Nearest neighbor parameters for Watson-Crick complementary heteroduplexes formed between 2′-O-methyl RNA and RNA oligonucleotides

Nucleic Acids Research

Volumn 34, Issue 13, 2006, Pages 3609-3614

  Kierzek, Elzbieta ^a,b   Mathews, David H ^c   Ciesielska, Anna ^b   Turner, Douglas H ^a,c   Kierzek, Ryszard ^b  

^a UNIVERSITY OF ROCHESTER   (United States)

^b INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

^c UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

2' O METHYL RNA; HETERODUPLEX; HYDROGEN; OLIGONUCLEOTIDE; RNA; UNCLASSIFIED DRUG; DOUBLE STRANDED RNA; OLIGORIBONUCLEOTIDE;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; HYDROGEN BOND; PREDICTION; PRIORITY JOURNAL; PROTEIN DENATURATION; RNA CONFORMATION; RNA SEQUENCE; RNA STABILITY; RNA STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; THERMODYNAMICS; CHEMISTRY; METHYLATION;

BASE PAIRING; METHYLATION; OLIGORIBONUCLEOTIDES; RNA, DOUBLE-STRANDED; THERMODYNAMICS;

EID: 33746488366     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl232     Document Type: Article

References (46)

1. Bodrossy,L. and Sessitsch,A. (2004) Oligonucleotide microarrays in microbial diagnostics. Curr. Opin. Microbiol., 7, 245-254.
2. Heller,R.A., Schena,M., Chai,A., Shalon,D., Bedilion,T., Gilmore,J., Woolley,D.E. and Davis,R.W. (1997) Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc. Natl Acad. Sci. USA, 94, 2150-2155.
3. Li,H.X. and Rothberg,L.J. (2004) Label-free colorimetric detection of specific sequences in genomic DNA amplified by the polymerase chain reaction. J. Am. Chem. Soc., 126, 10958-10961.
4. Long,W.H., Xiao,H.S., Gu,X.M., Zhang,Q.H., Yang,H.J., Zhao,G.P. and Liu,J.H. (2004) A universal microarray for detection of SARS coronavirus. J. Virol. Methods, 121, 57-63.
5. Zamecnik,P.C. and Stephenson,M.L. (1978) Inhibition of Rous-sarcoma virus-replication and cell transformation by a specific oligodeoxynucleotide. Proc. Natl Acad. Sci. USA, 75, 280-284.
6. Milligan,J.F., Matteucci,M.D. and Martin,J.C. (1993) Current concepts in antisense drug design. J. Med. Chem., 36, 1923-1937.
7. Burmeister,P.E., Lewis,S.D., Silva,R.F., Preiss,J.R., Horwitz,L.R., Pendergrast,P.S., McCauley,T.G., Kurz,J.C., Epstein,D.M., Wilson,C. et al. (2005) Direct in vitro selection of a 2′-O-methyl aptamer to VEGF. Chem. Biol., 12, 25-33.
8. Ruckman,J., Green,L.S., Beeson,J., Waugh,S., Gillette,W.L., Henninger,D.D., Claesson-Welsh,L. and Janji,N. (1998) 2′-fluoropyrimidine RNA-based aptamers to the 165-amino acid form of vascular endothelial growth factor (VEGF165). J. Biol. Chem., 273, 20556-20567.
9. Goodchild,J. (2004) Oligonucleotide therapeutics: 25 years agrowing. Curr. Opin. Mol. Ther., 6, 120-128.
10. Chworos,A., Severcan,I., Koyfman,A.Y., Weinkam,P., Oroudjev,E., Hansma,H.G. and Jaeger,L. (2004) Building programmable jigsaw puzzles with RNA. Science, 306, 2068-2072.
11. Seeman,N.C. (2005) From genes to machines: DNA nanomechanical devices. Trends Biochem. Sci., 30, 119-125.
12. Matveeva,O.V., Mathews,D.H., Tsodikov,A.D., Shabalina,S.A., Gesteland,R.F., Atkins,J.F. and Freier,S.M. (2003) Thermodynamic criteria for high hit rate antisense oligonucleotide design. Nucleic Acids Res., 31, 4989-4994.
13. Schwarz,D.S, Hutvagner,G., Du,T., Xu,Z.S., Aronin,N. and Zamore,P.D. (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell, 115, 199-208.
14. Dirks,R.M., Lin,M., Winfree,E. and Pierce,N.A. (2004) Paradigms for computational nucleic acid design. Nucleic Acids Res., 32, 1392-1403.
15. SantaLucia,J. and Hicks,D. (2004) The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomolec. Struct., 33, 415-440.
16. SantaLucia,J.,Jr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA, 95, 1460-1465.
17. Mathews,D.H., Disney,M.D., Childs,J.L., Schroeder,S.J., Zuker,M. and Turner,D.H. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl Acad. USA, 101, 7287-7292.
18. Xia,T.B., SantaLucia,J., Burkard,M.E., Kierzek,R., Schroeder,S.J., Jiao,X.Q., Cox,C. and Turner,D.H. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry, 37, 14719-14735.
19. Sugimoto,N., Nakano,S., Katoh,M., Matsumura,A., Nakamuta,H., Ohmici,T., Yoneyama,M. and Sasaki,M. (1995) Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry, 34, 11211-11216.
20. Borer,P.N., Dengler,B., Tinoco,I. and Uhlenbeck,O.C. (1974) Stability of ribonucleic-acid double-stranded helices. J. Mol. Biol., 86, 843-853.
21. Gray,D.M. (1997) Derivation of nearest-neighbor properties from data on nucleic acid oligomers.1. Simple sets of independent sequences and the influence of absent nearest neighbors. Biopolymers, 42, 783-793.
22. Gray,D.M. (1997) Derivation of nearest-neighbor properties from data on nucleic acid oligomers.2. Thermodynamic parameters of DNA - RNA hybrids and DNA duplexes. Biopolymers, 42, 795-810.
