title: Theoretical analysis of 'addressed' chemical modification of DNA.
abstract: Chemical "addressed" modification of DNA involves treatment of single-stranded DNA with oligonucleotides complementary to certain target sequences in this DNA and bearing a groupings reactive towards DNA bases. The binding of oligonucleotides can occur both at completely (specific) and incompletely (nonspecific) complementary sites. We analyse the modification of a fragment that is flanked by two target sequences complementary to a given oligonucleotide address, contains no more such targets and has some randomly distributed sites for nonspecific binding. Conditions for the maximum ratio between specific and non-specific modification are determined. We find the probability of both target termini being specifically modified without any non-specific modification occurring within the fragment up to a given moment in time. Quantitative analysis is based on the use of known features of the specific and non-specific binding of an oligonucleotide to DNA sites. This analysis shows the possibility of specific cutting of DNA based on addressed modification.
authors: Novosibirsk Institute of Bioorganic Chemistry, Siberian Division of the Academy of Sciences, USSR.
authors: M P
authors: MP
authors: Perelroyzen
authors: A V
authors: AV
authors: Vologodskii
mesh_terms: D001482:Base Composition; D003001:Cloning, Molecular / Q000379:methods; D004277:DNA, Single-Stranded / Q000235:genetics*; D008433:Mathematics; D008962:Models, Theoretical; D009838:Oligodeoxyribonucleotides; D013816:Thermodynamics
chemical_list: D004277:DNA, Single-Stranded; D009838:Oligodeoxyribonucleotides