-
1
-
-
0019883193
-
Thermodynamics of (dG-dC)3 double-helix formation in water and deuterium oxide
-
Albergo, D., L. A. Marky, K. J. Breslauer, and D. H. Turner. 1981. Thermodynamics of (dG-dC)3 double-helix formation in water and deuterium oxide. Biochemistry. 20:1409-1413.
-
(1981)
Biochemistry
, vol.20
, pp. 1409-1413
-
-
Albergo, D.1
Marky, L.A.2
Breslauer, K.J.3
Turner, D.H.4
-
2
-
-
0030875847
-
Thermodynamics and NMR of internal G-T mismatches in DNA
-
Allawi, H. T., and J. SantaLucia, Jr. 1997. Thermodynamics and NMR of internal G-T mismatches in DNA. Biochemistry. 97:10581-10594.
-
(1997)
Biochemistry
, vol.97
, pp. 10581-10594
-
-
Allawi, H.T.1
SantaLucia Jr., J.2
-
3
-
-
0013769174
-
Theory of effects of concentration and chain length on helix-coil equilibria in two-stranded nucleic acids
-
Applequist, J., and V. Damle. 1963. Theory of effects of concentration and chain length on helix-coil equilibria in two-stranded nucleic acids. J. Chem. Phys. 39:2719-2721.
-
(1963)
J. Chem. Phys.
, vol.39
, pp. 2719-2721
-
-
Applequist, J.1
Damle, V.2
-
4
-
-
0015257704
-
∞ from the dependence of the temperature of the helix-coil transition on oligomer concentrations
-
∞ from the dependence of the temperature of the helix-coil transition on oligomer concentrations. Biopolymers. 11:913-933.
-
(1972)
Biopolymers
, vol.11
, pp. 913-933
-
-
Blake, R.D.1
-
5
-
-
0024469373
-
Effects of base sequence on the loop folding in DNA hairpins
-
Blommers, M. J., J. A. Walters, C. A. Haasnoot, J. M. Aelen, G. A. van der Marel, J. H. van Boom, and C. W. Hilbers. 1989. Effects of base sequence on the loop folding in DNA hairpins. Biochemistry. 28:7491-7498.
-
(1989)
Biochemistry
, vol.28
, pp. 7491-7498
-
-
Blommers, M.J.1
Walters, J.A.2
Haasnoot, C.A.3
Aelen, J.M.4
Van Der Marel, G.A.5
Van Boom, J.H.6
Hilbers, C.W.7
-
6
-
-
0003803285
-
-
University Science Books, Sausalito, CA
-
Bloomfield, V. A., D. M. Crothers, and I. Tinoco, Jr. 2000. Nucleic Acids. Structure, Properties and Functions. University Science Books, Sausalito, CA.
-
(2000)
Nucleic Acids. Structure, Properties and Functions
-
-
Bloomfield, V.A.1
Crothers, D.M.2
Tinoco Jr., I.3
-
7
-
-
0016189342
-
Stability of ribonucleic acid double-stranded helices
-
Borer, P. N., B. Dengler, I. Tinoco, Jr., and O. C. Uhlenbeck. 1974. Stability of ribonucleic acid double-stranded helices. J. Mol. Biol. 86:843-853.
-
(1974)
J. Mol. Biol.
, vol.86
, pp. 843-853
-
-
Borer, P.N.1
Dengler, B.2
Tinoco Jr., I.3
Uhlenbeck, O.C.4
-
8
-
-
0026687954
-
Calorimetry: A tool for DNA and ligand-DNA studies
-
Breslauer, K. J., E. Freire, and M. Straume. 1992. Calorimetry: a tool for DNA and ligand-DNA studies. Methods Enzymol. 211:533-567.
-
(1992)
Methods Enzymol.
, vol.211
, pp. 533-567
-
-
Breslauer, K.J.1
Freire, E.2
Straume, M.3
-
9
-
-
0016656309
-
Calorimetric and spectroscopic investigation of the helix-to-coil transition of a ribo-oligonucleotide: rA7U7
-
Breslauer, K. J., J. M. Sturtevant, and I. Tinoco, Jr. 1975. Calorimetric and spectroscopic investigation of the helix-to-coil transition of a ribo-oligonucleotide: rA7U7. J. Mol. Biol. 99:549-565.
