By Nancy C. Stellwagen, Udayan Mohanty
Curvature and Deformation of Nucleic Acids: fresh Advances, New Paradigms provides an updated assessment at the curvature and deformation of nucleic acids. bankruptcy 1 units a few of the chapters in context, in addition to describing numerous debatable themes. bankruptcy 2 supplies a complete overview of the literature on DNA bending and describes the present prestige of molecular dynamics simulations of DNA and protein-DNA complexes. bankruptcy three describes the structural foundation for A-tract DNA helix bending, according to fresh NMR constructions and different biophysical measurements. bankruptcy four describes the localization of Mg++ ions within the crystal constitution of a B-form DNA dodecamer and discusses the relevance of those sure ions to sequence-dependent bending. bankruptcy five discusses the electrostatic strength consequences that outcome from phosphate crowding in curved DNA oligomers. bankruptcy 6 provides a quantitative version that predicts the significance of the bend brought on by uneven cost neutralization of DNA phosphate residues. bankruptcy 7 experiences the structural and dynamic houses of four-way DNA junctions within the presence of steel ions, and it describes the alternate among substitute stacking conformers in answer. bankruptcy eight files the truth that a conserved pseudouridine residue in an RNA duplex containing a precursor messenger department web site makes a big contribution to the constitution of the molecule. bankruptcy nine describes structural perturbations which are saw in disease-related mutants of human mitochondrial move RNAs. bankruptcy 10 stories the thermodynamics of the folding and unfolding of DNA oligomers distorted through the binding of small ligands. bankruptcy eleven describes a mode of creating DNA fragments for cyclization reviews that makes use of unmarried strand gaps as versatile hinges that permit the proper torsional orientation of the helix ends. bankruptcy 12 experiences a statistical mechanical version that predicts the steadiness of reconstituted nucleosomes in response to sequence-dependent DNA curvature and flexibility.
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With no B ' / B differentiation, there is no structural helix phasing, and the bending enhancement disappears. ch002 32 treated in M D and make interesting problems in the area of conformational stability and transitions accessible to more rigorous theoretical study. Cheatham and Kollman  reported M D on d ( C C A A C G T T G G ) in which the expected A / B conformational preferences were observed in water, including an A to B transition. However, at low water activity, a simulation beginning in the B form did not make the expected conformational transition to the A in a trajectory of 500 ps.
Due to the palindromic symmetry of the sequence, fully converged ion distribution results should exhibit symmetry with respect to the midpoint of the dodecamer, the A p T step. ch002 28 classes, Suzuki and coworkers  show that a) A-form oligonucleotides show relatively little differentiation with respect to sequence and b) B - form oligonucleotides show clear evidence of sequence effect, with values for Y R , Y Y and R Y steps forming essentially non-overlapping clusters in roll/slide/twist space.
19] have provided a schematic of possible ion binding sites in the major and minor groove of D N A (Figure 4) which indicate possible major groove as well as minor groove electrostatic pockets. Williams and coworkers , based on the idea of structural deformations arising from the modulation of phosphate repulsions , have argued the case for "cations in charge" of D N A structure. This idea has been recently argued , based on the crystal structure of a cross-linked dodecamer in environmental conditions without appreciable monovalent cations.