Solution Structure of an LNA Hybridized to DNA: NMR Study of the d(CTLGCTLTLCTLGC):d(GCAGAAGCAG) Duplex Containing Four Locked Nucleotides
- 23 February 2000
- journal article
- research article
- Published by American Chemical Society (ACS) in Bioconjugate Chemistry
- Vol. 11 (2) , 228-238
- https://doi.org/10.1021/bc990121s
Abstract
We have used two-dimensional 1H NMR spectroscopy at 750 MHz to determine a high-resolution solution structure of an oligonucleotide containing restricted nucleotides with a 2‘-O, 4‘-C-methylene bridge (LNA) hybridized to the complementary DNA strand. The LNA:DNA duplex examined contained four thymidine LNA modifications (T L), d(C1T L2G3C4T L5T L6C7T L8G9C10):d(G11C12A13G14A15A16G17C18A19G20). A total relaxation matrix approach was used to obtain interproton distance bounds from NOESY cross-peak intensities. These distance bounds were used as restraints in molecular dynamics (rMD) calculations. Forty final structures were generated for the duplex from A-form and B-form DNA starting structures. The root-mean-square deviation (RMSD) of the coordinates for the 40 structures of the complex was 0.6 Å. The sugar puckerings are averaged values of a dynamic interchange between N- and S-type conformation except in case of the locked nucleotides that were found 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 in a mixed conformation. The furanose rings of the nucleotides in the unmodified complementary strand are almost exclusively in the S-type conformation. Due to these different conformations of the sugars in the two strands, there is a structural strain between the A-type modified strand and the B-type unmodified complementary strand. This strain is relaxed by decreasing the value of rise and compensating with tip, buckle, and propeller twist. The values of twist vary along the strand but for a majority of the base pairs a value even lower than that of A-DNA is observed. The average twist over the sequence is 32 ± 1°. On the basis of the structure, we conclude that the high stability of LNA:DNA duplexes is caused by a local change of the phosphate backbone geometry that favors a higher degree of stacking.Keywords
This publication has 20 references indexed in Scilit:
- Investigation of restricted backbone conformations as an explanation for the exceptional thermal stabilities of duplexes involving LNA (Locked Nucleic Acid):† synthesis and evaluation of abasic LNAChemical Communications, 1999
- LNA (Locked Nucleic Acid): An RNA Mimic Forming Exceedingly Stable LNA:LNA DuplexesJournal of the American Chemical Society, 1998
- Novel convenient syntheses of LNA [2.2.1]bicyclo nucleosidesTetrahedron Letters, 1998
- Stabilizing effects of the RNA 2′-substituent: crystal structure of an oligodeoxynucleotide duplex containing 2′-O-methylated adenosinesChemistry & Biology, 1994
- Solution structure of a conserved DNA sequence from the HIV-1 genome: Restrained molecular dynamics simulation with distance and torsion angle restraints derived from two-dimensional NMR spectraBiochemistry, 1993
- Solution structure of a DNA octamer containing the pribnow box via restrained molecular dynamics simulation with distance and torsion angle constraints derived from two-dimensional nuclear magnetic resonance spectral fittingJournal of Molecular Biology, 1992
- Antisense oligonucleotides: a new therapeutic principleChemical Reviews, 1990
- Solution structure of phage .lambda. half-operator DNA by use of NMR, restrained molecular dynamics, and NOE-based refinementBiochemistry, 1990
- Relaxation matrix analysis of 2D NMR dataProgress in Nuclear Magnetic Resonance Spectroscopy, 1990
- Sequential resonance assignments in DNA proton NMR spectra by two-dimensional NOE spectroscopyJournal of the American Chemical Society, 1983