135D

SOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX CONTAINING G(DOT)GC AND T(DOT)AT TRIPLES


SOLUTION NMR
NMR Refinement
MethodDetailsSoftware
RESTRAINED MOLECULAR DYNAMICS, DISTANCE GEOMETRYRESTRAINED 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.X-PLOR
NMR Ensemble Information
Conformer Selection Criteria
Conformers Calculated Total Number
Conformers Submitted Total Number1
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementX-PLORBRUNGER