-
(1975)
J. Mol. Biol.
, vol.99
, pp. 549-565
-
-
Breslauer, K.J.1
Sturtevant, J.M.2
Tinoco Jr., I.3
-
10
-
-
0033529318
-
A more unified picture for the thermodynamics of nucleic acid duplex melting: A characterization by calorimetric and volumetric techniques
-
Chalikian, T. V., J. Volker, G. E. Plum, and K. J. Breslauer. 1999. A more unified picture for the thermodynamics of nucleic acid duplex melting: a characterization by calorimetric and volumetric techniques. Proc. Natl. Acad. Sci. USA. 96:7853-7858.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 7853-7858
-
-
Chalikian, T.V.1
Volker, J.2
Plum, G.E.3
Breslauer, K.J.4
-
11
-
-
0025689277
-
Thermodynamic stability of the 5′ dangling-ended DNA hairpins formed from sequences 5′-(XY)2GGATAC(T)4GTATCC-3′, where X,Y=A,T, G,C
-
Doktycz, M. J., T. M. Paner, M. Amaratunga, and A. S. Benight. 1990. Thermodynamic stability of the 5′ dangling-ended DNA hairpins formed from sequences 5′-(XY)2GGATAC(T)4GTATCC-3′, where X,Y=A,T, G,C. Biopolymers. 30:829-845.
-
(1990)
Biopolymers
, vol.30
, pp. 829-845
-
-
Doktycz, M.J.1
Paner, T.M.2
Amaratunga, M.3
Benight, A.S.4
-
12
-
-
0019886913
-
A 300-MHz proton nuclear magnetic resonance investigation of deoxyribonucleic acid restriction fragments: Dynamic properties
-
Early, T. A., D. R. Kearns, W. Hillen, and R. D. Wells. 1981. A 300-MHz proton nuclear magnetic resonance investigation of deoxyribonucleic acid restriction fragments: dynamic properties. Biochemistry. 20:3764-3769.
-
(1981)
Biochemistry
, vol.20
, pp. 3764-3769
-
-
Early, T.A.1
Kearns, D.R.2
Hillen, W.3
Wells, R.D.4
-
13
-
-
0017587485
-
Theory of DNA melting curves
-
Fixman, M., and J. J. Freire. 1977. Theory of DNA melting curves. Biopolymers. 16:2693-2704.
-
(1977)
Biopolymers
, vol.16
, pp. 2693-2704
-
-
Fixman, M.1
Freire, J.J.2
-
14
-
-
0001613489
-
Contribution of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes
-
Freier, S. M., D. Alkema, A. Sinclair, T. Neilson, and D. H. Turner. 1983. Contribution of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes. Biochemistry. 22:6198-6206.
-
(1983)
Biochemistry
, vol.22
, pp. 6198-6206
-
-
Freier, S.M.1
Alkema, D.2
Sinclair, A.3
Neilson, T.4
Turner, D.H.5
-
15
-
-
0019883234
-
Solvent effects on the kinetics and thermodynamics of stacking in poly (cytidylic acid)
-
Freier, S. M., K. O. Hill, T. G. Dewey, L. A. Marky, K. J. Breslauer, and D. H. Turner. 1981. Solvent effects on the kinetics and thermodynamics of stacking in poly (cytidylic acid). Biochemistry. 20:1419-1426.
-
(1981)
Biochemistry
, vol.20
, pp. 1419-1426
-
-
Freier, S.M.1
Hill, K.O.2
Dewey, T.G.3
Marky, L.A.4
Breslauer, K.J.5
Turner, D.H.6
-
16
-
-
0015914592
-
Free energy of imperfect nucleic acid helices. II. Small hairpin loops
-
Gralla, J., and D. M. Crothers. 1973. Free energy of imperfect nucleic acid helices. II. Small hairpin loops. J. Mol. Biol. 73:497-511.
-
(1973)
J. Mol. Biol.
, vol.73
, pp. 497-511
-
-
Gralla, J.1
Crothers, D.M.2
-
18
-
-
34249772381
-
Fast folding and comparison of RNA secondary structures
-
Hofacker, I. L., W. Fontana, P. F. Stadler, S. Bonhöffer, M. Tacker, and P. Schuster. 1994. Fast folding and comparison of RNA secondary structures. Monatsh. Chem. 125:167-188.
-
(1994)
Monatsh. Chem.
, vol.125
, pp. 167-188
-
-
Hofacker, I.L.1
Fontana, W.2
Stadler, P.F.3
Bonhöffer, S.4
Tacker, M.5
Schuster, P.6
-
19
-
-
0033614819
-
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
-
Holbrook, J. A., M. W. Capp, R. M. Saecker, and M. T. Record. 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.
