Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale.

ABSTRACT: The human telomeric DNA sequence with four repeats can fold into a parallel-stranded propeller-type topology. NMR structures solved under molecular crowding experiments correlate with the crystal structures found with crystal-packing interactions that are effectively equivalent to molecular crowding. This topology has been used for rationalization of ligand design and occurs experimentally in a number of complexes with a diversity of ligands, at least in the crystalline state. Although G-quartet stems have been well characterized, the interactions of the TTA loop with the G-quartets are much less defined. To better understand the conformational variability and structural dynamics of the propeller-type topology, we performed molecular dynamics simulations in explicit solvent up to 1.5 μs. T

SUBMITTER: Islam B 

PROVIDER: S-EPMC3575793 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature