Solution structure of an LNA hybridized to DNA: NMR study of the d(CT(L)GCT(L)T(L)CT(L)GC):d(GCAGAAGCAG) duplex containing four locked nucleotides

Bioconjugate Chemistry

Volumn 11, Issue 2, 2000, Pages 228-238

  Nielsen, Katrine E ^a   Singh, Sanjay K ^b   Wengel, Jesper ^b   Jacobsen, Jens Peter ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

BASE PAIRING; COMPLEMENTARY DNA; DNA CONFORMATION; DNA STRAND; FURANOSE; LNA DNA HYBRIDIZATION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE;

DNA; LOCKS (FASTENERS); MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; OLIGONUCLEOTIDES;

COMPLEMENTARY STRAND; DISTANCE BOUND; DNA DUPLEXES; FURANOSE RING; H NMR SPECTROSCOPY; HIGH RESOLUTION; METHYLENE BRIDGE; NMR STUDIES; SOLUTION STRUCTURES; TWO-DIMENSIONAL;

CONFORMATIONS;

EID: 0034023314     PISSN: 10431802     EISSN: None     Source Type: Journal    
DOI: 10.1021/bc990121s     Document Type: Article

References (44)

1. 2, an RNA duplex at 1.30 Å Resolution. Hydration Pattern of 2′-O-methylated RNA. Nucleic Acids Res. 25, 4599-4607.
2. Baleja, J. D., pon, R. T., and Sykes, B. D. (1990) Solution Structure of Phage Lamda Half-Operator DNA by Useof NMR, Restrained Molecular Dynamics, and NOE-Based Refinement. Biochemistry 29, 4828-4839.
3. Blommers, M. J. J., Pieles, U., and De Mesmaeker, A. (1994) An Approach to the Structure Determination of Nucleic Acid Analogues Hybridized to RNA. NMR Studies of a Duplex Between 2′-O-Me RNA and an Oligonucleotide Containing a Single Backbone Modification. Nucleic Acids Res. 22, 4187-4194.
4. 1H NMR Spectra of Oligonucleotides by Two-Dimensional NMR Spectroscopy. Application to lac Operator Fragment. J. Magn. Reson. 62, 378-386.
5. Borgias, B. A., and James, T. L. (1990) MARDIGRAS-A Procedure for Matrix Analysis of Relaxation for Discerning Geometry of an Aqueous Structure. J. Magn. Reson. 87, 475-487.
6. Borgias, B. A., Gochin, M., Kerwood, D., and James, T. L. (1990) Relaxation Matrix Analysis of 2D NMR Data. Prog. NMR Spectrosc. 22, 83-100.
7. Breslauer, Frank, R., Blücker, H., and Marky, L. (1986) Predicting DNA Duplex Stability from Base Sequence. Proc. Natl. Acad. Sci. 83, 3746-3750.
8. De Mesmaeker, A., Häner, R., Martin, P., and Moser, H. E. (1995) Antisense Oligonucleotides. Acc. Chem. Res. 28, 366-374.
9. Dickerson, R. E., Bansal, M., Calladine, C. R., Diekmann, S., Hunter, W. N., Kennard, O., von Kitzing, E., Nelson, H. C. M., Lavery, R., Olson, W. K., Saenger, W., Shakked, Z., Soumpasis, D. M., Tung, C.-S., Sklenar, H., Wang, A. H. J., and Zhurkin, V. B. (1989) Definitions and Nomenclature of Nucleic Acid Structure Parameters. EMBO J. 8, 1-4.
10. 2. Biochemistry 22, 5943-5951.
11. Gotfredsen, C. H., Spielmann, H. P., Wengel, J., and Jacobsen, J. P. (1996) Structure of a DNA duplex Containing a Single 2′-O-Methyl-beta-D-araT: Combined Use of NMR, Restrained Molecular Dynamics and Full Relaxation Matrix Refinement. Bioconjugate Chem. 7, 680-688.
