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Nucleic Acids Research, 1988, Vol. 16, No. 10 4693-4704
© 1988

Articles

Theoretical analysis of ‘addressed’ chemical modification of DNA

M.P. Perelroyzen and A.V. Vologodskii*

Novosibirsk Institute of Bioorganic Chemistry, Siberian Division of the Academy of Sciences of USSR Novosibirsk 630090 Institute of Molecular Genetics Acadamy of Sciences of USSR Moscow 123182, USSR

* To whom all correspondence should be addressed.

Received December 8, 1988. Revised April 19, 1988. Accepted April 19, 1988.

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 oligonucnucleotides can occus 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 specificaly 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.


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