Duplex dissociation rate constants

Poly(dA-dT) Duplex Dissociation Rate Constants in 0.1 M Phosphate Solution... 

BNA (also known as LNA) has been used in TFOs in a pyrimidine motif at neutral pH. The binding constant of the BNA TFO was about 20 times larger than that of DNA as a result of a large decrease in the dissociation rate constant. A 3 -amino-2, 4 -BNA nucleotide has been prepared to introduce N3 -P5 phosphoramidate linkages. It is introduced as a dinucleotide unit (61), and in thermal stability studies was shown to exhibit superior duplex and triplex stability compared to either BNA or DNA, and shows enhanced resistance to digestion by SVPDE. These properties have previously been observed for N3 -P5 phosphoramidate linkages in DNA. ... 

This reaction can be treated as the forward association rate (kf) ratioed against the backward dissociation rate (kj. In a positively cooperative system, multiple contact points join to form completely folded states directly after the first contact between the two strands. As a consequence, the forward association process is highly favored and a very large can be realized. In a system that displays negative cooperativ-ity, the duplex is likely to undergo complete dissociation when one pair of interactions is lost. In such cases, the backward rate constant is likely to dominate and a small is observed. 

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