Solution Structure of an LNA Hybridized to DNA: NMR Study of the d(CTLGCTLTLCTLGC):d(GCAGAAGCAG) Duplex Containing Four Locked Nucleotides
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- 作者：Katrine E. Nielsen ; Sanjay K. Singh ; Jesper Wengel ; and Jens Peter Jacobsen
- 刊名：Bioconjugate Chemistry
- 出版年：2000
- 出版时间：March 2000
- 年：2000
- 卷：11
- 期：2
- 页码：228 - 238
- 全文大小：272K
- 年卷期：v.11,no.2(March 2000)
- ISSN：1520-4812
文摘
We have used two-dimensional 1H NMR spectroscopy at 750 MHz to determine a high-resolutionsolution structure of an oligonucleotide containing restricted nucleotides with a 2'-O, 4'-C-methylenebridge (LNA) hybridized to the complementary DNA strand. The LNA:DNA duplex examined containedfour thymidine LNA modifications (TL), d(C1TL2G3C4TL5TL6C7TL8G9C10):d(G11C12A13G14A15A16G17C18A19G20). A total relaxation matrix approach was used to obtain interproton distancebounds from NOESY cross-peak intensities. These distance bounds were used as restraints in moleculardynamics (rMD) calculations. Forty final structures were generated for the duplex from A-form andB-form DNA starting structures. The root-mean-square deviation (RMSD) of the coordinates for the40 structures of the complex was 0.6 Å. The sugar puckerings are averaged values of a dynamicinterchange between N- and S-type conformation except in case of the locked nucleotides that werefound to be fixed in the C3'-endo conformation. Among the other nucleotides in the modified strand,the furanose ring of C7 and G9 is predominatly in the N-type conformation whereas that of G3 is ina mixed conformation. The furanose rings of the nucleotides in the unmodified complementary strandare almost exclusively in the S-type conformation. Due to these different conformations of the sugarsin the two strands, there is a structural strain between the A-type modified strand and the B-typeunmodified complementary strand. This strain is relaxed by decreasing the value of rise andcompensating with tip, buckle, and propeller twist. The values of twist vary along the strand but fora majority of the base pairs a value even lower than that of A-DNA is observed. The average twistover the sequence is 32 ± 1
. On the basis of the structure, we conclude that the high stability ofLNA:DNA duplexes is caused by a local change of the phosphate backbone geometry that favors ahigher degree of stacking.
. On the basis of the structure, we conclude that the high stability ofLNA:DNA duplexes is caused by a local change of the phosphate backbone geometry that favors ahigher degree of stacking.