SOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX CONTAINING G(DOT)GC AND T(DOT)AT TRIPLES
Solution structure of a purine.purine.pyrimidine DNA triplex containing G.GC and T.AT triples.
Solution Structure of an Intramolecular Purine(Dot)Purine(Dot)Pyrimidine DNA Triplex
(DT)(DC)(DC)(DT)(DC)(DC)(DT)(DT)(DT)(DT)(DT)(DT)(DA)(DG)(DG)(DA)(DG)(DG)(DA)(DT) (DT)(DT)(DT)(DT)(DT)(DG)(DG)(DT)(DG)(DG)(DT)
RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE DONE ONIDEALIZED A'- AND B-FORM STARTING STRUCTURES. ONLY THE TRIPLEX REGION AND THE FIRST AND LAST RESIDUES OF EACH OF THE TWO LOOPS IN THE SEQUENCE WERE CONSIDERED. THE REFINEMENT WAS CONDUCTED IN TWO STAGES. IN THE FIRST STAGE, SIX STRUCTURES WERE CALCULATED (THREE FROM EACH STARTING STRUCTURE) USING DISTANCE RESTRAINTS. IN THE SECOND STAGE, TWO OF THE SIX STRUCTURES WERE REFINED DIRECTLY AGAINST PRIMARY NOE DATA. THE R(1/6) VALUE WAS USED TO MONITOR THE REFINEMENT DURING THIS STAGE. THE FINAL R(1/6) VALUES FOR THE TWO AVERAGED MINIMIZED STRUCTURES WERE 0.04 AND 0.045.
RESTRAINED MOLECULAR DYNAMICS, DISTANCE GEOMETRY