DNA BENDING EFFECT OF REPLACING ADENINE W/ GUANINE NMR & COMPUTER EXPERIMENTS

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The width of the minor groove was determined in the following three closely related I I-mer B-DNA duplexes code named AAA, GAA and GGA C-C-T-C-A-A-A-C-T-C-C G-G-A-G-T-T-T-G-A-G-G AAA C-C-T-C-A-A-A-C-T-C-C G-G-A-G-T-T-T-G-A-G-G GAA C-C-T-C-A-A-A-C-T-C-C G-G-A-G-T-T-T-G-A-G-G GGA III by monitoring the interstrand NOE between the H2 of adenine and Hl' of the 3'-neighboring residue from the complementary strand at 500 MHz. It has been shown that the width of the minor groove was narrow in the GC rich oligonucleotides and that the narrow minor groove was not something endemic to A-tract DNA. The width of the groove is dictated by local sequence contexts and independent of neighboring A-tract DNA. It is also known that DNA bending is associated with nucleotidyl units assuming trans conformation about C4'-C5' at the 5' end of A-tract, and heteronomous structures at the 3' end of the A-tract. In view of our previous observation that DNA bends and kinks also occur in GC rich oligomers GAA and GGA, we have carried out a series of 'H-H, 'H-"P and 'H- 13C COSY NMR experiments to determine 'H-'H, 'H_31 p, 31 p_ I 3C, three bond couplings. The various coupling constants of the sugar phospahte backbone in GAA and GGA along each chain of the duplex are being extracted using computer simulation. In addition to extracting the coupling constants, we have also recorded the NOESY spectra for GAA and GGA at various mixing times. The coupling data and the NOESY distance data on these oligomers will be used to derive an ensemble of spatial configurations in equilibrium. It is believed that these data will lead to a better understanding of the DNA bending problem.