-
(1999)
Biochemistry
, vol.38
, pp. 8409-8422
-
-
Holbrook, J.A.1
Capp, M.W.2
Saecker, R.M.3
Record, M.T.4
-
22
-
-
0025729926
-
Thermodynamic characterization of deoxyribooligonucleotide duplexes containing bulges
-
LeBlanc, D. A., and K. M. Morden. 1991. Thermodynamic characterization of deoxyribooligonucleotide duplexes containing bulges. Biochemistry. 30:4042-4047.
-
(1991)
Biochemistry
, vol.30
, pp. 4042-4047
-
-
LeBlanc, D.A.1
Morden, K.M.2
-
23
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
Mathews, D. H., J. Sabina, M. Zuker, and D. H. Turner. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 87:911-940.
-
(1999)
J. Mol. Biol.
, vol.87
, pp. 911-940
-
-
Mathews, D.H.1
Sabina, J.2
Zuker, M.3
Turner, D.H.4
-
24
-
-
0029955048
-
RNAdraw: An integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows
-
Matzura, O., and A. Wennborg. 1996. RNAdraw: an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows. Comput. Appl. Biosci. 12:247-249.
-
(1996)
Comput. Appl. Biosci.
, vol.12
, pp. 247-249
-
-
Matzura, O.1
Wennborg, A.2
-
25
-
-
0025264854
-
The equilibrium partition function and base pair binding probabilities for RNA secondary structure
-
McCaskill, J. S. 1990. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers. 29:1105-1119.
-
(1990)
Biopolymers
, vol.29
, pp. 1105-1119
-
-
McCaskill, J.S.1
-
26
-
-
0031432735
-
Predicting sequence-dependent melting stability of short duplex DNA oligomers
-
Owczarzy, R., P. M. Vallone, F. J. Gallo, T. M. Paner, M. J. Lane, and A. S. Benight. 1997. Predicting sequence-dependent melting stability of short duplex DNA oligomers. Biopolymers. 44:217-239.
-
(1997)
Biopolymers
, vol.44
, pp. 217-239
-
-
Owczarzy, R.1
Vallone, P.M.2
Gallo, F.J.3
Paner, T.M.4
Lane, M.J.5
Benight, A.S.6
-
27
-
-
0020674698
-
Base-stacking and base-pairing contribution to helix stability: Thermodynamic of double-helix formation with CCGG, CCGGp, CCGGAp, CCGGUp, and ACCGGUp
-
Petersheim, M., and D. H. Turner. 1983. Base-stacking and base-pairing contribution to helix stability: Thermodynamic of double-helix formation with CCGG, CCGGp, CCGGAp, CCGGUp, and ACCGGUp. Biochemistry. 22:256-263.
-
(1983)
Biochemistry
, vol.22
, pp. 256-263
-
-
Petersheim, M.1
Turner, D.H.2
-
28
-
-
0028783875
-
Influence of the oxidatively damaged adduct 8-oxodeoxyguanosine on the conformation, energetics, and thermodynamic stability of a DNA duplex
-
Plum, G. E., A. P. Grollman, F. Johnson, and K. J. Breslauer. 1995. Influence of the oxidatively damaged adduct 8-oxodeoxyguanosine on the conformation, energetics, and thermodynamic stability of a DNA duplex. Biochemistry. 34:16148-16160.
-
(1995)
Biochemistry
, vol.34
, pp. 16148-16160
-
-
Plum, G.E.1
Grollman, A.P.2
Johnson, F.3
Breslauer, K.J.4
-
29
-
-
0015846852
-
Thermodynamics and kinetics of the helix-coil transition of oligomers containing GC basepairs
-
Poerschke, D., O. C. Uhlenbeck, and F. H. Martin. 1973. Thermodynamics and kinetics of the helix-coil transition of oligomers containing GC basepairs. Biopolymers. 12:1313-1335.
-
(1973)
Biopolymers
, vol.12
, pp. 1313-1335
-
-
Poerschke, D.1
Uhlenbeck, O.C.2
Martin, F.H.3
-
30
-
-
0016266885
-
Recursion relation generation of probability profiles for specific-sequence macromolecules with long-range correlations
-
Poland, D. 1974. Recursion relation generation of probability profiles for specific-sequence macromolecules with long-range correlations. Biopolymers. 13:1859-1871.
-
(1974)
Biopolymers
, vol.13
, pp. 1859-1871
-
-
Poland, D.1
-
32
-
-
0024804759
-
Absorbance melting curves of RNA
-
Puglisi, J. D., and I. Tinoco, Jr. 1989. Absorbance melting curves of RNA. Methods Enzymol. 180:304-325.
-
(1989)
Methods Enzymol.
