-
2
-
-
0028933039
-
Optical melting of 128 octamer DNA duplexes
-
Doktycz MJ, Morris MD, Dormady SJ, Beattie KL, Jacobson KB (1995) Optical melting of 128 octamer DNA duplexes. J Biol Chem 270: 8439-8445.
-
(1995)
J Biol Chem
, vol.270
, pp. 8439-8445
-
-
Doktycz, M.J.1
Morris, M.D.2
Dormady, S.J.3
Beattie, K.L.4
Jacobson, K.B.5
-
3
-
-
11144291466
-
Stability of DNA duplexes with Watson-Crick base pairs: A predicted model
-
Sundaralingam M, Ponnuswamy PK (2004) Stability of DNA duplexes with Watson-Crick base pairs: A predicted model. Biochemistry 43: 16467-16476.
-
(2004)
Biochemistry
, vol.43
, pp. 16467-16476
-
-
Sundaralingam, M.1
Ponnuswamy, P.K.2
-
4
-
-
34250663391
-
On the nature of DNA-duplex stability
-
Rezac J, Hobza P (2007) On the nature of DNA-duplex stability. Chemistry A Eur J 13: 2983-2989.
-
(2007)
Chemistry a Eur J
, vol.13
, pp. 2983-2989
-
-
Rezac, J.1
Hobza, P.2
-
5
-
-
0000160803
-
Biomolecular dynamics of DNA: Statistical mechanics and dynamical models
-
Peyrard M, Dauxois T, Hoyet H, Willis CR (1993) Biomolecular dynamics of DNA: statistical mechanics and dynamical models. Physica D 68: 104-115.
-
(1993)
Physica D
, vol.68
, pp. 104-115
-
-
Peyrard, M.1
Dauxois, T.2
Hoyet, H.3
Willis, C.R.4
-
6
-
-
0343648651
-
Free energy of an arbitrary charge distribution imbedded in coaxial cylindrical dielectric continua: Application to conformational preferences of DNA in aqueous solutions
-
Jayaram B, Beveridge DL (1990) Free energy of an arbitrary charge distribution imbedded in coaxial cylindrical dielectric continua: Application to conformational preferences of DNA in aqueous solutions. J Phys Chem 94: 4666-4671.
-
(1990)
J Phys Chem
, vol.94
, pp. 4666-4671
-
-
Jayaram, B.1
Beveridge, D.L.2
-
7
-
-
0000435148
-
Energetics of base pairs in B-DNA in solution: An appraisal of potential functions and dielectric treatments
-
Arora N, Jayaram B (1998) Energetics of base pairs in B-DNA in solution: An appraisal of potential functions and dielectric treatments. J Phys Chem B 102: 6139-6144.
-
(1998)
J Phys Chem B
, vol.102
, pp. 6139-6144
-
-
Arora, N.1
Jayaram, B.2
-
9
-
-
0002459355
-
Thermal denaturation of DNA molecules: A comparison of theory with experiment
-
Wartell RM, Benight AS (1985) Thermal denaturation of DNA molecules: A comparison of theory with experiment. Physics Reports 126: 67-107.
-
(1985)
Physics Reports
, vol.126
, pp. 67-107
-
-
Wartell, R.M.1
Benight, A.S.2
-
10
-
-
77957870764
-
-
Gene VIII. Pearson Prentice Hall, NJ
-
Lewin B (2004) Gene VIII. Pearson Prentice Hall, NJ.
-
(2004)
-
-
Lewin, B.1
-
11
-
-
84985641585
-
Cooperative non-enzymic base recognition II. Thermodynamics of the helix-coil transition of oligoadenylic + oligouridylic acids
-
Porschke, D (1971) Cooperative non-enzymic base recognition II. Thermodynamics of the helix-coil transition of oligoadenylic + oligouridylic acids. Biopolymers 10: 1989-2013.
-
(1971)
Biopolymers
, vol.10
, pp. 1989-2013
-
-
Porschke, D.1
-
12
-
-
0023374525
-
Cooperative lengths of DNA during melting
-
Blake RD (1987) Cooperative lengths of DNA during melting. Biopolymers 26: 1063-1074.
-
(1987)
Biopolymers
, vol.26
, pp. 1063-1074
-
-
Blake, R.D.1
-
15
-
-
0025808064
-
Stacking energies in DNA
-
Delcourt SG, Blake RD (1991) Stacking energies in DNA. J Biol Chem 266: 15160-15169.
