Thermodynamic contributions of single internal rAdA, rCdC, rGdG and rUdT mismatches in RNA/DNA duplexes

Nucleic Acids Research

Volumn 39, Issue 5, 2011, Pages 1894-1902

  Watkins Jr , Norman E ^a   Kennelly, William J ^a   Tsay, Mike J ^a   Tuin, Astrid ^a   Swenson, Lara ^a   Lee, Hyung Ran ^a   Morosyuk, Svetlana ^a   Hicks, Donald A ^a   Santalucia, John ^a  

^a DNA Software Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; DOUBLE STRANDED RNA; SODIUM CHLORIDE;

ARTICLE; BASE MISPAIRING; BASE PAIRING; COMPUTER PROGRAM; CONTROLLED STUDY; CURVE FITTING; DINUCLEOTIDE REPEAT; DNA DENATURATION; DNA DETERMINATION; MELTING POINT; MOLECULAR STABILITY; MOLECULAR WEIGHT; PRIORITY JOURNAL; RNA ANALYSIS; SINGLE INTERNAL MISMATCH; TEMPERATURE SENSITIVITY; THERMODYNAMICS; TREND STUDY;

ADENINE; BASE PAIR MISMATCH; CYTOSINE; DNA; GUANINE; RNA; THERMODYNAMICS; THYMINE; URACIL;

EID: 79953129880     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq905     Document Type: Article

References (51)