12. Hare, D. R., Wemmer, D. E., Chou, S.-H., Drobny, G., and Reid, B. R. (1983) Assignment of the Non-Exchangeable Proton Resonances of d(C-G-C-G-A-A-T-T-C-G-C-G) Using Two-Dimensional Nuclear Magnetic Resonance Methods. J. Mol. Biol. 171, 319-336.
13. Hélène, C. (1991) The Anti-Gene Strategy: Control of Gene Expression by Triplex-Forming-Oligonucleotides. Anti-Cancer Drug Des. 6, 569-584.
14. Hélène, C., and Toulmé, J.-J. (1990) Specific Regulation of Gene Expression by Antisense, Sense and Antigene Nucleic Acids. Biochim. Biophys. Acta 1049, 99-125.
15. Johansen, F., and Jacobsen, J. P. (1998) Site Selective Bis-Intercalation of a Homodimeric Oxazole Yellow dye in DNA Oligonucleotides. J. Biomol. Struct. Dyn. 16, 205-222.
16. Koshkin, A. A., Singh, S. K., Nielsen, P., Rajwanshi, V. K., Kumar, R., Meldgaard, M., Olsen, C. E., and Wengel, J. (1998a) LNA (Locked Nucleic Acids): Synthesis of the Adenine, Cytosine, Guanine, 5-Methylcytosine, Thymine and Uracil Bicyclonucleoside Monomers, Oligomerisation, and Unprecedented Nuclei Acid Recognition. Tetrahedron 54, 3607-3630.
17. Koshkin, A. A., Rajwanshi, V. K., and Wengel, J. (1998b) Novel Convinient Syntheses of LNA [2.2.1]Bicyclo Nucleosides. Tetrahedron Lett. 39, 4381-4384.
18. Koshkin, A. A., Nielsen, P., Meldgaard, M., Rajwanshi, V. K., Singh, S. K., and Wengel, J. (1998c) LNA (Locked Nucleic Acid): An RNA Mimic Forming Exceedingly Stable LNA:LNA Duplexes. J. Am. Chem. Soc. 120, 13252-13253.
19. Kværnø, I., and Wengel, J. (1999) 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 LNA. Chem. Commun. 1999, 657-658.
20. Lavery, R., and Sklenar, H. (1988) The Definition of Generalized Helicoidal Parameters and of Axis Curvature of Irregular Nucleic Acids. J. Biomol. Struct. Dyn. 6, 63-91.
21. Lavery, R., and Sklenar, H. (1989) Defining the Structure of Irregular Nucleic Acids: Conventions and Principles. J. Biomol. Struct. Dyn. 7, 655-667.
22. Liu, H., Spielmann, H. P., Ulyanov, N. A., Wemmer, D. E., and James, T. L. (1995) Interproton Distances Bounds from 2D-NOE Intensities: Effect of Experimental Noise and Peak Integrations Errors. J. Biol. NMR 6, 390-402.
23. Lubini, P., Zürcher, W., and Egli, M. (1994) Stabilizing Effects of the RNA 2′-Substituent: Crystal Structure of an Oligodeoxynucleotide Duplex Containing 2′-O-Methylated Adenosines. Chem. Biol. 1, 39-45.
24. Mujeeb, A., Kerwin, S. M., Kenyon, G. L., and James, T. L. (1993) 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 Spectra. Biochemistry 32, 13419-13431.
25. Nielsen, C. B., Singh, S. K., Wengel, J., and Jacobsen, J. P. (1999) The Solution Structure of a Locked Nucleic Acid (LNA) Hybridized to DNA. J. Biomol. Struct. Dyn. 17, 175-191.
26. Nielsen, P. E. (1991) Sequence-Selective DNA Recognition by Synthetic Ligands. Bioconjugate Chem. 2, 1-12.
27. Obika, S., Nanbu, D., Hari, Y., Mon, K., In, Y., Ishida, T., and Imanishi, T. (1997) Synthesis of 2′-O, 4′-C-Methyleneuridine and -Cytidine. Novel Bicyclic Nucleosides Having a Fixed C3′-endo Sugar Puckering. Tetrahedron Lett. 38, 8735
