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Volumn 21, Issue 3, 2009, Pages

Thermal equivalence of DNA duplexes for probe design

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENES; MELTING POINT; METAL MELTING; NUCLEIC ACIDS; PROBES;

EID: 63649127168     PISSN: 09538984     EISSN: 1361648X     Source Type: Journal    
DOI: 10.1088/0953-8984/21/3/034106     Document Type: Article
Times cited : (39)

References (53)
  • 1
    • 33645072440 scopus 로고    scopus 로고
    • Gene sequencing: The race for the $1000 genome
    • Service R F 2006 Gene sequencing: the race for the $1000 genome Science 311 1544-6
    • (2006) Science , vol.311 , Issue.5767 , pp. 1544-1546
    • Service, R.F.1
  • 2
    • 1942499454 scopus 로고    scopus 로고
    • Advanced sequencing technologies: Methods and goals
    • Shendure J, Mitra R D and Church G M 2004 Advanced sequencing technologies: methods and goals Nat. Rev. Gen. 5 335-44
    • (2004) Nat. Rev. Gen. , vol.5 , Issue.5 , pp. 335-344
    • Shendure, J.1    Mitra, R.D.2    Church, G.M.3
  • 3
    • 17044426694 scopus 로고    scopus 로고
    • Advances in sequencing technology
    • Chan E Y 2005 Advances in sequencing technology Mutat. Res. 573 13-40
    • (2005) Mutat. Res. , vol.573 , Issue.1-2 , pp. 13-40
    • Chan, E.Y.1
  • 4
    • 84984934752 scopus 로고    scopus 로고
    • Resequencing and mutational analysis using oligonucleotide microarrays
    • Hacia J G 1999 Resequencing and mutational analysis using oligonucleotide microarrays Nat. Genet. 21 42-7
    • (1999) Nat. Genet. , vol.21 , pp. 42-47
    • Hacia, J.G.1
  • 5
    • 33750882505 scopus 로고    scopus 로고
    • Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
    • Berger M F, Philippakis A A, Qureshi A M, He F S, Estep P W III and Bulyk M L 2006 Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities Nat. Biotechnol. 24 1429-35
    • (2006) Nat. Biotechnol. , vol.24 , Issue.11 , pp. 1429-1435
    • Berger, M.F.1    Philippakis, A.A.2    Qureshi, A.M.3    He, F.S.4    Estep, P.W.5    Bulyk, M.L.6
  • 7
    • 25444518699 scopus 로고    scopus 로고
    • A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus
    • Charbonnier Y, Gettler B, Francois P, Bento M, Renzoni A, Vaudaux P, Schlegel W and Schrenzel J 2005 A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus BMC Genomics 6 95
    • (2005) BMC Genomics , vol.6 , Issue.1 , pp. 95
    • Charbonnier, Y.1    Gettler, B.2    Francois, P.3    Bento, M.4    Renzoni, A.5    Vaudaux, P.6    Schlegel, W.7    Schrenzel, J.8
  • 8
    • 33746361200 scopus 로고    scopus 로고
    • Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations
    • Okoniewski M and Miller C 2006 Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations BMC Bioinformatics 7 276
    • (2006) BMC Bioinformatics , vol.7 , Issue.1 , pp. 276
    • Okoniewski, M.1    Miller, C.2
  • 10
    • 0029968822 scopus 로고    scopus 로고
    • Improved nearest-neighbour parameters for predicting DNA duplex stability
    • SantaLucia J Jr, Allawi HT and Seneviratne PA 1996 Improved nearest-neighbour parameters for predicting DNA duplex stability Biochemistry 35 3555-62
    • (1996) Biochemistry , vol.35 , Issue.11 , pp. 3555-3562
    • Santalucia, J.1    Allawi, H.T.2    Seneviratne, P.A.3
  • 13
    • 3042735602 scopus 로고    scopus 로고
    • Prediction of hybridization and melting for double-stranded nucleic acids
    • Dimitrov R A and Zuker M 2004 Prediction of hybridization and melting for double-stranded nucleic acids Biophys. J. 87 215-26
