A kinked model for the solution structure of DNA tridecamers with inserted adenosines: energy minimization and molecular dynamics.
Structural modelling techniques using energy minimization and molecular dynamics have been employed to generate kinked models for the solution structure of two DNA tridecamer sequences containing inserted adenosines: d(CGCAGAATTCGCG)2 and d(CGCAGAGCTCGCG)2. These models are consistent with NMR studies of these sequences in solution. The overall shapes of the two models are similar, consisting of three B-DNA sections: two outer segments on the same side of the central portion, with the additional adenosines acting as wedges to kink the structure. An alternative scheme for the hydrogen bond pairing at the kink site is suggested as a way for the additional adenosines to be stabilized in the duplex.
Hirshberg
M
M
Department of Chemical Physics, Weizmann Institute of Science, Rehovot, ISRAEL.
Sharon
R
R
Sussman
J L
JL
D000241:Adenosine; D004247:DNA / Q000648:ultrastructure*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation
D004247:DNA; D000241:Adenosine