Design, synthesis, and amplification of DNA pools for in vitro selection

Current Protocols in Molecular Biology

Volumn , Issue SUPPL. 88, 2009, Pages

  Hall, Bradley ^a   Micheletti, John M ^a   Satya, Pooja ^a   Ogle, Krystal ^a   Pollard, Jack ^b   Ellington, Andrew D ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b 3rd Millennium Corporation   (United States)

Author keywords

DNA pool synthesis; In vitro selection; Phosphoramidite DNA synthesis; Randomization

Indexed keywords

ACETONITRILE; APTAMER; BACTERIOPHAGE DNA; DNA POLYMERASE REV1; PHOSPHORAMIDOUS ACID; PROTEIN KINASE C BETA; REX PROTEIN; RIBOZYME;

ARTICLE; BACTERIOPHAGE T4; BINDING SITE; CHEMICAL REACTION; CONTROLLED STUDY; DNA PURIFICATION; DNA SYNTHESIS; GENE AMPLIFICATION; GENETIC ANALYSIS; IN VITRO STUDY; MOLECULAR WEIGHT; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROMOTER REGION; RANDOMIZATION; RNA TRANSCRIPTION; STRATEGIC PLANNING; DNA SEQUENCE; IN VITRO SELECTION; PROCESS DESIGN; SEQUENCE ANALYSIS;

DIRECTED MOLECULAR EVOLUTION; DNA; DNA, SINGLE-STRANDED; MOLECULAR BIOLOGY; RANDOM ALLOCATION; SELEX APTAMER TECHNIQUE;

EID: 78651361023     PISSN: 19343639     EISSN: 19343647     Source Type: Journal    
DOI: 10.1002/0471142727.mb2402s88     Document Type: Article

References (49)

