Hamming chromatography

Mol Divers. 1996 May;1(3):187-92. doi: 10.1007/BF01544957.

Abstract

Selection of molecules with desired properties from random pools of biopolymers has become a powerful tool in biotechnology. On designing an evolution experiment, a certain knowledge of the concomitant fitness landscape is clearly helpful to set up the optimal experimental conditions. The correlation function is a useful means of characterizing a given landscape, since it can be efficiently measured if one has a method of separating a pool of random sequences according to their Hamming distance from a moderately small number of test sequences. In this paper we describe a special type of hybridization chromatography, where a mixture of oligomers (partially) complementary to a given test sequence is hybridized to the test sequence, covalently bound to a matrix. DNA oligomers are eluted in an 'effective temperature gradient' using conditions that minimize the differences of effects of GC versus AT pairs on the melting temperatures. This method should be a means to quickly separate error classes and thus be the crucial step in characterizing fitness landscapes of biopolymers through an experimental approach. It would also be a useful tool to design sequence pools with a bias towards desired mutant spectra.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteriophage T7 / genetics
  • Base Sequence
  • Chromatography / methods*
  • Cloning, Molecular
  • DNA / chemistry
  • DNA / genetics*
  • DNA / isolation & purification*
  • DNA, Viral / chemistry
  • DNA, Viral / genetics
  • DNA, Viral / isolation & purification
  • Directed Molecular Evolution / methods*
  • Nucleic Acid Hybridization / methods*
  • Promoter Regions, Genetic
  • RNA, Transfer, Phe / chemistry
  • RNA, Transfer, Phe / genetics
  • RNA, Transfer, Phe / isolation & purification

Substances

  • DNA, Viral
  • RNA, Transfer, Phe
  • DNA