C CC A UCC AUCC CCAAC CAG GC CGG GCC A A ||| |||| ||||| ||| || ||| ||| U G AGG UAGG GGUUG GUC-CG GCC CGG U C A-UAA ACCC C-GAC C-A-A AAU CA G-C G-C C | G-C C-G C-G C-G U-A U-A A \ A G G-C A-U G-U G G
B4 Reactive blue binder
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Tuerk & Gold
SELEX- systematic evolution of ligands byexponential enrichment.
Selected RNA for binding to T4 DNA polymerase. 65,536 possible sequences. Wild-type T4 bacteriophage mRNA sequence found
and a variant with 50% identity to wild-type.
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Tuerk & Gold
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Tuerk & Gold
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Bartel & Szostak
220 random positions 1.6x1015 diversity
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Bartel & Szostak
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In vitro evolution of nucleic acids.
Random pool
Select for desired phenotype
Selected poolMultiplecycles
Final selected ensemble
Amplify and/or mutate geneotype
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Review
In vitro selection requires linking of genotype andphenotype.
Binding targets: simple ions, small molecules,peptides, proteins, organelles, and cells.
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Review AMP binding aptamer
Selectivity: theophyllineaptamer shows 10,000-folddecrease in binding tocaffeine which differs byone additional methyl group.
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Review
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In vitro selection and directedevolution of peptides and proteins
Goal: find protein/peptide with desired function(binding, catalyst, stability, etc.)
In vivo vs In vitro selection. Rational design vs. Library methods. Combinatorial peptide libraries.
Geysen. Discontinuous epitope mapping. Solid phasepeptide synthesis. Birth of combinatorial chemistry.
Phage display. mRNA fusion. Ribosome stalling. Antibody engineering and evolution. Primerless PCR. DNA shuffling. Sexual PCR.
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Scott & Smith
Filamentous bacteriophage (M13, fd)
Cloning into p3 (pIII) coat protein
NNK codons: N=ACTG, K=GT.Encodes 32 triples, all 20 aminoacids and only one stop codon.
antigenantibody
epitope
antigen combining region
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Scott & Smith
64 million possible hexapeptides Library contained 1.3 x 1014 phage from
2 x 108 clones
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Phage display
Enzyme selection. Note: hidden in vivo
selection too...
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mRNA-proteinfusion
Ribosomedisplay
Other. Cro?
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Phage display of Ab libraries
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Artificial immune maturation
Gene library from human,animal, or synthetic source.
Maturation: Saturation mutagenesis of
CDRs. Chain shuffling. Growth in mutagenic E. coli
strains.
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Diabodies and triabodies
In vitro selection/evolution of bifunctional antibodyfragments.
Universal protein-based adapter/address system.
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Stemmer
http://www.maxygen.com/science-pub.php
Gene reassembly Whole plasmid reassembly
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Stemmer
Can natural diversity accelerate the evolution process? Goal: obtain moxalactamase activity from four
cephalosporinase genes. DNA shuffling within genesor between genes...
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Stemmer
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Stemmer
Can natural diversity accelerate the evolution process? Goal: obtain moxalactamase activity from four cephalosporinase
genes. DNA shuffling within genes or between genes... One cycle: ~8-fold improvements from separately evolved genes. One cycle: 270- to 540-fold improvement from the four genes
shuffled together. Best clone contained 8 segments from 3 of the 4 genes & 33
amino-acid point mutations.
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stemmer
2003
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stemmer
2003
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Belcher(2000) Nature 405, 665-668
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Belcher
GaAs (100),GaAs(111), InP,GaN, ZnS, CdS,Fe3O4, CaCO3,etc.
(2000) Nature 405, 665-668