Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations

Nucleic Acids Research

Volumn 36, Issue 5, 2008, Pages 1508-1516

  Pande, Vineet ^a   Nilsson, Lennart ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOHYDRATE; DNA; LOCKED NUCLEIC ACID; PHOSPHATE; RNA; WATER;

ARTICLE; CHEMICAL MODIFICATION; CONTROLLED STUDY; DNA HYBRIDIZATION; DNA STRAND; HYDRATION; MOLECULAR DYNAMICS; NUCLEIC ACID HYBRIDIZATION; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; PROCESS MODEL; PROTEIN CONFORMATION; RNA HYBRIDIZATION; STRUCTURAL HOMOLOGY; THERMOSTABILITY;

BASE PAIRING; CARBOHYDRATE CONFORMATION; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DNA; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; RNA; WATER;

EID: 41149107472     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm1182     Document Type: Article

References (40)

1. Crooke,S.T. (2004) Progress in antisense technology. Annu. Rev. Med. 55, 61-95.
2. Braasch,D.A. and Corey,D.R. (2001) Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA. Chem. Biol. 8, 1-7.
3. Koshkin,A.A., Nielsen,P., Meldgaard,M., Rajwanshi,V.K., Singh,S.K. and Wengel.J. (1998) LNA (locked nucleic acid): An RNA mimic forming exceedingly stable LNA: LNA duplexes. J. Am. Chem. Soc., 120 13252-13253.
4. Obika,S., Nanbu,D., Hari,Y., Andoh,J., Morio,K., Doi,T. and Imanishi,T. (1998) Stability and structural features of the duplexes containing nucleoside analogues with a fixed N-type conformation, 2'-O,4'-C-methyleneribonucleosides. Tetrahedron Lett., 39, 5401-5404.
5. Crinelli,R., Bianchi,M., Gentilini,L. and Magnani,M. (2002) Design and characterization of decoy oligonucleotides containing locked nucleic acids. Nucleic Acids Res., 30, 2435-2443.
6. Vester,B., Lundberg,L.B., Sorensen,M.D., Babu,B.R., Douthwaite,S. and Wengel,J. (2002) LNAzymes: Incorporation of LNA-type monomers into DNAzymes markedly increases RNA cleavage. J. Am. Chem. Soc., 124, 13682-13683.
7. Wang,L., Yang,C.Y.J., Medley,C.D., Benner,S.A. and Tan,W.H. (2005) Locked nucleic acid molecular beacons. J. Am. Chem. Soc., 127 15664-15665.
8. Kloosterman,W.P., Wienholds,E., de Bruijn,E., Kauppinen,S. and Plasterk,R.H.A. (2006) In situ detection of miRNAs in animal embryos using LNA-modified oligonucteotide probes. Nat. Methods, 3, 27-29.
9. Thomsen,R., Nielsen,P.S. and Jensen,T.H. (2005) Dramatically improved RNA in situ hybridization signals using LNA-modified probes. RNA, 11, 1745-1748.
10. Elmen,J., Thonberg,H., Ljungberg,K., Frieden,M., Westergaard,M., Xu,Y.H., Wahren,B., Liang,Z.C., Urum,H. et al. (2005) Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality. Nucleic Acids Res., 33, 439-447.
11. Bondensgaard,K., Petersen,M., Singh,S.K., Rajwanshi,V.K., Kumar,R., Wengel,J. and Jacobsen,J.P.(2000) Structural studies of LNA : RNA duplexes by NMR: Conformations and implications for RNase H activity. Chemistry, 6, 2687-2695.
12. Nielsen,K.E., Singh,S.K., Wengel,J. and Jacobsen,J.P. (2000) 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. Bioconjug. Chem., 11, 228-238.
13. Petersen,M., Bondensgaard,K., Wengel,J. and Jacobsen,J.P. (2002) Locked nucleic acid (LNA) recognition of RNA: NMR solution structures of LNA : RNA hybrids. J. Am. Chem. Soc., 124, 5974-5982.
14. Nielsen,K.E., Rasmussen,J., Kumar,R., Wengel,J., Jacobsen,J.P. and Petersen,M. (2004) NMR studies of fully modified locked nucleic acid (LNA) hybrids: Solution structure of an LNA: RNA hybrid and characterization of an LNA : DNA hybrid. Bioconjug. Chem., 15 449-457.
15. Nielsen,K.E. and Spielmann,H.P. (2005) The structure of a mixed LNA/DNA : RNA duplex is driven by conformational coupling between LNA and deoxyribose residues as determined from C-13 relaxation measurements. J. Am. Chem. Soc., 127, 15273-15282.
16. Foloppe,N. and Nilsson,L. (2005) Toward a full characterization of nucleic acid components in aqueous solution: Simulations of nucleosides. J. Phys. Chem. B, 109, 9119-9131.
