Bubble-bound state of triple-stranded DNA: Efimov physics in DNA with repulsion

Abstract

The presence of a thermodynamic phase of a three-stranded DNA, namely, a mixed phase of bubbles of two bound strands and a single one, is established for large dimensions ($d\geqslant 5$ ) by using exact real space renormalization group transformations and exact computations of specific heat for finite length chains. Similar exact computations for the fractal Sierpinski gasket of dimension d  <  2 establish the stability of the phase in the presence of a repulsive three chain interaction. Although, for d  <  2, cooperativity factors for bubbles or noncrossing conditions are needed for the melting transition, the mixed phase may exist even in absence of those. In contrast to the Efimov DNA, where three strands are bound though no two are bound, the mixed phase appears at temperatures less than the two chain melting temperature. Both the Efimov-DNA and the mixed phase are formed essentially due to the strand exchange mechanism.