TAILIEUCHUNG - Báo cáo khoa học: Structural basis for poor uracil excision from hairpin DNA An NMR study

Two-dimensional NMR and molecular dynamics simula-tions have been used to determine the three-dimensional structures of two hairpin DNA structures: d-CTAGAG GATCCUTTTGGATCCT (abbreviated as U1-hairpin) and d-CTAGAGGATCCTTUTGGATCCT (abbreviated as U3-hairpin). The 1 H resonances of both of these hairpin structures have been assigned almost completely. | Eur. J. Biochem. 269 1886-1894 2002 FEBS 2002 doi Structural basis for poor uracil excision from hairpin DNA An NMR study Mahua Ghosh1 Nidhi Rumpal2 Umesh Varshney2 and Kandala V. R. Chary1 1 Department of Chemical Sciences Tata Institute of Fundamental Research Colaba Mumbai India department of Microbiology and Cell Biology Indian Institute of Science Bangalore India Two-dimensional NMR and molecular dynamics simulations have been used to determine the three-dimensional structures of two hairpin DNA structures d-CTAGAG GATCCUTTTGGATCCT abbreviated as U1-hairpin and d-CTAGAGGATCCTTUTGGATCCT abbreviated as U3-hairpin . The H resonances of both of these hairpin structures have been assigned almost completely. NMR restrained molecular dynamics and energy minimization procedures have been used to describe the three-dimensional structures of these hairpins. This study and concurrent NMR structural studies on two other d-CTAGAGGA TCCTUTTGGATCCT abbreviated as U2-hairpin and d-CTAGAGGATCCTTTUGGATCCT abbreviated as U4-hairpin have shed light upon various interactions reported between Echerichia coli uracil DNA glycosylase UDG and uracil-containing DNA. The backbone torsion angles which partially influence the local conformation of U12 and U14 in U1 and U3-hairpins respectively are probably locked in the trans conformation as in the case of U13 in the U2-hairpin. Such a stretched-out backbone conformation in the vicinity of U12 and U14 is thought to be the reason why the Km value is poor for U1- and U3-hairpins as it is for the U2-hairpin. Furthermore the bases U12 and U14 in both U1- and U3-hairpins adopt an anti conformation in contrast with the base conformation of U13 in the U2-hair-pin which adopts a syn conformation. The clear discrepancy observed in the U-base orientation with respect to the sugar moieties could explain why the Vmax value is 10- to 20-fold higher for the U1- and U3-hairpins compared with the U2-hairpin. Taken together

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