-
(1991)
J Biol Chem
, vol.266
, pp. 15160-15169
-
-
Delcourt, S.G.1
Blake, R.D.2
-
16
-
-
0033884290
-
Optimization of nucleic acid sequences
-
Lafontaine I, Lavery R (2000) Optimization of nucleic acid sequences. Biophys J 79: 680-685.
-
(2000)
Biophys J
, vol.79
, pp. 680-685
-
-
Lafontaine, I.1
Lavery, R.2
-
17
-
-
73649209034
-
Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature
-
Marmur J, Doty P (1962) Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5: 109-118.
-
(1962)
J Mol Biol
, vol.5
, pp. 109-118
-
-
Marmur, J.1
Doty, P.2
-
18
-
-
0029967168
-
Thermodynamics effect of formamide on DNA stability
-
Blake RD, Delcourt SD (1996) Thermodynamics effect of formamide on DNA stability. Nucleic Acid Res 24: 2095-2103.
-
(1996)
Nucleic Acid Res
, vol.24
, pp. 2095-2103
-
-
Blake, R.D.1
Delcourt, S.D.2
-
19
-
-
34247626260
-
A swift all-atom energy based computational protocol to predict DNA ligand binding affinity and DTm
-
Shaikh SA, Jayaram B (2007) A swift all-atom energy based computational protocol to predict DNA ligand binding affinity and DTm. J Med Chem 50: 2240-2244.
-
(2007)
J Med Chem
, vol.50
, pp. 2240-2244
-
-
Shaikh, S.A.1
Jayaram, B.2
-
20
-
-
0013822867
-
Dependence of the melting temperature of DNA on salt concentration
-
Schildkraut C, Lifson S (1965) Dependence of the melting temperature of DNA on salt concentration. Biopolymers 3: 195-208.
-
(1965)
Biopolymers
, vol.3
, pp. 195-208
-
-
Schildkraut, C.1
Lifson, S.2
-
21
-
-
36849151531
-
How the double helix breathes
-
Frank-Kamenetskii MD (1987) How the double helix breathes. Nature 328: 17-18.
-
(1987)
Nature
, vol.328
, pp. 17-18
-
-
Frank-Kamenetskii, M.D.1
-
22
-
-
0041779020
-
Helicoidal model for DNA opening
-
Barbi M, Cocco S, Peyrard M (1999) Helicoidal model for DNA opening. Phys Lett A 253: 358-369.
-
(1999)
Phys Lett A
, vol.253
, pp. 358-369
-
-
Barbi, M.1
Cocco, S.2
Peyrard, M.3
-
23
-
-
41449108360
-
A breathing wormlike chain model on DNA denaturation and bubble: Effects of stacking interactions
-
055101-055101-6
-
Kim J-Y, Jeon J-H, Sung W (2008) A breathing wormlike chain model on DNA denaturation and bubble: Effects of stacking interactions. J Chem Phys 128: 055101-055101-6.
-
(2008)
J Chem Phys
, vol.128
-
-
Kim, J.-Y.1
Jeon, J.-H.2
Sung, W.3
-
24
-
-
32844469596
-
Thermal denaturation of double-stranded DNA: Effect of base stacking
-
Kohandel M, Ha B-Y (2006) Thermal denaturation of double-stranded DNA: Effect of base stacking. Physical Review E 73: 011905.
-
(2006)
Physical Review E
, vol.73
, pp. 011905
-
-
Kohandel, M.1
Ha, B.-Y.2
-
25
-
-
32644434270
-
Base-stacking and base-pairing contributions into thermal stability of the DNA double helix
-
Yakovchuk P, Protozanova E, Frank-Kamenetskii MD (2006) Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res 34: 564-574.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 564-574
-
-
Yakovchuk, P.1
Protozanova, E.2
Frank-Kamenetskii, M.D.3
-
26
-
-
13244287791
-
A novel method for prokaryotic promoter prediction based on DNA stability
-
Kanhere A, Bansal M (2005) A novel method for prokaryotic promoter prediction based on DNA stability. BMC Bioinformatics 6: 1.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 1
-
-
Kanhere, A.1
Bansal, M.2
-
27
-
-
0000754002
-
Theory of ''Melting'' of the helical form in double chains of the DNA type
-
Zimm BH (1960) Theory of ''Melting'' of the helical form in double chains of the DNA type. J Chem Phys 33: 1349-1356.
-
(1960)
J Chem Phys
, vol.33
, pp. 1349-1356
-
-
Zimm, B.H.1
-
28
-
-
0000333671
-
On the theory of helix-coil transition in polypeptides
-
Lifson S, Roig A (1961) On the theory of helix-coil transition in polypeptides. J Chem Phys 34: 1963-1974.