28. Petersen, M., and Jacobsen, J. P. (1998) Solution Structure of a DNA Complex with the Fluorescent Bis-Intercalator TOTO Modified in the Major Groove. Bioconjugate Chem. 9, 331-340.
29. Petersen, M., Nielsen, C. B., Nielsen, K. E., Jensen, G. A., Bondensgaard, K., Singh, S. K., Rajwanshi, V. K., Koshkin, A. A., Dahl, B. M., Wengel, J., and Jacobsen, J. P. (2000) Conformation of Locked Nucleic Acid (LNA) Hybridized to DNA. J. Mol. Recognit. 13, 44-53.
30. 2 under Low Salts Conditions. Nucleic Acids Res. 25, 4589-4598.
31. Saenger, W. (1984) Principles of Nucleic Acid Structure, Springer-Verlag, New York.
32. 1H NMR Spectra by Two-Dimensional NOE Spectroscopy. J. Am. Chem. Soc. 105, 2914-2916.
33. Schmitz, U., Sethson, I., Egan, W. M., and James, T. L. (1992) Solution Structure of a DNA Octamer Containing the Pribnow Box via Restrained Molecular Dynamics Simulation with Distance and Torsional Angle Constraints Derived from Two-Dimensional Nuclear Magnetic Resonance Spectral Fitting. J. Mol. Biol. 227, 510-531.
34. Searle, M. S., and Williams, D. H. (1993) On the Stability of Nucelic Acid Structures in Solution: Enthalpy - Entropy Compensations, Internal Rotations and Reversability. Nucleic Acid Res. 21, 2051-2056.
35. Singh, S. K., and Wengel, J. (1998) Universality of LNA-Mediated High-Affinity Acid Recognition. Chem. Commun. 1247-1248.
36. Singh, S. K., Nielsen, P., Koshkin, A. A., and Wengel, J. (1998) LNA (Locked Nucleic Acids): Synthesis and High-Affinity Acid Recognition. Chem. Commun. 1998, 455-456.
37. Spielmann, H. P., Wemmer, D. E., and Jacobsen, J. P. (1995) The Solution Structure of a DNA Complex with the Fluorescent TOTO Determined by NMR Spectroscopy. Biochemistry 34, 8542-8553.
38. Stein, P. C., Jacobsen, J. P., and Spielmann, H. P. (1995) Design and Implementation of a Simple Shaped Notch Filter. J. Magn. Res., Ser. B 109, 93-96.
39. Thuong, N. T., and Hélène, C. (1993) Sequence-Specific Recognition and Modification of Double-Helical DNA by Oligonucleotides. Angew. Chem., Int. Ed. Engl. 32, 666-690.
40. Uhlmann, E., and Peyman, A. (1990) Antisense Oligonucleotides: A New Therapeutic Principle. Chem. Rev. 90, 543-584.
41. Weisz, K., Shafer, R. H., Egan, W., and James, T. L. (1994) Solution Structure of the Octamer Motif in Immunoglobulin Genes via Restrained Molecular Dynamics Calculations. Biochemistry 33, 354-366.
42. Wengel, J. (1998) Synthesis of 3′-C-and 4′-C-Branched Oligonucleotides and the Development of Locked Nucleic Acid (LNA). Acc. Chem. Res. 32, 301-310.
43. Wengel, J., Koshkin, A., Singh, S. K., Nielsen, P., Meldgaard, M., Rajwanshi, V. K., Kumar, R., Skouv, J., Nielsen, C. B., Jacobsen, J. P., Jacobsen, N., and Olsen, C. E. (1999) LNA (Locked Nucleic Acids). Nucleosides Nucleotides 18, 1365-1370.
44. Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids, John Wiley & Sons, New York.