-
2
-
-
0028933039
-
Optical melting of 128 octamer DNA duplexes. Effects of base pair location and nearest neighbors on thermal stability
-
Doktycz MJ, Morris MD, Dormady SJ, Beattie KL, Jacobson KB: Optical melting of 128 octamer DNA duplexes. Effects of base pair location and nearest neighbors on thermal stability. J Biol Chem 1995, 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
-
-
0027997526
-
DNA lesions. A thermodynamic perspective
-
Plum GE, Breslauer KJ: DNA lesions. A thermodynamic perspective. Ann NY Acad Sci 1994, 726:45-56.
-
(1994)
Ann NY Acad Sci
, vol.726
, pp. 45-56
-
-
Plum, G.E.1
Breslauer, K.J.2
-
4
-
-
0016189342
-
Stability of ribonucleic acid double-stranded helices
-
Borer PN, Dengler B, Tinoco I, Uhlenbeck OC: Stability of ribonucleic acid double-stranded helices. J Mol Biol 1974, 86:843-853.
-
(1974)
J Mol Biol
, vol.86
, pp. 843-853
-
-
Borer, P.N.1
Dengler, B.2
Tinoco, I.3
Uhlenbeck, O.C.4
-
5
-
-
0000075467
-
Improved free-energy parameters for predictions of RNA duplex stability
-
Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Caruthers MH, Neilson T, Turner DH: Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci USA 1986, 83:9373-9377.
-
(1986)
Proc Natl Acad Sci USA
, vol.83
, pp. 9373-9377
-
-
Freier, S.M.1
Kierzek, R.2
Jaeger, J.A.3
Sugimoto, N.4
Caruthers, M.H.5
Neilson, T.6
Turner, D.H.7
-
6
-
-
0001550068
-
Predicting DNA duplex stability from the base sequence
-
Breslauer KA, Frank R, Blocker H, Marky LA: Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA 1986, 83:3746-3750,
-
(1986)
Proc Natl Acad Sci USA
, vol.83
, pp. 3746-3750
-
-
Breslauer, K.A.1
Frank, R.2
Blocker, H.3
Marky, L.A.4
-
7
-
-
0029968822
-
Improved nearest-neighbor parameters for predicting DNA duplex stability
-
SantaLucia J Jr, Allawi HT, Seneviratne PA: Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 1996, 35:3555-3562. This paper describes the first determination based on optical melting curves of oligonucleotides for all 10 nearest-neighbor parameters and an initiation parameter for DNA duplexes containing only Watson-Crick pairs. The results should provide more reliable predictions of melting temperatures and equilibrium constants for applications involving Watson-Crick pairing.
-
(1996)
Biochemistry
, vol.35
, pp. 3555-3562
-
-
SantaLucia J., Jr.1
Allawi, H.T.2
Seneviratne, P.A.3
-
8
-
-
0026314940
-
Thermodynamic and structural properties of pentamer DNA-DNA, RNA-RNA and DNA-RNA duplexes of identical sequence
-
Hall KB, WcLaughlin, LW: Thermodynamic and structural properties of pentamer DNA-DNA, RNA-RNA and DNA-RNA duplexes of identical sequence. Biochemistry 1991, 30:10606-10613.
-
(1991)
Biochemistry
, vol.30
, pp. 10606-10613
-
-
Hall, K.B.1
Wclaughlin, L.W.2
-
9
-
-
0028318228
-
Sequence specific thermodynamic and structural properties for DNA-RNA duplexes
-
Ratmeyer L, Vinayak R, Zhong YY, Zon G, Wilson WD: Sequence specific thermodynamic and structural properties for DNA-RNA duplexes. Biochemistry 1994, 33:5298-5304.