1. Dasu M.R. Devaraj S. Park S. and Jialal I. (2010) Increased tolllike receptor (TLR) activation and TLR ligands in recently diagnosed type 2 diabetic subjects. Diabetes Care 33 861-868.
2. Eis P.S. Olson M.C. Takova T. Curtis M.L. Olson S.M. Vener T.I. Ip H.S. Vedvik K.L. Bartholomay C.T. Allawi H.T. et al. (2001) An invasive cleavage assay for direct quantitation of specific RNAs. Nat. Biotechnol. 19 673-676. (Pubitemid 32625440)
3. Fleischer A. Duhamel M. Lopez-Fernandez L.A. Munoz M. Rebollo M.P. Alvarez-Franco F. and Rebollo A. (2007) Cascade of transcriptional induction and repression during IL-2 deprivation-induced apoptosis. Immunol. Lett. 112 9-29. (Pubitemid 47331685)
4. Murray E.L. and Schoenberg D.R. (2008) Application of the invader RNA assay to the polarity of vertebrate mRNA decay. Methods Mol. Biol. 419 259-276.
5. Neelima P.S. and Rao A.J. (2008) Gene expression profiling during Forskolin induced differentiation of BeWo cells by differential display RT-PCR. Mol. Cell Endocrinol. 281 37-46. (Pubitemid 350296602)
6. Streit S. Michalski C.W. Erkan M. Kleeff J. and Friess H. (2009) Northern blot analysis for detection and quantification of RNA in pancreatic cancer cells and tissues. Nat. Protoc. 4 37-43.
7. Yu X.H. Zhang H. Wang Y.H. Liu L.J. Teng Y. and Liu P. (2009) Time-dependent reduction of glutamine synthetase in retina of diabetic rats. Exp. Eye Res. 89 967-971.
8. Alwine J.C. Kemp D.J. and Stark G.R. (1977) Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc. Natl Acad. Sci. USA 74 5350-5354.
9. Jin L. and Lloyd R.V. (1997) In situ hybridization: methods and applications. J. Clin. Lab. Anal. 11 2-9. (Pubitemid 27053382)
10. Orlando C. Pinzani P. and Pazzagli M. (1998) Developments in quantitative PCR. Clin. Chem. Lab. Med. 36 255-269. (Pubitemid 28325354)
11. Kulesh D.A. Clive D.R. Zarlenga D.S. and Greene J.J. (1987) Identification of interferon-modulated proliferation-related cDNA sequences. Proc. Natl Acad. Sci. USA 84 8453-8457.
12. Fluiter K. Mook O.R. Vreijling J. Langkjaer N. Hojland T. Wengel J. and Baas F. (2009) Filling the gap in LNA antisense oligo gapmers: the effects of unlocked nucleic acid (UNA) and 40-C-hydroxymethyl-DNA modifications on RNase H recruitment and efficacy of an LNA gapmer. Mol. Biosyst. 5 838-843.
13. Koizumi M. (2007) True antisense oligonucleotides with modified nucleotides restricted in the N-conformation. Curr. Top Med. Chem. 7 661-665. (Pubitemid 46681849)
14. Dmochowski I.J. and Tang X. (2007) Taking control of gene expression with light-activated oligonucleotides. Biotechniques 43 161 163 165 passim.
15. SantaLucia J. Jr (2007) Physical principles and visual-OMP software for optimal PCR design. Methods Mol. Biol. 402 3-34.
16. Allawi H.T. and SantaLucia J. Jr (1997) Thermodynamics and NMR of internal G.T mismatches in DNA. Biochemistry 36 10581-10594. (Pubitemid 27374152)
17. Allawi H.T. and SantaLucia J. Jr (1998) Thermodynamics of internal C.T mismatches in DNA. Nucleic Acids Res. 26 2694-2701. (Pubitemid 28297384)
18. Peyret N. Seneviratne P.A. Allawi H.T. and SantaLucia J. Jr (1999) Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A C.C G.G and T.T mismatches. Biochemistry 38 3468-3477.
19. Allawi H.T. and SantaLucia J. Jr (1998) NMR solution structure of a DNA dodecamer containing single G.T mismatches. Nucleic Acids Res. 26 4925-4934. (Pubitemid 28491172)
20. Davis A.R. and Znosko B.M. (2007) Thermodynamic characterization of single mismatches found in naturally occurring RNA. Biochemistry 46 13425-13436. (Pubitemid 350136381)
21. Saito H. and Richardson C.C. (1981) Processing of mRNA by ribonuclease III regulates expression of gene 1.2 of bacteriophage T7. Cell 27 533-542. (Pubitemid 12200790)
22. Saito M. and Nakamura T. (2005) Two point mutations identified in emmer wheat generate null Wx-A1 alleles. Theor. Appl. Genet. 110 276-282. (Pubitemid 40181225)
23. Bae S.H. and Choi B.S. (2001) Structure of influenza a virus promoter and its implications for viral RNA synthesis. Scientific World J. 1 812-814.
24. Sugimoto N. Nakano S. Katoh M. Matsumura A. Nakamuta H. Ohmichi T. Yoneyama M. and Sasaki M. (1995) Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry 34 11211-11216.
25. SantaLucia J. Jr (1998) A unified view of polymer dumbbell and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA 95 1460-1465. (Pubitemid 128624151)
26. Pont-Kingdon G. Margraf R.L. Sumner K. Millson A. Lyon E. and Schutz E. (2008) Design and application of noncontinuously binding probes used for haplotyping and genotyping. Clin. Chem. 54 990-999. (Pubitemid 351793405)
