Thermodynamic analysis of conformational transitions in oligonucleotide complexes in presence of Na⁺and Mg²⁺ions, using “Staggering Zipper” model

Abstract

Curves of transitions in double (2-->1 transition) and triple (3-->2 transition) complexes of oligonucleotides dA(N1)with dT(N2) in solutions with Na(+) and Mg(2+) are calculated for the case of oligomer lengths from 10 to 500 nucleotides in the wide range of ion concentrations. The calculated curves of transitions and their differential analogs reflect rather exactly the position and form of experimental curves and describe dependences of transition temperatures on the length of molecules, their concentration, and ionic conditions. Values of the nucleation parameter beta for the systems studied are determined by comparison of the calculated and experimental data obtained in a number of works. The average beta value equal to 10(-3) l/mole is in an agreement with values reported for similar systems earlier. It is shown that disordering of duplex and triplex ends ("end fraying") has an essential influence on the form of melting curves, their asymmetry and the increase of the transition interval.

Hybridization of poly(rI) with poly(rC) adsorbed to the carbon nanotube surface

“…Due to some distribution in the length, the duplexes obtained after hybridization are characterized with the presence of dangling ends composed of single strands. This state manifests itself in the melting curve [42], the shape of which acquires the slight slope in the low-temperature part and the broadening of helix → coil transition in comparison with the initial duplex (18°C vs 8°C). Note that there is a difference in absolute values of hypochromic (Figure  2, curve 1) and hyperchromic (Figure  3, curve 1) coefficients.…”

ssDNA templated assembly of oligonucleotides and bivalent naphthalene guests

“…Hence, the hybridization of two single strands under given conditions can be predicted accurately. 12 In an elegant study, the hybridization of oligomeric strands, dAm (Scheme 1) and deoxyuracil nucleotides of equal 13,14 and unequal 14 length has been evaluated with a zipper model to get information on the intra-strand base-stacking interaction. The interaction between the bases within one strand makes sure that binding of a whole strand to the complementary strand is favored.…”