CC/GG Contacts Facilitate the B to A Transition of DMA in Solution

Abstract

Self-complementary decadeoxynucleotides, CCGATATCGG, CCAGATCTGG, CCCTGCAGGG, GGGGGCCCCC, were designed and synthesized to estimate the A-philic free energy of CC/GG contacts. First, regions of temperature-stability of the double-stranded conformation were determined for each 10-mer. Then, circular dichroism spectra were recorded for the B-family forms at different temperatures, counter-ion concentrations and trifluoroethanol contents. A cooperative change typical of the B-A transition is observed in the CD spectra at a trifluoroethanol content specific for each duplex. The positions of half-transition points were functions not only of the nucleotide sequence but of the duplex length as well: the B to A transitions were hindered in these 10-mers in comparison with a lengthy DNA. The B-phility value was estimated to be 3 kcal/mol of 10-mer. The B-A transition point was shown to drop with an increase in the number of CC/GG contacts in a duplex. The designed 10-mers made it possible to estimate quantitatively the A-phility of CC/GG contact as compared with an average DNA: (FA-FB)CC = 0.2 Kcal/mol, (FA-FB)DNA = 0.7 Kcal/mol.

The structure of a stable intermediate in the A ↔ B DNA helix transition

“…Independent theoretical studies have predicted that the thermodynamic barrier between A and B forms for A-favoring Gtracts in solution is no more than 0.2 kcal͞mol (13,25). Electrostatic repulsion between stacked GC base pairs in the B DNA form creates a destabilizing tension that increases cooperatively with G-tract length (26).…”

“…Fiber diffraction and solution studies have shown that Gtracts, or runs of four of more GC base pairs, also have special structural properties. G-tracts favor the A DNA helix conformation and, depending on the local water activity, can induce a B-to-A DNA transition (10)(11)(12)(13). Sequences with long G tracts usually crystallize as A DNA (14,15).…”

Protein–DNA Hydrophobic Recognition in the Minor Groove is Facilitated by Sugar Switching

“…Further, changes in sugar pucker are often associated with larger alterations to DNA structure, such as the B-to-A transition that widens and flattens the minor groove, thereby providing a more readily accessible surface for interactions with proteins. 16 And, since the energy cost of this transition is sequence-dependent in solution, 24,25 it is plausible that the B-to-A switch can increase selectivity of the protein-DNA binding.…”

Photochemical probing of the B–A conformational transition in a linearized pUC19 DNA and its polylinker region

“…DNA can adopt an A-like double helix even when it contains sugars puckered in the B-like fashion [21,22]. Such a double helix is stabilized by G n ·C n runs [21][22][23][24][25][26]. This unusual B/A hybrid is interesting from the evolutionary point of view because it suggests a possible way of transmission of molecular mechanisms developed on RNA to DNA during the RNA-to-DNA world transition [21,22].…”