-
(1961)
J Chem Phys
, vol.34
, pp. 1963-1974
-
-
Lifson, S.1
Roig, A.2
-
29
-
-
34247642885
-
Stacking heterogeneity: A model for the sequence dependent melting cooperativity of duplex DNA
-
165101-165101-9
-
Grigoryan AV, Mamasakhlisov ESh, Buryakina TYu, Tsarukyan AV, Benight AS, et al. (2007) Stacking heterogeneity: A model for the sequence dependent melting cooperativity of duplex DNA. J Chem Phys 126: 165101-165101-9.
-
(2007)
J Chem Phys
, vol.126
-
-
Grigoryan, A.V.1
Mamasakhlisov, E.2
Buryakina, T.3
Tsarukyan, A.V.4
Benight, A.S.5
-
31
-
-
0001040631
-
Theory of DNA melting based on the Peyrard-Bishop model
-
Zhang Y-L, Zheng W-M, Liu J-X, Chen YZ (1997) Theory of DNA melting based on the Peyrard-Bishop model. Phys Rev E 56: 7100-7115.
-
(1997)
Phys Rev E
, vol.56
, pp. 7100-7115
-
-
Zhang, Y.-L.1
Zheng, W.-M.2
Liu, J.-X.3
Chen, Y.Z.4
-
32
-
-
33644879263
-
Thermal equivalence of DNA duplexes without calculation of melting temperature
-
Weber G, Haslam N, Whiteford N, Prugel-Bennett A, Essex JW, et al. (2006) Thermal equivalence of DNA duplexes without calculation of melting temperature. Nature Physics 2: 55-59.
-
(2006)
Nature Physics
, vol.2
, pp. 55-59
-
-
Weber, G.1
Haslam, N.2
Whiteford, N.3
Prugel-Bennett, A.4
Essex, J.W.5
-
33
-
-
0000104103
-
Experimental tests of the Peyrard-Bishop model applied to the melting of very short DNA chains
-
Campa A, Giansanti A (1998) Experimental tests of the Peyrard-Bishop model applied to the melting of very short DNA chains. Physics Review E 58: 3585-3588.
-
(1998)
Physics Review E
, vol.58
, pp. 3585-3588
-
-
Campa, A.1
Giansanti, A.2
-
34
-
-
0029859713
-
Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes
-
Sugimoto N, Nakano S, Yoneyama M, Honda K (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res 24: 4501-4505.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 4501-4505
-
-
Sugimoto, N.1
Nakano, S.2
Yoneyama, M.3
Honda, K.4
-
35
-
-
0032539693
-
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 95: 1460-1465.
-
(1998)
Proc Natl Acad Sci
, vol.95
, pp. 1460-1465
-
-
Santalucia Jr., J.1
-
37
-
-
15944415071
-
Comparison of different melting temperature calculation methods for short DNA sequences
-
Panjkovich A, Melo F (2005) Comparison of different melting temperature calculation methods for short DNA sequences. Bioinformatics 21: 711-722.
-
(2005)
Bioinformatics
, vol.21
, pp. 711-722
-
-
Panjkovich, A.1
Melo, F.2
-
38
-
-
1642380887
-
Effects of sodium ions on DNA duplex oligomers: Improved predictions of melting temperatures
-
Owczarzy R, You Y, Moreira BG, Manthey JA, Huang L, et al. (2004) Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures. Biochemistry 43: 3537-3554.
-
(2004)
Biochemistry
, vol.43
, pp. 3537-3554
-
-
Owczarzy, R.1
You, Y.2
Moreira, B.G.3
Manthey, J.A.4
Huang, L.5
-
39
-
-
0029830638
-
Experimental measurement of aromatic stacking in the context of duplex DNA
-
Guckian KM, Schweitzer BA, Ren RX-F, Sheils CJ, Paris PL, et al. (1996) Experimental measurement of aromatic stacking in the context of duplex DNA. J Am Chem Soc 118: 8182-8183.
-
(1996)
J Am Chem Soc
, vol.118
, pp. 8182-8183
-
-
Guckian, K.M.1
Schweitzer, B.A.2
Ren, R.X.-F.3
Sheils, C.J.4
Paris, P.L.5
-
40
-
-
28444490422
-
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps
-
Dixit SB, Beveridge DL, Case DA, Cheatham TE, 3rd, Giudice E, et al. (2005) Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. Biophys J 89: 3721-3740.
