Propagation of Melting Cooperativity along the Phosphodiester Backbone of DNA

Abstract

The role of the DNA phosphodiester backbone in the transfer of melting cooperativity between two helical domains was experimentally addressed with a helix-bulge-helix DNA model, in which the bulge consisted of a varying number of either conformationally flexible propanediol or conformationally constrained bicyclic anucleosidic phosphodiester backbone units. We found that structural communication between two double helical domains is transferred along the DNA backbone over the equivalent of ca. 12-20 backbone units, depending on whether there is a symmetric or asymmetric distribution of the anucleosidic units on both strands. We observed that extension of anucleosidic units on one strand only suffices to disrupt cooperativity transfer in a similar way as if extension occurs on both strands, indicating that the length of the longest anucleosidic inset determines cooperativity transfer. Furthermore, conformational rigidity of the sugar unit increases the distance of coopertivity transfer along the phosphodiester backbone. This is especially the case when the units are asymmetrically distributed in both strands.

Electrostatic assembly of a DNA superparamagnetic nano-tool for simultaneous intracellular delivery and in situ monitoring

“…In fact, DNA duplex formation or denaturation is known to be a highly cooperative process determined by the stacking interactions between neighboring base pairs formed sequentially and also by the conformational properties of the sugarphosphate backbone. 44 UV-melting experiments show that even if the duplex is slightly destabilized by the interaction between the phosphate groups and the maghemite, its structure is at least partially conserved in our experimental conditions.…”

Bipyridyl‐ and Biphenyl‐DNA: A Recognition Motif Based on Interstrand Aromatic Stacking

“…This T m is only 5.7 K lower than that of the duplex containing natural base pairs at both ends (Table 5, entry 5) and is 42.4 K higher than that of the natural hexamer duplex consisting of the first six base pairs (T m = 8.9 8C). [34] From these experiments we conclude that stable I pairs can exist also in duplexes with natural base pairs on one end and a 5'-overhang of natural bases on the other end, while duplexes with bluntended I pairs or a 3'-overhang tend to aggregate. The reason of the differential behavior of duplexes with 5'-or 3'-overhang is unknown at present, but is expected to be due to stacking of the overhang on the neighboring I pair.…”

Hydrophobic Organic Linkers in the Self-Assembly of Small Molecule-DNA Hybrid Dimers: A Computational–Experimental Study of the Role of Linkage Direction in Product Distributions and Stabilities

“…39 The second factor has been ascribed by Leumann and co-workers as due to close structural communications between the two linked helical domains. 67 While chelate cooperativity may be important, our thermal data clearly point to hydrophobic interactions between the cores as a major effect.…”