-
(1994)
Biochemistry
, vol.33
, pp. 5298-5304
-
-
Ratmeyer, L.1
Vinayak, R.2
Zhong, Y.Y.3
Zon, G.4
Wilson, W.D.5
-
10
-
-
0029121625
-
Relative thermodynamic stability of DNA, RNA, and DNA-RNA hybrid duplexes-relationship with base composition and structure
-
Lesnik EA, Freier SM: Relative thermodynamic stability of DNA, RNA, and DNA-RNA hybrid duplexes-relationship with base composition and structure. Biochemistry 1995, 34:10807-10815.
-
(1995)
Biochemistry
, vol.34
, pp. 10807-10815
-
-
Lesnik, E.A.1
Freier, S.M.2
-
11
-
-
0029134549
-
Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes
-
Sugimoto N, Nakano S, Katoh M, Matsumura A, Nakamuta H, Ohmichi T, Yoneyama M, Sasaki M: Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry 1995, 34:11211-11216. This paper describes the first determination of nearest-neighbor parameters for RNA-DNA hybrids. The results allow the prediction of melting temperatures and equilibrium constants for these duplexes. No simple model seems to predict the hybrid results from the RNA-RNA and DNA-DNA results (see Fig. 1).
-
(1995)
Biochemistry
, vol.34
, pp. 11211-11216
-
-
Sugimoto, N.1
Nakano, S.2
Katoh, M.3
Matsumura, A.4
Nakamuta, H.5
Ohmichi, T.6
Yoneyama, M.7
Sasaki, M.8
-
12
-
-
0028000994
-
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding
-
Walter AE, Turner DH, Kim J, Lyttle MH, Muller P, Mathews DH, Zuker M: Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci USA 1994, 91:9218-9222. The first measurements of the thermodynamic effects of coaxial stacking of helixes show that this is an important, favorable interaction.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, pp. 9218-9222
-
-
Walter, A.E.1
Turner, D.H.2
Kim, J.3
Lyttle, M.H.4
Muller, P.5
Mathews, D.H.6
Zuker, M.7
-
13
-
-
0028143014
-
Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces
-
Walter AE, Turner DH: Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces. Biochemistry 1994, 33:12715-12719. The order of stability increments for the coaxial stacking of Watson-Crick pairs follows that observed for Watson-Crick pairs in the middle of continuous helixes.
-
(1994)
Biochemistry
, vol.33
, pp. 12715-12719
-
-
Walter, A.E.1
Turner, D.H.2
-
14
-
-
0028222102
-
Influence of base composition, base sequence, and duplex structure on DNA hydration: Apparent molar volumes and apparent molar adiabatic compressibilities of synthetic and natural DNA duplexes at 25•C
-
Chalikian TV, Sarvazyan AP, Plum GE, Breslauer KJ: Influence of base composition, base sequence, and duplex structure on DNA hydration: apparent molar volumes and apparent molar adiabatic compressibilities of synthetic and natural DNA duplexes at 25•C. Biochemistry 1994, 33:2394-2401. Measurements of molar volumes and compressibilities provide new thermodynamic parameters that will be important in the development of theories of helix formation.
-
(1994)
Biochemistry
, vol.33
, pp. 2394-2401
-
-
Chalikian, T.V.1
Sarvazyan, A.P.2
Plum, G.E.3
Breslauer, K.J.4
-
15
-
-
0027964661
-
Differential hydration of dA-dT base pairs in parallel-stranded DNA relative to antiparallel DNA
-
Rentzeperis D, Kupke DW, Marky LA: Differential hydration of dA-dT base pairs in parallel-stranded DNA relative to antiparallel DNA. Biochemistry 1994, 33:9588-9591. The authors describe measurements of volume changes that will be important in the development of theories of helix formation.
-
(1994)
Biochemistry
, vol.33
, pp. 9588-9591
-
-
Rentzeperis, D.1
Kupke, D.W.2
Marky, L.A.3
-
16
-
-
0028917227
-
A periodic table of symmetric tandem mismatches in RNA
-
Wu M, McDowell JA, Turner DH: A periodic table of symmetric tandem mismatches in RNA. Biochemistry 1995, 34:3204-3211. A large sequence dependence of stabilities of symmetric tandem mismatches is reported. NMR spectra indicate the more stable mismatches have hydrogen bonds between the bases. Subsequent work (JA McDowell, DH Turner, unpublished data) shows that all the tandem GU mismatches involve imino proton hydrogen bonds, as expected.
