Theoretical Principles of In Vitro Selection Using Combinatorial Nucleic Acid Libraries

Barry Vant‐Hull1, Larry Gold1, Dominic A. Zichi1

1 NeXstar Pharmaceuticals, Boulder, Colorado
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 9.1
DOI:  10.1002/0471142700.nc0901s00
Online Posting Date:  February, 2000
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

Abstract

A new paradigm for drug discovery and biological research has developed from technologies that integrate combinatorial chemistry with rounds of selection and amplification, a technique called in vitro selection or systematic evolution of ligands by exponential enrichment (SELEX). This overview unit discusses nucleic acid libraries that can be used, affinity probability distributions, an equilibrium model for SELEX, and optimal conditions including concentrations and signal‐to‐noise ratios.

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • Nucleic Acid Libraries
  • Affinity Probability Distributions
  • An Equilibrium Model for SELEX
  • Optimal Conditions for In Vitro Selection
  • Concluding Remarks
  • Acknowledgments
  • Literature Cited
  • Figures
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

Literature Cited
   Berg, O.G. and von Hippel, P.H. 1987. Selection of DNA binding sites by regulatory proteins: Statistical‐mechanical theory and application to operators and promoters. J. Mol. Biol. 193:723‐750
   Blackwell, T.K. and Weintraub, H. 1990. Differences and similarities in DNA‐binding preferences of MyoD and E2A protein complexes revealed by binding site selection. Science 250:1104‐1110
   Breaker, R.R. 1997. In vitro selection of catalytic polynucleotides. Chem. Rev. 97:371‐390
   Ciesiolka, J., Illangasekare, M., Majerfeld, I., Nickles, T., Welch, M., Yarus, M., and Zinnen, S. 1996. Affinity selection‐amplification from randomized ribooligonucleotide pools. Methods Enzymol. 267:315‐335
   Cwirla, S.E., Peters, E.A., Barrett, R.W., and Dower, W.J. 1990. Peptides on phage: A vast library of peptides for identifying ligands. Proc. Natl. Acad. Sci. U.S.A. 87:6378‐6382
   Ellington, A.D. and Szostak, J.W. 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346:818‐822
   Gold, L. 1995. Oligonucleotides as research, diagnostic, and therapeutic agents. J. Biol. Chem. 95:13581‐13584 270:13581‐13584.
   Gold, L., Polisky, B., Uhlenbeck, O., and Yarus, M. 1995. Diversity of oligonucleotide functions. Annu. Rev. Biochem. 64:763‐797.
   Hager, A.J., Pollard, J.D., Jr., and Szostak, J.W. 1996. Ribozymes: Aiming at RNA replication and protein synthesis. Chem. Biol. 3:717‐725
   Irvine, D., Tuerk, C., and Gold, L. 1991. SELEXION: Systematic evolution of ligands by exponential enrichment with integrated optimization by nonlinear analysis. J. Mol. Biol. 222:739‐761
   Kauffman, S.A. and Macready, W.G. 1995. Search strategies for applied molecular evolution. J. Theor. Biol. 173:427‐440
   Kay, B.K. 1994. Biologically displayed random peptides as reagents in mapping protein‐protein interactions. Persp. Drug Discovery Design 2:251‐268
   Klug, S.J. and Famulok, M. 1994. All you wanted to know about SELEX. Mol. Biol. Rep. 20:97‐107
   Levitan, B. 1998. Stochastic modeling and optimization of phage display. J. Mol. Biol. 277:893‐916
   Mathieu‐Daudi, F., Welsh, J., Vogt, T., and McClelland, M. 1996. DNA rehybridization during PCR: the ‘C0t effect’ and its consequences. Nucl. Acids Res. 24:2080‐2086
   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. 4:767‐774
   Schneider, D., Gold, L., and Platt, T. 1993. Selective enrichment of RNA species for tight binding to Escherichia coli rho factor. FASEB J. 7:201‐201
   Schuster, P. 1995. How to search for RNA structures. Theoretical concepts in evolutionary biotechnology. J. Biotechnol. 41:239‐257
   Scott, J.K. and Smith, G.P. 1990. Searching for peptide ligands with an epitope library. Science 249:386‐390
   Stormo, G.D. and Yoshioka, M. 1991. Specificity of the mnt protein determined by binding to randomized operators. Proc. Natl. Acad. Sci. U.S.A. 88:5699‐9743
   Sun, F., Galas, D., and Waterman, M.S. 1996. A mathematical analysis of in vitro molecular selection‐amplification. J. Mol. Biol. 258:650‐660
   Tuerk, C. and Gold, L. 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505‐510
   Vant‐Hull, B., Payano‐Baez, A.R., Davis, R.H., and Gold, L. 1998. The mathematics of SELEX against complex targets. J. Mol.Biol. 278:579‐597
   Winter, G., Griffiths, A.D., Hawkins, R.E., and Hoogenboom, H.R. 1994. Making antibodies by phage display technology. Annu. Rev. Immunol. 12:433‐455
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library