-
(2005)
Biophys J
, vol.89
, pp. 3721-3740
-
-
Dixit, S.B.1
Beveridge, D.L.2
Case, D.A.3
Cheatham III, T.E.4
Giudice, E.5
-
41
-
-
0014030864
-
On the exclusivity of hydrogen-bonded pairing between the Watson-Crick complementary bases
-
Pullman B, Claverie P, Caillet J (1966) On the exclusivity of hydrogen-bonded pairing between the Watson-Crick complementary bases. J Mol Biol 22: 373-375.
-
(1966)
J Mol Biol
, vol.22
, pp. 373-375
-
-
Pullman, B.1
Claverie, P.2
Caillet, J.3
-
42
-
-
58749098268
-
Destabilization of DNA duplexes by oxidative damage at guanine: Implications for lesion recognition and repair
-
Jiranusornkul S, Laughton CA (2008) Destabilization of DNA duplexes by oxidative damage at guanine: implications for lesion recognition and repair. J R Soc 5: 191-198.
-
(2008)
J R Soc
, vol.5
, pp. 191-198
-
-
Jiranusornkul, S.1
Laughton, C.A.2
-
43
-
-
0030780913
-
Increased DNA binding and sequence discrimination of PNA oligomers containing 2,6- diaminopurine
-
Haaima A, Hansen HF, Christensen L, Dahl O, Nielsen PE (1997) Increased DNA binding and sequence discrimination of PNA oligomers containing 2,6- diaminopurine. Nucleic Acids Res 25: 4639-4643.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 4639-4643
-
-
Haaima, A.1
Hansen, H.F.2
Christensen, L.3
Dahl, O.4
Nielsen, P.E.5
-
44
-
-
0037012360
-
Substituted 1,8- naphthyridin-2 (1H)-ones are superior to thymine in the recognition of adenine in duplex as well as triplex structures
-
Eldrup AB, Christensen C, Haaima G, Nielsen PE (2002) Substituted 1,8- naphthyridin-2 (1H)-ones are superior to thymine in the recognition of adenine in duplex as well as triplex structures. J Am Chem Soc 124: 3254-3262.
-
(2002)
J Am Chem Soc
, vol.124
, pp. 3254-3262
-
-
Eldrup, A.B.1
Christensen, C.2
Haaima, G.3
Nielsen, P.E.4
-
45
-
-
0031451044
-
Beyond the wobble: The rule of conjugates
-
Jayaram B (1997) Beyond the wobble: The rule of conjugates. J Mol Evol 45: 704-705.
-
(1997)
J Mol Evol
, vol.45
, pp. 704-705
-
-
Jayaram, B.1
-
46
-
-
33947647510
-
Irreducible representation for nucleotide sequence physical properties and self consistency of nearest-neighbor dimer sets
-
Licino P, Guerra JCO (2007) Irreducible representation for nucleotide sequence physical properties and self consistency of nearest-neighbor dimer sets. Biophys J 92: 2000-2006.
-
(2007)
Biophys J
, vol.92
, pp. 2000-2006
-
-
Licino, P.1
Guerra, J.C.O.2
-
47
-
-
0028963346
-
Enthalpy-entropy compensation in DNA melting thermodynamics
-
Petruska J, Goodman MF (1995) Enthalpy-entropy compensation in DNA melting thermodynamics. J Biol Chem 270: 746-750.
-
(1995)
J Biol Chem
, vol.270
, pp. 746-750
-
-
Petruska, J.1
Goodman, M.F.2
-
48
-
-
77957860788
-
-
Analyse-it for Microsoft Excel (version 220) Analyse-it Software, Ltd
-
Analyse-it for Microsoft Excel (version 220) Analyse-it Software, Ltd http://wwwanalyse-itcom/.
-
-
-
-
49
-
-
0014734528
-
Correlation of melting temperature and cesium chloride buoyant density of bacterial deoxyribonucleic acid
-
Mandel M, Igambi I, Bergendahl J, Dodson ML, Jr., Scheltgen E (1970) Correlation of melting temperature and cesium chloride buoyant density of bacterial deoxyribonucleic acid. J Bacteriology 101: 333-338.