-
(1995)
Biochemistry
, vol.34
, pp. 3204-3211
-
-
Wu, M.1
McDowell, J.A.2
Turner, D.H.3
-
17
-
-
0024283266
-
Unusual duplex formation in purine rich oligodeoxyribonucleotides
-
Wilson WD, Hoa DTM, Zuo ET, Zon G: Unusual duplex formation in purine rich oligodeoxyribonucleotides. Nucleic Acids Res 1988, 16:5137-5151.
-
(1988)
Nucleic Acids Res
, vol.16
, pp. 5137-5151
-
-
Wilson, W.D.1
Hoa, D.T.M.2
Zuo, E.T.3
Zon, G.4
-
18
-
-
0025082690
-
Effects of GA mismatches on the structure and thermodynamics of RNA internal loops
-
SantaLucia J Jr, Kierzek R, Turner DH: Effects of GA mismatches on the structure and thermodynamics of RNA internal loops. Biochemistry 1990, 29:8813-8819.
-
(1990)
Biochemistry
, vol.29
, pp. 8813-8819
-
-
SantaLucia J., Jr.1
Kierzek, R.2
Turner, D.H.3
-
19
-
-
0028897382
-
Purine-purine mismatches in RNA helices. Evidence for protonated G-A pairs and next-nearest neighbor effects
-
Morse SE, Draper DE: Purine-purine mismatches in RNA helices. Evidence for protonated G-A pairs and next-nearest neighbor effects. Nucleic Acids Res 1995, 23:302-306. Non-nearest neighbor effects and surprising sequence dependence were observed for both single and tandem purine-purine base pairs. Certain sequences with single GA mismatches also exhibit pH dependence.
-
(1995)
Nucleic Acids Res
, vol.23
, pp. 302-306
-
-
Morse, S.E.1
Draper, D.E.2
-
20
-
-
0028354874
-
Properties of multiple G-A mismatches in stable oligonucleotide duplexes
-
Lane A, Ebel SY, Brown T: Properties of multiple G-A mismatches in stable oligonucleotide duplexes. Eur J Biochem 1994, 220:717-727. This paper shows that multiple tandem GA mismatches in a deoxyoligonucleotide can be amazingly stable, and presents a model for the structure based on NMR data.
-
(1994)
Eur J Biochem
, vol.220
, pp. 717-727
-
-
Lane, A.1
Ebel, S.Y.2
Brown, T.3
-
21
-
-
0028296359
-
Thermodynamic stability and solution conformation of tandem G-A mismatches in RNA and RNA-DNA hybrid duplexes
-
Ebel S, Brown T, Lane AN: Thermodynamic stability and solution conformation of tandem G-A mismatches in RNA and RNA-DNA hybrid duplexes. Eur J Biochem 1994, 220:703-715. The authors describe thermodynamics for tandem GA mismatches in RNA-RNA and RNA-DNA duplexes, along with a three-dimensional model for the RNA-RNA duplex based on NMR data.
-
(1994)
Eur J Biochem
, vol.220
, pp. 703-715
-
-
Ebel, S.1
Brown, T.2
Lane, A.N.3
-
22
-
-
0028085964
-
The stability and structure of tandem GA mismatches in RNA depend on closing base pairs
-
Walter AE, Wu M, Turner DH: The stability and structure of tandem GA mismatches in RNA depend on closing base pairs. Biochemistry 1994, 33:11349-11354. The formation of structures with imino hydrogen bonded or sheared GA tandem mismatches in RNA depends on the adjacent base pair, and the rules differ from those observed for DNA [24•,25,26].