1. Abd-Elsalam, K.A. 2003. Bioinformatic tools and guideline for PCR primer design. Afr. J. Biotech. 2:91-95.
2. Bartel, D.P. and Szostak, J.W. 1993. Isolation of new ribozymes from a large pool of random sequences. Science 261:1411-1418.
3. Bartel, D.P., Zapp, M.L., Green, M.R., and Szostak, J.W. 1991. HIV-1 Rev regulation involves recognition of non-Watson-Crick base pairs in viral RNA. Cell 67:529-536.
4. Baskerville, S., Zapp, M., andEllington, A.D. 1995. High-resolution mapping of the human T-cell leukemia virus type 1 rex-binding element by in vitro selection. J. Virol. 69:7559-7569.
5. Beaucage, S.L. and Caruthers, M.H. 1981. Deoxynucleoside phosphoramidites. A new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Lett. 22:1859-1862.
6. Beaucage, S.L. and Caruthers, M. 2000. Synthetic strategies and parameters involved in the synthesis of oligodeoxyribonucleotides according to the phosphoramidite method. Curr. Protoc. Nucl. Acid Chem. 00:3.3.1-3.3.20.
7. Beaucage, S.L. and Iyer, R.P. 1992. Advances in the synthesis of oligonucleotides by the phosphoramidite approach. Tetrahedron 48:2223-2311.
8. Boutros, R., Stokes, N., Bekaert, M., and Teeling, E.C. 2009. UniPrime2: A web service providing easier Universal Primer design. Nucl. Acids Res. 37:w209-w213.
9. Breaker, R.R. 1997. In vitro selection of catalytic polynucleotides. Chem. Rev. 97:371-390.
10. Brown, D.M. 1993. A brief history of oligonucleotide synthesis. Methods Mol. Biol. 20:1-17.
11. Chandra, S. and Gopinath, B. 2007. Methods developed for SELEX. Anal. Bioanal. Chem. 387:171-182.
12. Chen, C.K. 2007. Complex SELEX against target mixture: Stochastic computer model, simulation, and analysis. Comput. Methods Programs Biomed. 87:189-200.
13. Chen, Z. and Ruffner, D.E. 1996. Modified crushand-soak method for recovering oligodeoxynucleotides from Polyacrylamide gel. BioTechniques 21:820-822. (Pubitemid 26380347)
14. Conrad, R., Keranen, L.M., Ellington, A.D., and Newton, A.C. 1994. Isozyme-specific inhibition of protein kinase C by RNA aptamers. J. Biol. Chem. 269:32051-32054.
15. 20-fold aptamer library amplification without gel purification. Nucl. Acids Res. 21:4410.
16. Fitzwater, T. and Polisky, B. 1996. A SELEX primer. Methods Enzymol. 267:275-301.
17. Giver, L., Bartel, D., Zapp, M., Pawul, A., Green, M., and Ellington, A.D. 1993. Selective optimization of the Rev-binding element of HIV-1. Nucl. Acids Res. 21:5509-5516. (Pubitemid 23348621)
18. Gold, L., Polisky, B., Uhlenbeck, O., and Yarus, M. 1995. Diversity of oligonucleotide functions. Annu. Rev. Biochem. 64:163-191.
19. Hermes, J.D., Parekh, S.M., Blacklow, S.C., Koster, H., and Knowles, J.R. 1989. A reliable method for random mutagenesis: The generation of mutant libraries using spiked oligodeoxyribonucleotide primers. Gene 84:143-151.
20. Hesselberth, J.R., Miller, D., Robertus, J., and Ellington, A.D. 2000. In vitro selection of RNA molecules that inhibit the activity of ricin achain. J. Biol. Chem. 275:4937-4942. (Pubitemid 30108888)
21. Iyer, R.P. and Beaucage, S.L. 1999. Oligonucleotide synthesis. In Comprehensive Natural Products Chemistry, Vol. 7: DNA and Aspects of Molecular Biology (E.T. Kool, ed.) pp. 105-152. Elsevier, London.
22. Jaeger, J.A., Turner, D.H., andZuker, M. 1989. Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol. 183:281-306.
23. Jaeger, L. 1997. The new world of ribozymes. Curr. Opin. Struct. Biol. 7:324-335.
24. Kim, N., Gan, H.H., and Schlick, T. 2007. A computational proposal for designing structured RNA pools for in vitro selection of RNAs. RNA. 13:478-492. (Pubitemid 46506931)
25. Legiewicz, M., Lozupone, C., Knight, R., and Yarus, M. 2005. Size, constant sequences, and optimal selection. RNA 11:1701-1709. (Pubitemid 41505544)
26. Lorsch, J.R. and Szostak, J.W. 1994. In vitro evolution of new ribozymes with polynucleotide kinase activity. Nature 371:31-36.
27. Lyamichev, V., Brow, M.A., and Dahlberg, J.E. 1993. Structure-specific endonucleolytic cleavage of nucleic acids by eubacterial DNA polymerases. Science 260:778-783. (Pubitemid 23167605)
28. Michelson, A.M. and Todd, A.R. 1955. Nucleotides. XXXII. Synthesis of a dithymidine dinucleotide containing a 3′,5′-internucleotidic linkage. J. Chem. Soc. 2632-2638.
29. Milligan, J.F., Groebe, D.R., Witherell, G.W., and Uhlenbeck, O.C. 1987. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucl. Acids Res. 15:8783-8798.
30. Oliphant, A.R. and Struhl, S. 1989. An efficient method for generating proteins with altered enzymatic properties: application to betalactamase. Proc. Natl. Acad. Sci. 86:9094-9098.
31. Oliphant, A.R., Brandi, C.J., and Struhl, K. 1990. Defining the sequence specificity of DNAbinding proteins by selecting binding sites from random-sequence oligonucleotides: Analysis of yeast GCN4 protein. Mol. Cell Biol. 9:2944-2949.
32. Pan, W. and Clawson, G.A. 2008. Catalytic DNAzymes: Derivations and functions. Expert Opin. Biol. Ther. 8:1071-1085.
33. Pan, W. and Clawson, G.A. 2009. The shorter the better: Reducing fixed primer regions of oligonucleotide libraries for aptamer selection. Molecules. 14:1353-1369.
34. PerSeptive Biosystems. 1998. Expedite Nucleic Acid Synthesis System: User's Guide. PerSeptive Biosystems, Framingham, Mass.
35. Piasecki, S.K., Hall, B., and Ellington, A.D. 2009. Nucleic acid pool preparation and characterization. Methods Mol. Biol. 535:3-18.
36. Piganeau, N. 2009. In vitro selection of allosteric ribozymes. Methods Mol. Biol. 535:45-57.
37. Reese, C.B. 2005. Oligo- and poly-nucleotides: 50 years of chemical synthesis. Org. Biomol. Chem. 3:3851-3868.
38. Sabeti, P.C., Unrau, P.J., and Bartel, D.P. 1997. Accessing rare activities from random RNA sequences: The importance of the length of molecules in the starting pool. Chem. Biol. 4:161-114.
39. Scott, W.G. 2007. Ribozymes. Curr. Opin. Struct. Biol. 17:280-286.
40. Singer, B.S., Shtatland, T., Brown, D., and Gold, L. 1997. Libraries for genomic SELEX. Nucl. Acids Res. 25:781-786.
41. Singh, V.K. and Kumar, A. 2001. PCR Primer Design. Mol. Biol. Today 2:27-32.
42. Stoltenburg, R., Reinemann, C., and Strehlitz, B. 2007. SELEX-A (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomol. Eng. 24:381-403. (Pubitemid 47391579)
43. Strömberg, R. and Stawinski, J. 2004. Synthetic strategies and parameters involved in the synthesis of oligodeoxyribo- and oligoribonucleotides according to the H-phosphonate method. Curr. Protoc. Nucl. Acid Chem. 19:3.4.1-3.4.15.
44. Tuerk, C and Gold, L. 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505-510 (Pubitemid 20248891)
45. Tuerk, C and MacDougal-Waugh, S. 1993. In vitro evolution of functional nucleic acids: High affinity RNA ligands of HIV-1 proteins. Gene 137:33-39. (Pubitemid 24053729)
46. Unrau, P.J. and Bartel, D.P., 1998. RNA-catalysed nucleotide synthesis. Nature. 395:260-263.
47. Vieux, E.F., Kwok, P.Y, and Miller, R.D. 2002. Primer design for PCR and sequencing in highthroughput analysis of SNPs. Biotechniques 32:S28-S32. (Pubitemid 34615021)
48. Zon, G., Gallo, K.A., Samson, C.J., Shao, K., Summers, M.F., and Byrd, R.A. 1985. Analytical studies of "mixed sequence" oligodeoxyribonucleotides synthesized by competitive coupling of either methyl- or β-cyanoethyl-,N,Ndiisopropy lamino phosphoramidite reagents, including 2′-deoxyinosine. Nucl. Acids Res. 13:8181-8196.
49. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31:3406-3415. (Pubitemid 37442169)