Study of the interaction of polynucleotide chains with oligomers by means of chromatography: II. Effect of magnesium ions and noncomplementary bases on the stability of complexes

• Published in: Biophysical chemistry Vol. 1; no. 3; pp. 227 - 235
• Main Authors: Chernajenko, V.M., Bresler, S.E.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.02.1974
• Subjects: Binding Sites; Chromatography, DEAE-Cellulose; Chromatography, Gel; Cytidine Monophosphate; Inosine Monophosphate; Magnesium; Oligonucleotides - isolation & purification; Poly U; Polynucleotides; Thermodynamics
• ISSN: 0301-4622; 1873-4200
• DOI: 10.1016/0301-4622(74)80009-8

The interaction of the oligonucleotides ApA, ApApA, ApApC and ApApU with poly(U) and (Ip) 5I and (Ip) 6 with poly(C) has been studied by means of equilibrium gelfiltration through Sephadex. From sorption isotherms the free energies, energies and entropies of complexing have been computed for different concentrations of magnesium ions in the medium. The stoichiometric ratio of polymers to oligomers has been measured and found equal to 2 in the case of ApApA and ApApC. This shows that the cytidylic acid residue is included in the ternary complex. But in the case of ApApU the noncomplementary base is partly squeezed out of the complex. The stacking free energy of neighbouring oligomers has been found to be in the range 1000–3000 cal mole depending on the conditions. The stoichimetric ratio has been found to be 1 in the case of poly(C): oligo(I), the stacking energy is equal to 1.2 kcal mole . The effect of magnesium is somewhat different in the case of double and triple helices and probably reflects the formation of coordination compounds with the nitrogen bases of nucleotides.