SOLUTION STRUCTURE AND HYDRATION PATTERNS OF A PYRIMIDINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX CONTAINING A NOVEL T(DOT)CG TRIPLE

Solution structure and hydration patterns of a pyrimidine.purine.pyrimidine DNA triplex containing a novel T.CG base-triple.

DNA (5'-D(*GP*AP*AP*CP*AP*GP*GP*TP*TP*TP*TP*T*CP*CP*TP*GP*TP*TP*CP*TP*TP*TP*TP*T*CP*TP*TP*TP*TP*CP*C)-3')

(DG)(DA)(DA)(DC)(DA)(DG)(DG)(DT)(DT)(DT)(DT)(DT)(DC)(DC)(DT)(DG)(DT)(DT)(DC)(DT)
(DT)(DT)(DT)(DT)(DC)(DT)(DT)(DT)(DT)(DC)(DC)

NUMBER OF NUCLEIC ACID ATOMS -- 415 RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE CONDUCTED ON IDEALIZED A'- AND B-FORM STARTING STRUCTURES. ONLY THE TRIPLEX REGION IN THE SEQUENCE WAS CONSIDERED. SIX STRUCTURES WERE CALCULATED INITIALLY USING DISTANCE RESTRAINTS. A MAJORITY OF THE DISTANCE RESTRAINTS WERE SUBSEQUENTLY REPLACED BY NOE INTENSITY RESTRAINTS. THE R(1/6) VALUE WAS MONITORED DURING THE REFINEMENTS. EACH STRUCTURE WAS SUBJECTED TO 500 CYCLES OF ENERGY MINIMIZATION AFTER THE DYNAMICS. NO AVERAGE STRUCTURE WAS CALCULATED. THE R(1/6) VALUE FOR THE MINIMIZED STRUCTURE REPRESENTING THE ENSEMBLE IS 0.024. THE DYNAMICS SIMULATIONS WERE PERFORMED IN THE PRESENCE OF EXPLICIT SOLVENT MOLECULES AND 15 NA+ COUNTER IONS. THE SUMMATION EXTENDS THROUGH ALL ASSIGNABLE, QUANTIFIABLE CROSS PEAK INTENSITIES IN NOESY SPECTRA RECORDED AT MIXING TIMES OF 40, 90 AND 150 MS. RMS DEVIATIONS FROM IDEALIZED GEOMETRY FOR THE MINIMIZED STRUCTURE `RM' REPRESENTING THE ENSEMBLE ARE AS FOLLOWS: RM BOND (ANGSTROMS) 0.016 (0.016) ANGLES (DEGREES) 3.825 (3.734) IMPROPERS (DEGREES) 0.552 (0.391) THE VALUES IN PARENTHESES CORRESPOND TO THE AVERAGE VALUES FOR THE ENSEMBLE OF SIX STRUCTURES.