Biopolym. Cell. 1988; 4(6):283-289.
http://dx.doi.org/10.7124/bc.00023A
Structure and Function of Biopolymers
Theoretical analysis of addressed modification of DNA
1Perelroyzen M. P., 2Vologodskii A. V.
  1. Institute of Bioorganic Chemistry, Siberian Branch of the Academy of Sciences of the USSR
    Novosibirsk, USSR
  2. Institute of Molecular Genetics, Academy of Sciences of the USSR
    Moscow, USSR

Abstract

Specific chemical addressed modification of DNA involves treatment of single-stranded DNA by oligonucleotides complementary to certain target sequences in this DNA and bearing groupings reactive towards the DNA bases. The binding with the partially complementary targets can cause non-specific modification. The selectivity of the addressed modification is the subject of the present investigation. Modification of a fragment is analyzed which is flanked by two target sequences complementary to a given oligonucleotide address and contains no more such exact targets over all its length. Conditions of maximum ratio between specific and non-specific modification are calculated. The probability of the process in which up to the given time both of the target termini will be specifically modified without any non-specific modification of the internal part of a fragment is determined.
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References

[1] Affinity modification of biopolymers. Ed. DG Knorre. Novosibirsk, Nauka, 1983; 243 p.
[2] Aboul-ela F, Koh D, Tinoco I Jr, Martin FH. Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,T). Nucleic Acids Res. 1985;13(13):4811-24.
[3] Craig ME, Crothers DM, Doty P. Relaxation kinetics of dimer formation by self complementary oligonucleotides. J Mol Biol. 1971;62(2):383-401.
[4] Porschke D, Eigen M. Co-operative non-enzymic base recognition. 3. Kinetics of the helix-coil transition of the oligoribouridylic--oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH. J Mol Biol. 1971;62(2):361-81.
[5] Porschke D, Uhlenbeck OC, Martin FH. Thermodynamics and kinetics of the helix-coil transition of oligomers containing GC base pairs. Biopolymers. 1973; 12(6):1313-1335.
[6] Cantor Ch, Schimmel P. Biophysical Chemistry. Moscow, Mir, 1985; Vol. 3; 534 p.
[7] Vedenov AA, Dykhne AM, Frank-Kamenetskii MD. The helix - coil transition in DNA. Usp Fiz Nauk. 1971; 105(3):479-519.
[8] Wada A, Yabuki S, Husimi Y. Fine structure in the thermal denaturation of DNA: high temperature-resolution spectrophotometric studies. CRC Crit Rev Biochem. 1980;9(2):87-144.
[9] Anshelevich VV, Vologodskii AV, Lukashin AV, Frank-Kamenetskii MD. Slow relaxational processes in the melting of linear biopolymers: a theory and its application to nucleic acids. Biopolymers. 1984;23(1):39-58.