… at specific DNA sites have been engineered to overcome the problem of competitive
inhibition by excess nonspecific binding sites on DNA. The formation of a specific protein–DNA …

… DNA than stacking, because H-bonding (unlike stacking) is penalized by a large desolvation
energy… simulations with a modified energy function. As has been shown, the stacking …

… In this paper the values of three free energy parameters governing the superhelical …
transition to a torsionally deformable alternative conformation, which takes place in a circular DNA …

… an energy source such as ATP, are abundant in biology 8 , 9 . It has been shown previously
that branched motifs of DNA can … device consisting of two rigid DNA ‘double-crossover’ (DX) …

… energy effects of 5-methylation of cytosine on the B - Z conformational equilibrium in DNA. …
Since for our purposes it was necessary to calculate the free energy effects of methylation in …

… The free energy parameters for the transition in dilute … of plasmidsat which the transition
occurs in alternating CG inserts … of the right-handed DNA duplex at each of the B/Z junctions. …

… DNA- and the homogeneous bacterial and phage DNA. Hence, in the B to A transition DNA
… It is reasonable further to assume that the free energy of the DNA chain in the body of the …

… , we have also calculated the electrostatic contributions to the transition free energy for DNA
modeled with a formal charge of −1 on each phophorus atom and all other atoms uncharged…

… the study of direct and indirect effects of low-energy electrons (LEEs) on DNA damage. In an
… plasmids, DNA bases, sugar analogs, phosphate groups, and longer DNA moieties. Here, …

… accessible conformation of the DNA duplex and provide … transition. In this Perspective, we
describe pathways and kinetics for this transition at an atomic level of detail, using the energy …