    • (2004) Biophys. J. , vol.87 , Issue.1 , pp. 215-226
    • Dimitrov, R.A.1    Zuker, M.2
  • 14
    • 4243187319 scopus 로고
    • Statistical mechanics of a nonlinear model for DNA denaturation
    • Peyrard M and Bishop A R 1989 Statistical mechanics of a nonlinear model for DNA denaturation Phys. Rev. Lett. 62 2755-7
    • (1989) Phys. Rev. Lett. , vol.62 , Issue.23 , pp. 2755-2757
    • Peyrard, M.1    Bishop, A.R.2
  • 16
    • 41549144880 scopus 로고    scopus 로고
    • DNA denaturation bubbles at criticality
    • Theodorakopoulos N 2008 DNA denaturation bubbles at criticality Phys. Rev. E 77 031919
    • (2008) Phys. Rev. , vol.77 , Issue.3 , pp. 031919
    • Theodorakopoulos, N.1
  • 17
    • 42749100398 scopus 로고    scopus 로고
    • Energy localization in the Peyrard-Bishop DNA model
    • DeLuca J, Drigo Filho E, Ponno A and Ruggiero J R 2004 Energy localization in the Peyrard-Bishop DNA model Phys. Rev. E 70 026213
    • (2004) Phys. Rev. , vol.70 , Issue.2 , pp. 026213
    • Deluca, J.1    Drigo Filho, E.2    Ponno, A.3    Ruggiero, J.R.4
  • 18
    • 40949116640 scopus 로고    scopus 로고
    • Solitonic speed in DNA
    • Zdravkovic S and Sataric M V 2008 Solitonic speed in DNA Phys. Rev. E 77 031906
    • (2008) Phys. Rev. , vol.77 , Issue.3 , pp. 031906
    • Zdravkovic, S.1    Sataric, M.V.2
  • 20
    • 33644893893 scopus 로고    scopus 로고
    • Sharp DNA denaturation due to solvent interaction
    • Weber G 2006 Sharp DNA denaturation due to solvent interaction Europhys. Lett. 73 806-11
    • (2006) Europhys. Lett. , vol.73 , Issue.5 , pp. 806-811
    • Weber, G.1
  • 21
    • 0001040631 scopus 로고    scopus 로고
    • Theory of DNA melting based on the Peyrard-Bishop model
    • Zhang Y-L, Zheng W-M, Liu J-X and Chen Y Z 1997 Theory of DNA melting based on the Peyrard-Bishop model Phys. Rev. E 56 7100-15
    • (1997) Phys. Rev. , vol.56 , Issue.6 , pp. 7100-7115
    • Zhang, Y.-L.1    Zheng, W.-M.2    Liu, J.-X.3    Chen, Y.Z.4
  • 22
    • 2542535189 scopus 로고    scopus 로고
    • General non-existence theorem for phase transitions in one-dimensional systems with short-range interactions, and physical examples of such transitions
    • Cuesta J A and Snches A 2004 General non-existence theorem for phase transitions in one-dimensional systems with short-range interactions, and physical examples of such transitions J. Stat. Phys. 115 869-93
    • (2004) J. Stat. Phys. , vol.115 , Issue.3-4 , pp. 869-893
    • Cuesta, J.A.1    Snches, A.2
  • 24
    • 5344259404 scopus 로고
    • Entropy-driven transition in a one-dimensional system
    • Dauxois T and Peyrard M 1995 Entropy-driven transition in a one-dimensional system Phys. Rev. E 51 4027-40
    • (1995) Phys. Rev. , vol.51 , Issue.5 , pp. 4027-4040
    • Dauxois, T.1    Peyrard, M.2
  • 25
    • 28844449314 scopus 로고    scopus 로고
    • Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation
    • Joyeux M and Buyukdagli S 2005 Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation Phys. Rev. E 72 051902
    • (2005) Phys. Rev. , vol.72 , Issue.5 , pp. 051902
    • Joyeux, M.1    Buyukdagli, S.2
  • 26
    • 33750618208 scopus 로고    scopus 로고
    • The relevance of nonlinear stacking interactions in simple models of double-stranded DNA
    • Saccomandi G and Sgura I 2006 The relevance of nonlinear stacking interactions in simple models of double-stranded DNA J. R. Soc. Interface 3 655-67
    • (2006) J. R. Soc. Interface , vol.3 , Issue.10 , pp. 655-667
    • Saccomandi, G.1    Sgura, I.2
  • 27
    • 0035151619 scopus 로고    scopus 로고