-
(1994)
Biochemistry
, vol.33
, pp. 11349-11354
-
-
Walter, A.E.1
Wu, M.2
Turner, D.H.3
-
23
-
-
0027146665
-
2 in solution from NMR and restrained molecular dynamics
-
2 in solution from NMR and restrained molecular dynamics. Biochemistry 1993, 32:12612-12623.
-
(1993)
Biochemistry
, vol.32
, pp. 12612-12623
-
-
SantaLucia J., Jr.1
Turner, D.H.2
-
24
-
-
0028344967
-
2, determined by 20 NMR and structural refinement methods
-
2, determined by 20 NMR and structural refinement methods. Biochemistry 1994, 33:1053-1062. This paper provides a three-dimensional structure for the surprisingly stable tandem GA mismatch motif in DNA.
-
(1994)
Biochemistry
, vol.33
, pp. 1053-1062
-
-
Greene, K.L.1
Jones, R.L.2
Li, Y.3
Robinson, H.4
Wang, A.H.5
Zon, G.6
Wilson, W.D.7
-
25
-
-
0026053768
-
NMR and molecular modeling evidence for a G-a mismatch base pair in a purine-rich DNA duplex
-
Li Y, Zon G, Wilson WD: NMR and molecular modeling evidence for a G-A mismatch base pair in a purine-rich DNA duplex. Proc Natl Acad Sci USA 1991, 88:26-30.
-
(1991)
Proc Natl Acad Sci USA
, vol.88
, pp. 26-30
-
-
Li, Y.1
Zon, G.2
Wilson, W.D.3
-
26
-
-
0027053974
-
Base pairing geometry in GA mismatches depends entirely on the neighboring sequence
-
Cheng J-W, Chou S-H, Reid BR: Base pairing geometry in GA mismatches depends entirely on the neighboring sequence. J Mol Biol 1992, 228:1037-1041.
-
(1992)
J Mol Biol
, vol.228
, pp. 1037-1041
-
-
Cheng, J.-W.1
Chou, S.-H.2
Reid, B.R.3
-
27
-
-
0028018868
-
Parallel-stranded duplex DNA containing blocks of trans purine-purine and purine-pyrimidine base pairs
-
Evertsz EM, Rippe K, Jovin TM: Parallel-stranded duplex DNA containing blocks of trans purine-purine and purine-pyrimidine base pairs. Nucleic Acids Res 1994, 22:3293-3303. This work shows that it is possible to make long parallel-stranded DNA duplexes with mixed sequences.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 3293-3303
-
-
Evertsz, E.M.1
Rippe, K.2
Jovin, T.M.3
-
28
-
-
0028963346
-
Enthalpy entropy compensation in DNA melting thermodynamics
-
Petruska J, Goodman MF: Enthalpy entropy compensation in DNA melting thermodynamics. J Biol Chem 1995, 270:746-750.
-
(1995)
J Biol Chem
, vol.270
, pp. 746-750
-
-
Petruska, J.1
Goodman, M.F.2
-
29
-
-
0027213193
-
On the stability of nucleic acid structures in solution: Enthalpy-entropy compensations, internal rotations and reversibility
-
Searle MS, Williams DH: On the stability of nucleic acid structures in solution: enthalpy-entropy compensations, internal rotations and reversibility. Nucleic Acids Res 1993, 21:2051-2056.
-
(1993)
Nucleic Acids Res
, vol.21
, pp. 2051-2056
-
-
Searle, M.S.1
Williams, D.H.2
-
30
-
-
0028332580
-
Sequence-dependent effects on DNA stability resulting from guanosine replacements by inosine
-
Reich NO, Sweetnam KR: Sequence-dependent effects on DNA stability resulting from guanosine replacements by inosine. Nucleic Acids Res 1994, 22:2089-2093.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 2089-2093
-
-
Reich, N.O.1
Sweetnam, K.R.2
-
32
-
-
0028003846
-
The 2,6-diaminopurine riboside5-methylisocytidine wobble base pair: An isoenergetic substitution for the study of G-U pairs in RNA
-
Strobel SA, Cech TR, Usman N, Beigelman L: The 2,6-diaminopurine riboside5-methylisocytidine wobble base pair: an isoenergetic substitution for the study of G-U pairs in RNA. Biochemistry 1994, 33:13824-13835. The authors describe the thermodynamic properties of several new base pairs, one of which is isosteric with GU, but with a different placement of functional groups.
