Induction of B-A transitions of deoxyoligonucleotides by multivalent cations in dilute aqueous solution

Abstract

Circular dichroism (CD) spectra of d(CCCCGGGG) in the presence of Co(NH3)6(3+) are very similar to spectra of r(CCCCGGGG). In contrast, B-form characteristics are observed for d(CCCCGGGG) in the presence of Na+ and Mg2+, even at high salt concentrations. Spermidine induces modest changes of the CD of d(CCCCGGGG). The NMR chemical shifts of the nonexchangeable protons of d(CCCCGGGG) in the absence and presence of Co(NH3)6(3+) were assigned by proton two-dimensional (2D) NOESY and COSY measurements. The chemical shifts of the GH8 protons of d(CCCCGGGG) move upfield upon titration with Co(NH3)6Cl3. The sums of the sugar H1' coupling constants decrease with added Co(NH3)6Cl3. Cross peak intensities in the 2D proton NOESY spectra show a transformation from B-DNA to A-DNA characteristics upon the addition of Co(NH3)6Cl3. The temperature-dependent 59Co transverse and longitudinal relaxation rates demonstrate that Co(NH3)6(3+) is site-bound to the oligomer. Such localization is not a general feature of Co(NH3)6(3+) binding to oligonucleotides. 59Co NMR relaxation and CD measurements demonstrate chiral discrimination by d(CCCCGGGG) for the two stereoisomers of Co(en)3(3+). Both stereoisomers bind tightly as judged by 59Co NMR, and both cause large (but nonequivalent) changes in the CD of this oligomer.

Mapping the B-A conformational transition along plasmid DNA

“…DNA contains deoxyribose instead of ribose, and deoxyribose is more stable in C2′-endo puckering in the aqueous solution to promote the B-form (40). However, DNA can undergo the B-A transition (6,7,32) that is induced by a number of agents, including spermine (16) and other multivalent cations (17,18), methanol (8) and, most importantly, proteins such as the catabolite activator protein (12) and numerous polymerases (9,10,13,41). The most common inducer of the A-form is ethanol (6,7,42) that was used to induce the B-A transition in the present study.…”

Conformational Preferences of DNA in Reduced Dielectric Environments

“…6,11,15,18,25 Calculated free energy differences between A- and B-form structures are given in Tables 3 and 4 with positive values indicating a preference for the A-form while negative values indicate a preference for the B-form.…”

B-DNA Helix Stability in a Solvent-Free Environment

“…Although the B-helix is recognized as the standard helix form for DNA, the B-to-A (B-A) transition is thought to be very important biologically as the presence of the TATA-binding protein [7,8] and certain polymerases have been observed to induce this transition [9 -14]. B-A transitions have also been observed when alcohols and some salts are added to a DNA solution, decreasing its relative humidity (RH) [15][16][17][18][19]. To further understand this dependence on RH, many different DNA duplex sequences have been analyzed with varying solution conditions.…”