    • Model simulations of DNA denaturation dynamics
    • Drukker K, Wu G and Schatz G C 2001 Model simulations of DNA denaturation dynamics J. Chem. Phys. 114 579-90
    • (2001) J. Chem. Phys. , vol.114 , Issue.1 , pp. 579-590
    • Drukker, K.1    Wu, G.2    Schatz, G.C.3
  • 28
    • 0034214822 scopus 로고    scopus 로고
    • Order of the phase transition in models of DNA thermal denaturation
    • Theodorakopoulos N, Dauxois T and Peyrard M 2000 Order of the phase transition in models of DNA thermal denaturation Phys. Rev. Lett. 85 6-9
    • (2000) Phys. Rev. Lett. , vol.85 , Issue.1 , pp. 6-9
    • Theodorakopoulos, N.1    Dauxois, T.2    Peyrard, M.3
  • 31
    • 0000104103 scopus 로고    scopus 로고
    • Experimental tests of the Peyard-Bishop model applied to the melting of very short DNA chains
    • Campa A and Giansanti A 1998 Experimental tests of the Peyard-Bishop model applied to the melting of very short DNA chains Phys. Rev. E 58 3585
    • (1998) Phys. Rev. , vol.58 , Issue.3 , pp. 3585
    • Campa, A.1    Giansanti, A.2
  • 32
    • 0032539693 scopus 로고    scopus 로고
    • A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    • SantaLucia J Jr 1998 A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics Proc. Natl Acad. Sci. USA 95 1460-5
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , Issue.4 , pp. 1460-1465
    • Santalucia, J.1
  • 33
    • 0036318088 scopus 로고    scopus 로고
    • Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation
    • Wu P, Nakano S and Sugimoto N 2002 Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation Eur. J. Biochem. 269 2821-30
    • (2002) Eur. J. Biochem. , vol.269 , Issue.12 , pp. 2821-2830
    • Wu, P.1    Nakano, S.2    Sugimoto, N.3
  • 35
    • 5744255023 scopus 로고    scopus 로고
    • Sequence-specific thermal fluctuations identify start sites for DNA transcription
    • Kalosakas G, Rasmussen K O, Bishop A R, Choi C H and Usheva A 2004 Sequence-specific thermal fluctuations identify start sites for DNA transcription Europhys. Lett. 68 127133
    • (2004) Europhys. Lett. , vol.68 , Issue.1 , pp. 127
    • Kalosakas, G.1    Rasmussen, K.O.2    Bishop, A.R.3    Choi, C.H.4    Usheva, A.5
  • 37
    • 33745205353 scopus 로고    scopus 로고
    • Comment on Can one predict DNA transcription start sites by studying bubbles?
    • Choi C H, Usheva A, Kalosakas G, Rasmussen K and Bishop A R 2006 Comment on Can one predict DNA transcription start sites by studying bubbles? Phys. Rev. Lett. 96 239801
    • (2006) Phys. Rev. Lett. , vol.96 , Issue.23 , pp. 239801
    • Choi, C.H.1    Usheva, A.2    Kalosakas, G.3    Rasmussen, K.4    Bishop, A.R.5
  • 39
    • 85009230331 scopus 로고    scopus 로고
    • Complexity of DNA sequencing by hybridization
    • Błazewicz J and Kasprzak M 2003 Complexity of DNA sequencing by hybridization Theor. Comput. Sci. 290 1459-73
    • (2003) Theor. Comput. Sci. , vol.290 , Issue.3 , pp. 1459-1473
    • Błazewicz, J.1    Kasprzak, M.2
  • 40
    • 10644247621 scopus 로고    scopus 로고
    • Applications of DNA tiling arrays for whole-genome analysis
    • Mockler T C and Ecker J R 2005 Applications of DNA tiling arrays for whole-genome analysis Genomics 85 1-15
    • (2005) Genomics , vol.85 , Issue.1 , pp. 1-15
    • Mockler, T.C.1    Ecker, J.R.2
  • 42
    • 0034121447 scopus 로고    scopus 로고
    • Universal DNA array detection of small insertions and deletions in BRCA1 and BRCA2
    • Favis R, Day J P, Gerry N P, Phelan C, Narod S and Barany F 2000 Universal DNA array detection of small insertions and deletions in BRCA1 and BRCA2 Nat. Biotechnol. 18 561-4
