DNA-SEQUENCING BY HYBRIDIZATION TO OLIGONUCLEOTIDE MATRIX - CALCULATION OF CONTINUOUS STACKING HYBRIDIZATION EFFICIENCY

In this paper we consider the efficiency of additional rounds of ''con tinuous stacking'' hybridization in DNA sequence reconstruction by hyb ridization with oligonucleotide matrix (SHOM). After the initial hybri dization of target DNA with the matrix of oligonucleotides of fixed le ngth L some additional hybridizations should be carried out in the pre sence of fluorescently labeled oligonucleotides of another length l. T hese additional oligonucleotides can hybridize in tandem with matrix t uples (continuous stacking hybridization) thus forming an extended dup lex with the target DNA strand. The additional data obtained allows re solutions of branching points arising in the reconstruction procedure. Multiple rounds of continuous stacking hybridization considerably inc rease the efficiency of the sequencing method, eventually approaching the power of (L+l)-matrix. We develop here an; algorithm that allows u s to minimize the number of additional hybridization steps, by assembl ing sets of I-tuples to be added together in each round of continuous stacking hybridization. For SHOM using a matrix of octanucleotides, co ntinuous stacking hybridization with pentanucleotides increases the le ngth of unambiguously sequenced DNA from 200 to several thousands of b ase pairs.