-
(1994)
Biochemistry
, vol.33
, pp. 13824-13835
-
-
Strobel, S.A.1
Cech, T.R.2
Usman, N.3
Beigelman, L.4
-
33
-
-
0028955347
-
Minor groove recognition of the conserved G-U pair at the Tetrahymena ribozyme reaction site
-
Strobel SA, Cech TR: Minor groove recognition of the conserved G-U pair at the Tetrahymena ribozyme reaction site. Science 1995, 267:675-679.
-
(1995)
Science
, vol.267
, pp. 675-679
-
-
Strobel, S.A.1
Cech, T.R.2
-
34
-
-
0029039457
-
Synthesis of oligonucleotides bearing the non-standard bases iso-C and iso-G. Comparison of iso-C-iso-G, C-G and U-A base-pair stabilities in RNA/DNA duplexes
-
Roberts C, Bandaru R, Switzer C: Synthesis of oligonucleotides bearing the non-standard bases iso-C and iso-G. Comparison of iso-C-iso-G, C-G and U-A base-pair stabilities in RNA/DNA duplexes. Tetrahedron Lett 1995, 36:3601-3604.
-
(1995)
Tetrahedron Lett
, vol.36
, pp. 3601-3604
-
-
Roberts, C.1
Bandaru, R.2
Switzer, C.3
-
35
-
-
0028886621
-
Hydrophobic, non-hydrogen-bonding bases and base pairs in DNA
-
Schweitzer BA, Kool ET: Hydrophobic, non-hydrogen-bonding bases and base pairs in DNA. J Am Chem Soc 1995, 117:1863-1872. The thermodynamic characterization of duplexes containing three new, hydrophobic bases provides some hints into interactions important for stability, and sets the stage for new applications. The hydrophobic bases are non-selective for pairing with A, C, G, and T, but are selective in pairing with each other.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 1863-1872
-
-
Schweitzer, B.A.1
Kool, E.T.2
-
36
-
-
0028886761
-
Synthesis, structure, and deoxyribonucleic-acid sequencing with a universal nucleoside-1-(2′-deoxy-beta-d-ribofuranosyl)-3-nitropyrrole
-
Bergstrom DE, Zhang PM, Toma PH, Andrews PC, Nichols R: Synthesis, structure, and deoxyribonucleic-acid sequencing with a universal nucleoside-1-(2′-deoxy-beta-d-ribofuranosyl)-3-nitropyrrole. J Am Chem Soc 1995, 117:1201-1209.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 1201-1209
-
-
Bergstrom, D.E.1
Zhang, P.M.2
Toma, P.H.3
Andrews, P.C.4
Nichols, R.5
-
37
-
-
0028983405
-
Oligonucleotide N3 to P5′ phosphoramidates
-
Gryaznov SM, Lloyd DH, Chen JK, Schultz RG, Dedionisio LA, Ratmeyer L, Wilson WD: Oligonucleotide N3 to P5′ phosphoramidates. Proc Natl Acad Sci USA 1995, 92:5798-5802. The properties of oligomers made with a new backbone, which may be useful for antisense applications, are reported.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 5798-5802
-
-
Gryaznov, S.M.1
Lloyd, D.H.2
Chen, J.K.3
Schultz, R.G.4
Dedionisio, L.A.5
Ratmeyer, L.6
Wilson, W.D.7
-
38
-
-
0029001386
-
Synthesis of the polycation thymidyl DNG, its fidelity in binding polyanionic DNA-RNA, and the stability and nature of the hybrid complexes
-
