1AUL

SOLUTION STRUCTURE OF A HIGHLY STABLE DNA DUPLEX CONJUGATED TO A MINOR GROOVE BINDER, NMR, MINIMIZED AVERAGE STRUCTURE

1AUL の概要

• エントリーDOI: 10.2210/pdb1aul/pdb
• 分子名称: DNA (5'-D(P*THXP*GP*AP*TP*TP*AP*TP*CP*TP*G)-3'), DNA (5'-D(*CP*AP*GP*AP*TP*AP*AP*TP*CP*A)-3') (2 entities in total)
• 機能のキーワード: deoxyribonucleic acid, cdpi3, dna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 6781.83

構造登録者

Kumar, S.,Reed, M.W.,Gamper Junior, H.B.,Gorn, V.V.,Lukhtanov, E.A.,Foti, M.,West, J.,Meyer Junior, R.B.,Schweitzer, B.I. (登録日: 1997-08-29, 公開日: 1997-12-24, 最終更新日: 2024-05-22)

主引用文献

Kumar, S.,Reed, M.W.,Gamper Jr., H.B.,Gorn, V.V.,Lukhtanov, E.A.,Foti, M.,West, J.,Meyer Jr., R.B.,Schweitzer, B.I.
Solution structure of a highly stable DNA duplex conjugated to a minor groove binder.
Nucleic Acids Res., 26:831-838, 1998

PubMed Abstract: The tripeptide 1,2-dihydro-(3 H )-pyrrolo[3,2- e ]indole-7-carboxylate (CDPI3) binds to the minor groove of DNA with high affinity. When this minor groove binder is conjugated to the 5'-end of short oligonucleotides the conjugates form unusually stable hybrids with complementary DNA and thus may have useful diagnostic and/or therapeutic applications. In order to gain an understanding of the structural interactions between the CDPI3minor groove binding moiety and the DNA, we have determined and compared the solution structure of a duplex consisting of oligodeoxyribonucleotide 5'-TGATTATCTG-3' conjugated at the 5'-end to CDPI3 and its complementary strand to an unmodified control duplex of the same sequence using nuclear magnetic resonance techniques. Thermal denaturation studies indicated that the hybrid of this conjugate with its complementary strand had a melting temperature that was 30 degrees C higher compared with the unmodified control duplex. Following restrained molecular dynamics and relaxation matrix refinement, the solution structure of the CDPI3-conjugated DNA duplex demonstrated that the overall shape of the duplex was that of a straight B-type helix and that the CDPI3moiety was bound snugly in the minor groove, where it was stabilized by extensive van der Waal's interactions.

PubMed: 9443977
DOI: 10.1093/nar/26.3.831

実験手法

SOLUTION NMR