23. Cramer,H. and Pfleiderer,W. (2000) Nucleotides LXIV[1]: Synthesis, hybridization and enzymatic degradation studies of 2′-O-methyl-oligoribonucleotides and 2_Pm-O-methyl/deoxy gapmers. Nucleosides Nucleotides Nucleic Acids, 19, 1765-1777.
24. Lesnik,E.A. and Freier,S.M. (1998) What affects the effect of 2′-alkoxy modifications? 1. Stabilization effect of 2′-methoxy substitutions in uniformly modified DNA oligonucleotides Biochemistry, 37, 6991-6997.
25. Majlessi,M., Nelson,N.C. and Becker,M.M. (1998) Advantages of 2′-O-methyl oligoribonucleotide probes for detecting RNA targets. Nucleic Acids Res., 26, 2224-2229.
26. Sproat,B.S., Lamond,A.I., Beijer,B., Neuner,P. and Ryder,U. (1989) Highly efficient chemical synthesis of 2′-O-methyloligoribonucleotides and tetrabiotinylated derivatives - novel probes that are resistant to degradation by RNA or DNA specific nucleases. Nucleic Acids Res., 17, 3373-3386.
27. Kierzek,E., Ciesielska,A., Pasternak,K., Mathews,D.H., Turner,D.H. and Kierzek,R. (2005) The influence of locked nucleic acid residues on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes. Nucleic Acids Res., 33, 5082-5093.
28. Borer,P.N. (1975) Optical properties of nucleic acids, absorption and circular dichroism spectra. In Fasman,G.D. (ed.), Handbook of Biochemistry and Molecular Biology: Nucleic Acids. 3rd edn. CRS Press, Cleveland, OH, vol. 1, pp. 589-595.
29. Richards,E.G. (1975) Use of tables in calculation of absorption, optical rotatory dispersion and circular dichroism of polyribonucleotides. In Fasman,G.D. (ed.), Handbook of Biochemistry and Molecular Biology: Nucleic Acids. 3rd edn. CRS Press, Cleveland, OH, vol. 1, pp. 596-603.
30. 2 by two-dimensional NMR and simulated annealing. Biochemistry, 35, 14077-14089.
31. SantaLucia,J.,Jr and Turner,D.H. (1998) Measuring the thermodynamics of RNA secondary structure formation. Biopolymers, 44, 309-319.
32. Allawi,H.T. and SantaLucia,J.,Jr (1997) Thermodynamics and NMR of internal G-T mismatches in DNA. Biochemistry, 36, 10581-10594.
33. Matveeva,O.V., Shabalina,S.A., Nemtsov,V.A., Tsodikov,A.D., Gesteland,R.F. and Atkins,J.F. (2003) Thermodynamic calculations and statistical correlations for oligo-probes design. Nucleic Acids Res., 31, 4211-4217.
34. Crooke,S.T., Lemonidis,K.M., Neilson,L., Griffey,R., Lesnik,E.A. and Monia,B.P. (1995) Kinetic characteristics of Escherichia coli RNase H1: cleavage of various antisense oligonucleotide-RNA duplexes. Biochem. J., 312, 599-608.
35. Kraynack,B.A. and Baker,B.F. (2006) Small interfering RNAs containing full 2′-O-methylribonucleotide-modified sense strands display Argonaute 2/eIF2C2-dependent activity. RNA, 12, 163-176.
36. Ding,Y. and Lawrence,C.E. (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res., 31, 7280-7301.
37. Rivas,E. and Eddy,S.R. (1999) A dynamic programming algorithm for RNA structure prediction including pseudokknots. J. Mol. Biol., 285, 2053-2068.
38. Wuchty,S., Fontana,W., Hofacker,I.L. and Schuster,P. (1999) Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers, 49, 145-165.
39. Freier,S.M. and Altmann,K.H. (1997) The ups and downs of nucleic acid duplex stability: Structure-stability studies on chemically-modified DNA:RNA duplexes. Nucleic Acids Res., 25, 4429-4443.
40. Gryaznov,S. and Chen,J.-K. (1994) Oligodeoxyribonucleotide N3′→P5′ phosphoramidates: Synthesis and hybridization properties. J. Amer. Chem. Soc., 116, 3143-3144.
41. Pieken,W.A., Olsen,D.B., Benseler,F., Aurup,H. and Eckstein,F. (1991) Kinetic characterization of ribonuclease-resistant 2′-modified hammerhead ribozymes. Science, 253, 314-317.
42. Heidenreich,O., Benseler,F., Fahrenholz,A. and Eckstein,F. (1994) High activity and stability of hammerhead ribozymes containing 2′-modified pyrimidine nucleosides and phosphorothioates. J. Biol. Chem., 269, 2131-2138.
43. Holbrook,J.A., Capp,M.W., Saecker,R.M. and Record,M.T.,Jr (1999) Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: Interpretation in terms of coupled processes of formation and association of single-stranded helices. Biochemistry, 38, 8409-8422.
44. Takach,J.C., Mikulecky,P.J. and Feig,A.L. (2004) Salt-dependent heat capacity changes for RNA duplex formation. J. Am. Chem. Soc., 126, 6530-6531.
45. Chaires,J.B. (1997) Possible origin of differences between van't Hoff and calorimetric enthalpy estimates. Biophys. Chem., 64, 15-23.
46. Petersheim,M. and Turner,D.H. (1983) Base-stacking and base-pairing contributions to helix stability: Thermodynamics of double-helix formation with CCGG, CCGGp, CGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry, 22, 256-263.