Dempcy RO, Browne KA, Bruice TC: Synthesis of the polycation thymidyl DNG, its fidelity in binding polyanionic DNA-RNA, and the stability and nature of the hybrid complexes. J Am Chem Soc 1995, 117:6140-6141. The synthesis and hybridization properties for a nucleic acid mimic with a positively charged backbone are reported.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 6140-6141
-
-
Dempcy, R.O.1
Browne, K.A.2
Bruice, T.C.3
-
39
-
-
0029077840
-
Characterization of fully 2′-modified oligoribonucleotide heteroduplex and homoduplex hybridization and nuclease sensitivity
-
Cummins LL, Owens SR, Risen LM, Lesnik EA, Freier SM, McGee D, Guinosso CJ, Cook PD: Characterization of fully 2′-modified oligoribonucleotide heteroduplex and homoduplex hybridization and nuclease sensitivity. Nucleic Acids Res 1995, 23:2019-2024. This paper reports the effects of modifications at the 2′ position on melting temperatures for duplexes formed with an RNA strand and for homo duplexes. Nuclease sensitivity was also measured. The results are important for the design of antisense compounds.
-
(1995)
Nucleic Acids Res
, vol.23
, pp. 2019-2024
-
-
Cummins, L.L.1
Owens, S.R.2
Risen, L.M.3
Lesnik, E.A.4
Freier, S.M.5
McGee, D.6
Guinosso, C.J.7
Cook, P.D.8
-
40
-
-
0028068751
-
On the conformational stability of oligonucleotide duplexes and tRNA molecules
-
Ponnuswamy PK, Gromiha MM: On the conformational stability of oligonucleotide duplexes and tRNA molecules. J Theor Biol 1994, 169:419-432.
-
(1994)
J Theor Biol
, vol.169
, pp. 419-432
-
-
Ponnuswamy, P.K.1
Gromiha, M.M.2
-
41
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell WD, Cieplak P, Bayly C, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA: A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995, 117:5179-5197. The authors provide improved parameters for theoretical calculations.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.3
Gould, I.R.4
Merz K.M., Jr.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
42
-
-
6344260593
-
An all-atom empirical energy function for the simulation of nucleic acids
-
MacKerell AD Jr, Wiorkiewicz-Kuczera J, Karplus M: An all-atom empirical energy function for the simulation of nucleic acids. J Am Chem Soc 1995, 117:11946-11975. The authors provide improved parameters for theoretical calculations.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 11946-11975
-
-
MacKerell A.D., Jr.1
Wiorkiewicz-Kuczera, J.2
Karplus, M.3
-
43
-
-
0028029749
-
Geometries, charges, dipole moments and interaction energies of normal, tautomeric and novel bases
-
Jiang SP, Raghunathan G, Ting KL, Xuan JC, Jernigan RL: Geometries, charges, dipole moments and interaction energies of normal, tautomeric and novel bases. J Biomol Struct Dyn 1994, 12:367-382.