    • (2000) Nat. Biotechnol. , vol.18 , Issue.5 , pp. 561-564
    • Favis, R.1    Day, J.P.2    Gerry, N.P.3    Phelan, C.4    Narod, S.5    Barany, F.6
  • 43
    • 0036725230 scopus 로고    scopus 로고
    • Rapid detection of hepatitis B virus mutations using real-time PCR and melting curve analysis
    • Zhang M, Gong Y, Osiowy C and Minuk G Y 2002 Rapid detection of hepatitis B virus mutations using real-time PCR and melting curve analysis Hepatology 36 723-8
    • (2002) Hepatology , vol.36 , Issue.3 , pp. 723-728
    • Zhang, M.1    Gong, Y.2    Osiowy, C.3    Minuk, G.Y.4
  • 45
    • 49449092312 scopus 로고    scopus 로고
    • Optimal probe length varies for targets with high sequence variation: Implications for probe library design for resequencing highly variable genes
    • Haslam N, Whiteford N, Weber G, Prügel-Bennett A, Essex J W and Neylon C 2008 Optimal probe length varies for targets with high sequence variation: implications for probe library design for resequencing highly variable genes PLoS ONE 3 e2500
    • (2008) PLoS ONE , vol.3 , Issue.6 , pp. 2500
    • Haslam, N.1    Whiteford, N.2    Weber, G.3    Prügel-Bennett, A.4    Essex, J.W.5    Neylon, C.6
  • 47
    • 0036106380 scopus 로고    scopus 로고
    • Salt dependence of the elasticity and overstretching transition of single DNA molecules
    • Wenner J R, Williams M C, Rouzina I and Bloomfield V A 2002 Salt dependence of the elasticity and overstretching transition of single DNA molecules Biophys. J. 82 3160-9
    • (2002) Biophys. J. , vol.82 , Issue.6 , pp. 3160-3169
    • Wenner, J.R.1    Williams, M.C.2    Rouzina, I.3    Bloomfield, V.A.4
  • 48
    • 38349173106 scopus 로고    scopus 로고
    • Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations
    • Harris S A, Laughton C A and Liverpool T B 2008 Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations Nucleic Acids Res. 36 2129
    • (2008) Nucleic Acids Res. , vol.36 , pp. 2129
    • Harris, S.A.1    Laughton, C.A.2    Liverpool, T.B.3
  • 49
    • 0032919143 scopus 로고    scopus 로고
    • Sequence-dependent mechanics of single DNA molecules
    • Rief M, Clausen-Schaumann H and Gaub H E 1999 Sequence-dependent mechanics of single DNA molecules Nat. Struct. Biol. 6 346-9
    • (1999) Nat. Struct. Biol. , vol.6 , Issue.4 , pp. 346-349
    • Rief, M.1    Clausen-Schaumann, H.2    Gaub, H.E.3
  • 50
    • 2442643901 scopus 로고    scopus 로고
    • The salt dependence of the stretching transition of double-stranded DNA molecules
    • Dong R, Yan X and Liu S 2004 The salt dependence of the stretching transition of double-stranded DNA molecules J. Phys.: Condens. Matter 37 4977-84
    • (2004) J. Phys.: Condens. Matter , vol.37 , pp. 4977-4984
    • Dong, R.1    Yan, X.2    Liu, S.3
  • 51
    • 0034607637 scopus 로고    scopus 로고
    • Structural stability of DNA in nonaqueous solvents
    • Bonner G and Klibanov A M 2000 Structural stability of DNA in nonaqueous solvents Biotechnol. Bioeng. 68 339-44
    • (2000) Biotechnol. Bioeng. , vol.68 , Issue.3 , pp. 339-344
    • Bonner, G.1    Klibanov, A.M.2
  • 52
    • 33748452868 scopus 로고    scopus 로고
    • The denaturation transition of DNA in mixed solvents
    • Hammouda B and Worcester D 2006 The denaturation transition of DNA in mixed solvents Biophys. J. 91 2237-42
    • (2006) Biophys. J. , vol.91 , Issue.6 , pp. 2237-2242
    • Hammouda, B.1    Worcester, D.2


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