SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING AN ALPHA-ANOMERIC ADENOSINE: INSIGHTS INTO SUBSTRATE RECOGNITION BY ENDONUCLEASE IV
THE CORE OF THE SEQUENCE CORRESPONDS TO THE RECOGNITION SITE OF E. COLI ENDONUCLEASE IV
FOR NON-EXCHANGEABLE PROTONS, NOESY EXPERIMENTS IN D2O WERE PERFORMED WITH 10S RELAXATION DELAYS AND MIXING TIMES OF 75MS, 150MS AND 250 MS. FOR EXCHANGEABLE PROTONS, A WATERGATE NOESY WAS PERFORMED WITH A RELAXATION DELAY OF 4S AND 150MS MIXING TIME.
THE STRUCTURE IS BASED ON A TOTAL OF 502 RESTRAINTS: 284 DISTANCE RESTRAINTS, 80 ENDOCYCLIC TORSION ANGLE RESTRAINTS, 50 WATSON-CRICK DISTANCE AND ANGLE RESTRAINTS, AND 88 BACKBONE TORSION ANGLE RESTRAINTS. THE ALPHAA DUPLEX STRUCTURE WAS ELUCIDATED BY A COMBINATION OF DYANA AND RMD/REM IN AMBER. ALL CALCULATIONS WERE PERFORMED IN VACUO. THE FINAL STRUCTURE DEPOSITED HERE WAS OBTAINED BY COORDINATE AVERAGING THE FINAL ENSEMBLE OF 10 RMD/REM STRUCTURES FOLLOWED BY RESTRAINED ENERGY MINIMIZATION. THIS STRUCTURE WAS FURTHER REFINED BY RMD IN VACUO WITH AN ADDITIONAL 25 C-H RESIDUAL DIPOLAR COUPLINGS, FOLLOWED BY REM.
TORSION ANGLE DYNAMICS MOLECULAR DYNAMICS
1.0 MM ALPHAA DUPLEX, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.1 MM EDTA, PH 6.6
DNA DOUBLE HELIX WITH ENLARGED MINER GROOVE AND HELICAL KINK, DNA