27. Kierzek R. Caruthers M.H. Longfellow C.E. Swinton D. Turner D.H. and Freier S.M. (1986) Polymer-supported RNA synthesis and its application to test the nearest-neighbor model for duplex stability. Biochemistry 25 7840-7846.
28. Marugg J.E. Piel N. McLaughlin L.W. Tromp M. Veeneman G.H. van der Marel G.A. and van Boom J.H. (1984) Polymer supported DNA synthesis using hydroxybenzotriazole activated phosphotriester intermediates. Nucleic Acids Res. 12 8639-8651.
29. Olmsted M.C. Anderson C.F. and Record M.T. Jr (1989) Monte Carlo description of oligoelectrolyte properties of DNA oligomers: range of the end effect and the approach of molecular and thermodynamic properties to the polyelectrolyte limits. Proc. Natl Acad. Sci. USA 86 7766-7770. (Pubitemid 19265266)
30. SantaLucia J. Jr Kierzek R. and Turner D.H. (1990) Effects of GA mismatches on the structure and thermodynamics of RNA internal loops. Biochemistry 29 8813-8819. (Pubitemid 20302780)
31. SantaLucia J. Jr and Hicks D. (2004) The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct. 33 415-440. (Pubitemid 38829966)
32. Sugimoto N. Nakano M. and Nakano S. (2000) Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes. Biochemistry 39 11270-11281.
33. Manning G.S. (1977) A field-dissociation relation for polyelectrolytes with an application to field-induced conformational changes of polynucleotides. Biophys. Chem. 7 189-192. (Pubitemid 8199337)
34. SantaLucia J. Jr (2000) The Use of Spectrosocopic Techniques in the Study of DNA Stability. University Press Oxford NY.
35. Bommarito S. Peyret N. and SantaLucia J. Jr (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res. 28 1929-1934. (Pubitemid 30229658)
36. Watkins N.E. Jr and SantaLucia J. Jr (2005) Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes. Nucleic Acids Res. 33 6258-6267. (Pubitemid 41742563)
37. SantaLucia J. Jr Allawi H.T. and Seneviratne P.A. (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35 3555-3562. (Pubitemid 26092574)
38. McDowell J.A. and Turner D.H. (1996) Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: solution structure of (rGAGGUCUC)2 by two-dimensional NMR and simulated annealing. Biochemistry 35 14077-14089. (Pubitemid 26384403)
39. 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.
40. Rouzina I. and Bloomfield V.A. (2001) Force-induced melting of the DNA double helix. 2. Effect of solution conditions. Biophys. J. 80 894-900. (Pubitemid 32128340)
41. Chaires J.B. (1997) Possible origin of differences between van't Hoff and calorimetric enthalpy estimates. Biophys. Chem. 64 15-23. (Pubitemid 27148653)
42. Freier S.M. Kierzek R. Jaeger J.A. Sugimoto N. Caruthers M.H. Neilson T. and Turner D.H. (1986) Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl Acad. Sci. USA 83 9373-9377. (Pubitemid 17223363)
43. Hall T.S. Pancoska P. Riccelli P.V. Mandell K. and Benight A.S. (2001) Sequence context and thermodynamic stability of a single base pair mismatch in short deoxyoligonucleotide duplexes. J. Am. Chem. Soc. 123 11811-11812. (Pubitemid 33121807)
44. Hammond N.B. Tolbert B.S. Kierzek R. Turner D.H. and Kennedy S.D. (2010) RNA internal loops with tandem AG pairs: the structure of the 50GAGU/30UGAG loop can be dramatically different from others including 50AAGU/30UGAA. Biochemistry 49 5817-5827.
45. Kierzek R. Burkard M.E. and Turner D.H. (1999) Thermodynamics of single mismatches in RNA duplexes. Biochemistry 38 14214-14223.
46. Borden K.L. Jenkins T.C. Skelly J.V. Brown T. and Lane A.N. (1992) Conformational properties of the G.G mismatch in d(CGC GAATTGGCG)2 determined by NMR. Biochemistry 31 5411-5422.
47. Faibis V. Cognet J.A. Boulard Y. Sowers L.C. and Fazakerley G.V. (1996) Solution structure of two mismatches G.G and I.I in the K-ras gene context by nuclear magnetic resonance and molecular dynamics. Biochemistry 35 14452-14464. (Pubitemid 26423704)
48. Freier S.M. Alkema D. Sinclair A. Neilson T. and Turner D.H. (1985) Contributions of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp XCCGGp XGGCCYp and XCCGGYp helixes. Biochemistry 24 4533-4539.
49. Gyi J.I. Lane A.N. Conn G.L. and Brown T. (1998) Solution structures of DNA.RNA hybrids with purine-rich and pyrimidine-rich strands: comparison with the homologous DNA and RNA duplexes. Biochemistry 37 73-80. (Pubitemid 28049109)
50. Gyi J.I. Conn G.L. Lane A.N. and Brown T. (1996) Comparison of the thermodynamic stabilities and solution conformations of DNA.RNA hybrids containing purine-rich and pyrimidine-rich strands with DNA and RNA duplexes. Biochemistry 35 12538-12548. (Pubitemid 26318051)
51. Petruska J. and Goodman M.F. (1995) Enthalpy-entropy compensation in DNA melting thermodynamics. J. Biol. Chem. 270 746-750.