17. Norberg,J. and Nilsson,L. (2002) Molecular dynamics applied to nucleic acids. Acc. Chem. Res., 35, 465-472.
18. Noy,A., Perez,A., Marquez,M., Luque,F.J. and Orozco,M. (2005) Structure, recognition properties, and flexibility of the DNA-RNA hybrid. J. Am. Chem. Soc., 127, 4910-4920.
19. Sen,S. and Nilsson,L. (1998) Molecular dynamics of duplex systems involving PNA: Structural and dynamical consequences of the nucleic acid backbone. J. Am. Chem. Soc., 120, 619-631.
20. Sen,S. and Nilsson,L. (2001) MD simulations of homomorphous PNA, DNA, and RNA single strands: Characterization and comparison of conformations and dynamics. J. Am. Chem. Soc., 123, 7414-7422.
21. Soliva,R., Sherer,E., Luque,F.J., Laughton,C.A. and Orozco,M. (2000) Molecular dynamics simulations of PNA center dot DNA and PNA center dot RNA duplexes in aqueous solution. J. Am. Chem. Soc., 122, 5997-6008.
22. Brooks,B.R., Bruccoleri,R.E., Olafson,B.D., States,D.J., Swaminathan,S. and Karplus,M. (1983) Charmm - a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem., 4 187-217.
23. Foloppe,N. and MacKerell,A.D. (2000) All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem., 21, 86-104.
24. Jorgensen,W.L., Chandrasekhar,J., Madura,J.D., Impey,R.W. and Klein,M.L. (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79, 926-935.
25. Ryckaert,J.P., Ciccotti,G. and Berendsen,H.J.C. (1977) Numerical-integration of Cartesian equations of motion of a system with constraints - molecular-dynamics of N-alkanes. J. Comput. Phys., 23, 327-341.
26. Feller,S.E., Zhang,Y.H., Pastor,R.W. and Brooks,B.R. (1995) Constant-pressure molecular-dynamics simulation - the Langevin Piston method. J. Chem. Phys., 103, 4613-4621.
27. Steinbach,P.J. and Brooks,B.R. (1994) New spherical-cutoff methods for long-range forces in macromolecular simulation. J. Comput. Chem., 15, 667-683.
28. Norberg,J. and Nilsson,L. (2000) On the truncation of long-range electrostatic interactions in DNA. Biophys. J., 79, 1537-1553.
29. Lavery,R. and Sklenar,H. (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic-acids. J. Biomol. Struct. Dyn., 6, 63-91.
30. Deloof,H., Nilsson,L. and Rigler,R. (1992) Molecular-dynamics simulation of Galanin in aqueous and nonaqueous solution. J. Am. Chem. Soc., 114, 4028-4035.
31. Andricioaei,I. and Karplus,M. (2001) On the calculation of entropy from covariance matrices of the atomic fluctuations. J. Chem. Phys., 115, 6289-6292.
32. 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. et al. (2000) The conformations of locked nucleic acids (LNA). J. Mol. Recognit. 13, 44-53.
33. Altona,C. and Sundaralingam,M. (1972) Conformational-analysis of sugar ring in nucleosides and nucleotides - new description using concept of pseudorotation. J. Am. Chem. Soc., 94, 8205.
34. Auffinger,P. and Westhof,E. (2000) Water and ion binding around RNA and DNA (C,G) oligomers. J. Mol. Biol., 300, 1113-1131.
35. Saenger,W., Hunter,W.N. and Kennard,O. (1986) DNA conformation is determined by economics in the hydration of phosphate groups. Nature 324, 385-388.
36. Auffinger,P. and Westhof,E. (2001) Water and ion binding around r(UpA)(12) and d(TpA)(12) oligomers - comparison with RNA and DNA (CpG)(12) duplexes. J. Mol. Biol., 305, 1057-1072.
37. Westhof,E. (1988) Water: An integral part of nucleic acid structure. Annu. Rev. Biophys. Biophys. Chem., 17, 125-144.
38. Kaur,H., Arora,A., Wengel,J. and Maiti,S. (2006) Thermodynamic, counterion, and hydration effects for the incorporation of locked nucleic acid nucleotides into DNA duplexes. Biochemistry, 45 7347-7355.
39. Pastor,N. (2005) The B- to A-DNA transition and the reorganization of solvent at the DNA surface. Biophys. J., 88, 3262-3275.
40. Sorensen,J.J., Nielsen,J.T. and Petersen,M. (2004) Solution structure of a dsDNA: LNA triplex. Nucleic Acids Res., 32, 6078-6085.