B-A Transition in DNA

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Abstract
The B-A transition is characterized by two main physical parameters which might be biologically important: the cooperativity length and free energy difference between the B and A states under physiological conditions. Earlier these values were determined by us in an experiment over the B-A shift in water-non-electrolyte solutions in the presence of small molecules (“ties”) affecting the B-A equilibrium. Now we report a new method of determining the cooperativity length which utilizes a phase diagram (B,A, coil). The coordinates are the fraction of non-electrolytes and temperature. Application of the Ising model for joint description of the B-A and helix-coil transitions makes possible to find the cooperativity length using the known thermodynamic parameters of the DNA melting and the appearance of the phase diagram near the triple point (B,A, coil). The value thus found (∼ 10′ base pairs) is in accord with the values obtained with ties. In the new method the junctions between the A and B segments actually play the role of ties, stabilizing the double-stranded state. A considerable effect of the melting curve widening within the B-A transition range was discovered. A possible explanation suggests the presence of the A-philic sequences in the natural DNA. The A-phility of the oligo G• oligo C sequence was estimated from the B-A transition curves of the synthetic decanucleotide duplexes.