1HG9

Solution structure of DNA:RNA hybrid

1HG9 の概要

• エントリーDOI: 10.2210/pdb1hg9/pdb
• 関連するPDBエントリー: 1HHW 1HHX
• 分子名称: 5- D(*CP*TP*GP*AP*TP*AP*TP*GP*C) -3, 5- R(*GP*CP*AP*UP*AP*UP*CP*AP*G) -3 (2 entities in total)
• 機能のキーワード: dna-rna hybrid, dna rna hybrid, dna/rna chimeric hybrid duplex, antisense, locked nucleic acid, dna, rna, hybrid, rnase h
• 由来する生物種: synthetic construct; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 5586.58

構造登録者

Petersen, M.,Bondensgaard, K.,Wengel, J.,Jacobsen, J.P. (登録日: 2000-12-13, 公開日: 2002-01-02, 最終更新日: 2024-05-15)

主引用文献

Bondensgaard, K.,Petersen, M.,Singh, S.K.,Rajwanshi, V.K.,Kumar, R.,Wengel, J.,Jacobsen, J.P.
Structural studies of LNA:RNA duplexes by NMR: conformations and implications for RNase H activity.
Chemistry, 6:2687-2695, 2000

PubMed Abstract: We have used NMR and CD spectroscopy to study the conformations of modified oligonucleotides (locked nucleic acid, LNA) containing a conformationally restricted nucleotide (T(L)) with a 2'-O,4'-C-methylene bridge. We have investigated two LNA:RNA duplexes, d(CTGAT(L)ATGC):r(GCAUAUCAG) and d(CT(L)GAT(L)AT(L)GC):r(GCAUAUCAG), along with the unmodified DNA:RNA reference duplex. Increases in the melting temperatures of +9.6 degrees C and +8.1 degrees C per modification relative to the unmodified duplex were observed for these two LNA:RNA sequences. The three duplexes all adopt right-handed helix conformations and form normal Watson-Crick base pairs with all the bases in the anti conformation. Sugar conformations were determined from measurements of scalar coupling constants in the sugar rings and distance information derived from 1H-1H NOE measurements; all the sugars in the RNA strands of the three duplexes adopt an N-type conformation (A-type structure), whereas the sugars in the DNA strands change from an equilibrium between S- and N-type conformations in the unmodified duplex towards more of the N-type conformation when modified nucleotides are introduced. The presence of three modified T(L) nucleotides induces drastic conformational shifts of the remaining unmodified nucleotides of the DNA strand, changing all the sugar conformations except those of the terminal sugars to the N type. The CD spectra of the three duplexes confirm the structural changes described above. On the basis of the results reported herein, we suggest that the observed conformational changes can be used to tune LNA:RNA duplexes into substrates for RNase H: Partly modified LNA:RNA duplexes may adopt a duplex structure between the standard A and B types, thereby making the RNA strand amenable to RNase H-mediated degradation.

PubMed: 10985717
DOI: 10.1002/1521-3765(20000804)6:15<2687::aid-chem2687>3.0.co;2-u

実験手法

SOLUTION NMR