-
(1970)
J Bacteriology
, vol.101
, pp. 333-338
-
-
Mandel, M.1
Igambi, I.2
Bergendahl, J.3
Dodson Jr., M.L.4
Scheltgen, E.5
-
50
-
-
0020426192
-
The similarities between Pseudomonas paucimobilis and allied bacteria derived from analysis of deoxyribonucleic acids and electrophoretic protein patterns
-
Owen RJ, Jackman PJH (1982) The similarities between Pseudomonas paucimobilis and allied bacteria derived from analysis of deoxyribonucleic acids and electrophoretic protein patterns. J Gen Microbiol 128: 2945-2954.
-
(1982)
J Gen Microbiol
, vol.128
, pp. 2945-2954
-
-
Owen, R.J.1
Jackman, P.J.H.2
-
51
-
-
0019241398
-
Fine structure in the thermal denaturation of DNA: High temperature-resolution spectrophotometric studies
-
Wada A, Yabuki S, Husimi Y (1980) Fine structure in the thermal denaturation of DNA: high temperature-resolution spectrophotometric studies. CRC Crit Rev Biochem 9: 87-144.
-
(1980)
CRC Crit Rev Biochem
, vol.9
, pp. 87-144
-
-
Wada, A.1
Yabuki, S.2
Husimi, Y.3
-
52
-
-
0036712053
-
Determination of base and backbone contributions to the thermodynamics of premelting and melting transitions in B-DNA
-
Movileanu L, Benevides JM, Thomas GJ, Jr. (2002) Determination of base and backbone contributions to the thermodynamics of premelting and melting transitions in B-DNA. Nucleic Acids Res 30: 3767-3777.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3767-3777
-
-
Movileanu, L.1
Benevides, J.M.2
Thomas Jr., G.J.3
-
53
-
-
55149118976
-
Helix-coil transition of a four-way DNA junction observed by multiple fluorescence parameters
-
Vamosi G, Clegg RM (2008) Helix-coil transition of a four-way DNA junction observed by multiple fluorescence parameters. J Phys Chem B 112: 13136-13148.
-
(2008)
J Phys Chem B
, vol.112
, pp. 13136-13148
-
-
Vamosi, G.1
Clegg, R.M.2
-
55
-
-
0031587824
-
Archaeal histones, nucleosomes and transcription initiation
-
Reeve JN, Sandman K, Daniels CJ (1997) Archaeal histones, nucleosomes and transcription initiation. Cell 89: 999-1002.
-
(1997)
Cell
, vol.89
, pp. 999-1002
-
-
Reeve, J.N.1
Sandman, K.2
Daniels, C.J.3
-
56
-
-
0034011209
-
Structure and functional relationships of archaeal and eukaryal histones and nucleosomes
-
First published on January 20, 2000, 101007/s002039900122
-
Sandman K, Reeve JN (2000) Structure and functional relationships of archaeal and eukaryal histones and nucleosomes. Arch Microbiol 173: 165-169. First published on January 20, 2000, 101007/s002039900122.
-
(2000)
Arch Microbiol
, vol.173
, pp. 165-169
-
-
Sandman, K.1
Reeve, J.N.2
-
57
-
-
33244465205
-
A physicochemical model for analyzing DNA sequences
-
Dutta S, Singhal P, Agrawal P, Tomer R, Kritee, et al. (2006) A physicochemical model for analyzing DNA sequences. J Chem Inf Model 46: 78-85.
-
(2006)
J Chem Inf Model
, vol.46
, pp. 78-85
-
-
Dutta, S.1
Singhal, P.2
Agrawal, P.3
Tomer, R.4
Kritee5
-
58
-
-
44849087728
-
Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations
-
Singhal P, Jayaram B, Dixit SB, Beveridge DL (2008) Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations. Biophys J 94: 4173-4183.
-
(2008)
Biophys J
, vol.94
, pp. 4173-4183
-
-
Singhal, P.1
Jayaram, B.2
Dixit, S.B.3
Beveridge, D.L.4
-
59
-
-
0027230594
-
Compilation of E coli mRNA promoter sequences
-
Lisser S, Margalit H (1993) Compilation of E coli mRNA promoter sequences. Nucleic Acids Res 21: 1507-1516.
-
(1993)
Nucleic Acids Res
, vol.21
, pp. 1507-1516
-
-
Lisser, S.1
Margalit, H.2
-
60
-
-
0022609327
-
Local stability of DNA and RNA secondary structure and its relation to biological functions
-
Wada A, Suyama A (1986) Local stability of DNA and RNA secondary structure and its relation to biological functions. Prog Biophys Mol Biol 47: 113-157.
-
(1986)
Prog Biophys Mol Biol
, vol.47
, pp. 113-157
-
-
Wada, A.1
Suyama, A.2
|