Calculating Melting Temperature of Native and Modified Oligonucleotide Complexes at Various Cation Concentrations with the Use of Enhanced Counterion Condensation Model

Abstract

A new model describing the influence of ionic strength on thermal stability of DNA comlexes of oligonucleotides is proposed. This model assumes that binding of cations with DNA polyanions influences solely the entropy of hybridization and has a saturating mode. The efficacy of counterion binding with single- and double-stranded DNA is different, and the number of cations which bind additionally with the oligonucleotide at duplex formation depends on bulk cation concentration. Analytical equations describing the influence of cation concentration on melting temperature of DNA-duplexes as function of the length of oligonucleotide, its GC-composition and presence of the modification (non-nucleotide insert) were obtained. The values of melting temperature (Tm ) and thermodynamic parameters ( o ∆H , o ∆S ) characterizing the hybridization of both native and «bridged» oligonucleotides (bearing non-nucleotide insert on the basis of diethylene glycol phosphodiester) with DNA in various concentrations of NaCl (0,01÷1 М) were obtained using the UV-melting technique. Based on both the data obtained and presented in literature the database (695 data sets) characterizing the influence of ionic strength on the thermal stability of oligonucleotide complexes of various structure is developed. The database analysis allows us to obtain the values of the equilibrium binding constants for condensation of caions on DNA and the number of ions required for saturation of a discrete binding site. The proposed enhanced model of cation condensation utilizing unified thermodynamic increments of dsDNA formation allows us to calculate melting temperatures of DNAduplexes in the wide range of ionic strength ([Na+] = 0,01÷1 М) with high accuracy.