Origin of the intrinsic rigidity of DNA.
The intrinsic rigidities of DNA and RNA helices are generally thought to arise from some combination of vertical base-stacking interactions and intra-helix phosphate-phosphate charge repulsion; however, the relative contributions of these two types of interaction to helix rigidity have not been quantified. To address this issue, we have measured the rotational decay times of a 'gapped-duplex' DNA molecule possessing a central, single-stranded region, dT24, before and after addition of the free purine base, N6-methyladenine ((me)A). Upon addition of (me)A, the bases pair with the T residues, forming a continuous stack within the gap region. Formation of the gapped duplex is accompanied by a nearly 2-fold increase in decay time, to values that are indistinguishable from the full duplex control for monovalent salt concentrations up to 90 mM. These results indicate that at least 90% of the rigidity of the dT(n)-dA(n) homopolymer derives from base pair stacking effects, with phosphate-phosphate interactions contributing relatively little to net helix rigidity at moderate salt concentrations.
Mills
Janine B
JB
Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, 4200 East Ninth Avenue, Denver, CO 80262, USA.
Hagerman
Paul J
PJ
D000225:Adenine / Q000031:analogs & derivatives* / Q000737:chemistry; D020029:Base Pairing; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry; D012399:Rotation; D013941:Thymine / Q000737:chemistry
D000225:Adenine; D004247:DNA; D004277:DNA, Single-Stranded; D013941:Thymine; C000730567:6-methyladenine