Hamming chromatography.
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.
Schwienhorst
A
A
Institute for Molecular Biotechnology, Jena, Germany.
Schober
A
A
Günther
R
R
Stadler
P F
PF
D017123:Bacteriophage T7 / Q000235:genetics; D001483:Base Sequence; D002845:Chromatography / Q000379:methods*; D003001:Cloning, Molecular; D004247:DNA / Q000737:chemistry / Q000235:genetics* / Q000302:isolation & purification*; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D019020:Directed Molecular Evolution / Q000379:methods*; D009693:Nucleic Acid Hybridization / Q000379:methods*; D011401:Promoter Regions, Genetic; D012360:RNA, Transfer, Phe / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification
D004279:DNA, Viral; D012360:RNA, Transfer, Phe; D004247:DNA