The solution structure of [d(CGC)r(aaa)d(TTTGCG)](2): hybrid junctions flanked by DNA duplexes

The solution structure and hydration of the chimeric duplex [d(CGC)r(aaa)d( TTTGCG)](2), in which the central hybrid segment is flanked by DNA duplexes at both ends, was determined using two-dimensional NMR, simulated annealin g and restrained molecular dynamics. The solution structure of this chimeri c duplex differs from the previously determined X-ray structure of the anal ogous B-DNA duplex [d(CGCAAATTTGCG)](2) as well as NMR structure of the ana logous A-RNA duplex [r(cgcaaauuugcg)](2). Long-lived water molecules with c orrelation time tau(c) longer than 0.3 ns were found close to the RNA adeni ne H2 and H1' protons in the hybrid segment, A possible long-lived water mo lecule was also detected close to the methyl group of TT in the RNA-DNA jun ction but not with the other two thymines (8T and 9T), This result correlat es with the structural studies that only DNA residue 7T in the RNA-DNA junc tion adopts an O4'-endo sugar conformation, while the other DNA residues in cluding 3C in the DNA-RNA junction, adopt C1'-exo or C2'-endo conformations . The exchange rates for RNA C2'-OH were found to be similar to 5-20 s(-1). This slow exchange rate may be due to the narrow minor groove width of [d( CGC)r(aaa)d(TTTGCG)](2), which may trap the water molecules and restrict th e dynamic motion of hydroxyl protons. The minor groove width of [d(CGC)r(aa a)d(TTTGCG)](2) is wider than its B-DNA analog but narrower than that of th e A-RNA analog. It was further confirmed by its titration with the minor gr oove binding drug distamycin. A possible 2:1 binding mode was found by the titration experiments, suggesting that this chimeric duplex contains a wide r minor groove than its B-DNA analog but still narrow enough to hold two di stamycin molecules. These distinct structural features and hydration patter ns of this chimeric duplex provide a molecular basis for further understand ing the structure and recognition of DNA RNA hybrid and chimeric duplexes.