-
(1994)
J Biomol Struct Dyn
, vol.12
, pp. 367-382
-
-
Jiang, S.P.1
Raghunathan, G.2
Ting, K.L.3
Xuan, J.C.4
Jernigan, R.L.5
-
44
-
-
0029110156
-
Toward the accurate modeling of DNA: The importance of long-range electrostatics
-
York DM, Yang W, Lee H, Darden T, Pedersen LG: Toward the accurate modeling of DNA: the importance of long-range electrostatics. J Am Chem Soc 1995, 117:5001-5002. A 2.2 ns simulation of a DNA dodecamer with full charges and explicit water and counterions is made possible by new methods for evaluating long-range Coulomb forces.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 5001-5002
-
-
York, D.M.1
Yang, W.2
Lee, H.3
Darden, T.4
Pedersen, L.G.5
-
45
-
-
0029109915
-
Molecular dynamics of RNA with the OPLS force field. Aqueous simulation of a hairpin containing a tetranucleotide loop
-
Zichi DA: Molecular dynamics of RNA with the OPLS force field. Aqueous simulation of a hairpin containing a tetranucleotide loop. J Am Chem Soc 1995, 117:2957-2969. The Ewald method permits long time simulations of an RNA hairpin loop.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 2957-2969
-
-
Zichi, D.A.1
-
46
-
-
0029170114
-
Molecular dynamics simulations on solvated biomolecular systems: The particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins
-
Cheatham TE III, Miller JL, Fox T, Darden TA, Kollman PA: Molecular dynamics simulations on solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. J Am Chem Soc 1995, 117:4193-4194. The Ewald method permits long time simulations of a DNA duplex and an RNA hairpin loop.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 4193-4194
-
-
Cheatham T.E. III1
Miller, J.L.2
Fox, T.3
Darden, T.A.4
Kollman, P.A.5
-
47
-
-
0029140885
-
Do C-H⋯O hydrogen bonds contribute to the stability of nucleic acid base pairs?
-
Leonard GA, McAuley-Hecht K, Brown T, Hunter WN: Do C-H⋯O hydrogen bonds contribute to the stability of nucleic acid base pairs? Acta Crystallogr D Biol Crystallogr 1995, 51:136-139. On the basis of crystal structures, the authors make the interesting suggestion that C-H⋯O hydrogen bonds can compensate for the desolvation of the carbonyl and thus contribute to duplex stability.
-
(1995)
Acta Crystallogr D Biol Crystallogr
, vol.51
, pp. 136-139
-
-
Leonard, G.A.1
McAuley-Hecht, K.2
Brown, T.3
Hunter, W.N.4
-
48
-
-
0026000848
-
Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs
-
Holbrook SR, Cheong C, Tinoco I Jr, Kim SH: Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs. Nature 1991, 353:579-581.
-
(1991)
Nature
, vol.353
, pp. 579-581
-
-
Holbrook, S.R.1
Cheong, C.2
Tinoco I., Jr.3
Kim, S.H.4
-
49
-
-
0028902990
-
Structure of an RNA double helix including uracil-uracil base pairs in an internal loop
-
Baeyens KJ, De Bondt HL, Holbrook SR: Structure of an RNA double helix including uracil-uracil base pairs in an internal loop. Nat Struct Biol 1995, 2:56-62. The authors describe a crystal structure that provides a detailed picture of both U-U and G-U mismatches in RNA.
-
(1995)
Nat Struct Biol
, vol.2
, pp. 56-62
-
-
Baeyens, K.J.1
De Bondt, H.L.2
Holbrook, S.R.3
-
50
-
-
0030044773
-
The structure of r(UUCGCG) has a 5′-UU- Overhang exhibiting Hoogsteen-like trans UU base pairs
-
Wahl MC, Rao ST, Sundaralingam M: The structure of r(UUCGCG) has a 5′-UU- overhang exhibiting Hoogsteen-like trans UU base pairs. Nat Struct Biol 1996, 3:24-31. This paper reports a crystal structure containing novel UU pairs with C-H⋯O hydrogen bonds similar to those discussed in [47•].
-
(1996)
Nat Struct Biol
, vol.3
, pp. 24-31
-
-
Wahl, M.C.1
Rao, S.T.2
Sundaralingam, M.3
-
51
-
-
0028908575
-
Tricyclic 2′-deoxycytidine analogs: Syntheses and incorporation into oligodeoxynucleotides which have enhanced binding to complementary RNA
-
Lin K-Y, Jones RJ, Matteucci M: Tricyclic 2′-deoxycytidine analogs: syntheses and incorporation into oligodeoxynucleotides which have enhanced binding to complementary RNA. J Am Chem Soc 1995, 117:3873-3874.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 3873-3874
-
-
Lin, K.-Y.1
Jones, R.J.2
Matteucci, M.3
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