, vol.180
, pp. 304-325
-
-
Puglisi, J.D.1
Tinoco Jr., I.2
-
33
-
-
0342699024
-
Fast algorithms to determine RNA secondary structures containing multiple loops
-
D. Sankoff and J. B. Kruskal, editors. Addison-Wesley, Reading, MA
-
Sankoff, D., J. B. Kruskal, S. Mainville, and R. J. Cedergren. 1983. Fast algorithms to determine RNA secondary structures containing multiple loops. In Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison. D. Sankoff and J. B. Kruskal, editors. Addison-Wesley, Reading, MA. 93-120.
-
(1983)
Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison
, pp. 93-120
-
-
Sankoff, D.1
Kruskal, J.B.2
Mainville, S.3
Cedergren, R.J.4
-
34
-
-
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. USA. 95:1460-1465.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 1460-1465
-
-
SantaLucia Jr., J.1
-
35
-
-
0035070585
-
Immobilized RNA switches for the analysis of complex chemical and biological mixture
-
Seetharaman, S., M. Zivarats, N. Sudarsan, and R. R. Braker. 2001. Immobilized RNA switches for the analysis of complex chemical and biological mixture. Nat. Biotechnol. 19:336-341.
-
(2001)
Nat. Biotechnol.
, vol.19
, pp. 336-341
-
-
Seetharaman, S.1
Zivarats, M.2
Sudarsan, N.3
Braker, R.R.4
-
36
-
-
0035865260
-
Experimental annotation of the human genome using microarray technology
-
Shoemaker, D. D., E. E. Schadt, C. D. Armour, Y. D. He, P. Garrett-Engele, P. D. McDonagh, and P. M. Loer. 2001. Experimental annotation of the human genome using microarray technology. Nature. 409:922-927.
-
(2001)
Nature
, vol.409
, pp. 922-927
-
-
Shoemaker, D.D.1
Schadt, E.E.2
Armour, C.D.3
He, Y.D.4
Garrett-Engele, P.5
McDonagh, P.D.6
Loer, P.M.7
-
37
-
-
0000826487
-
Biochemical applications of differential scanning calorimetry
-
Sturtevant, J. M. 1987. Biochemical applications of differential scanning calorimetry. Annu. Rev. Phys. Chem. 38:463-488.
-
(1987)
Annu. Rev. Phys. Chem.
, vol.38
, pp. 463-488
-
-
Sturtevant, J.M.1
-
38
-
-
0023653195
-
Sequence dependence for the energetics of dangling ends terminal base pairs in ribonucleic acid
-
Sugimoto, N., R. Kierzek, and D. H. Turner. 1987. Sequence dependence for the energetics of dangling ends terminal base pairs in ribonucleic acid. Biochemistry. 26:4554-4558.
-
(1987)
Biochemistry
, vol.26
, pp. 4554-4558
-
-
Sugimoto, N.1
Kierzek, R.2
Turner, D.H.3
-
39
-
-
0013549381
-
Sequence alignment in the neighborhood of the optimum with general application to dynamic programming
-
Waterman, M. S. 1983. Sequence alignment in the neighborhood of the optimum with general application to dynamic programming. Proc. Natl. Acad. Sci. USA. 80:3123-3124.
-
(1983)
Proc. Natl. Acad. Sci. USA
, vol.80
, pp. 3123-3124
-
-
Waterman, M.S.1
-
40
-
-
0022380106
-
A dynamic programming algorithm to find all solutions in a neighborhood of the optimum
-
Waterman, M. S., and T. H. Byers. 1985. A dynamic programming algorithm to find all solutions in a neighborhood of the optimum. Math. Biosci. 77:179-188.
-
(1985)
Math. Biosci.
, vol.77
, pp. 179-188
-
-
Waterman, M.S.1
Byers, T.H.2
-
41
-
-
0023045712
-
A dynamic programing algorithm for finding alternate RNA secondary structures
-
Williams, A. L., and I. Tinoco, Jr. 1986. A dynamic programing algorithm for finding alternate RNA secondary structures. Nucleic Acids Res. 14:299-315.
-
(1986)
Nucleic Acids Res.
, vol.14
, pp. 299-315
-
-
Williams, A.L.1
Tinoco Jr., I.2
-
42
-
-
0025896047
-
Differential hydration of dA-dT base pairing and dA and dT bulges in deoxyoligonucleotides
-
Zieba, K., T. M. Chu, D. W. Kupke, and L. A. Marky. 1991. Differential hydration of dA-dT base pairing and dA and dT bulges in deoxyoligonucleotides. Biochemistry. 30:8018-8026.
-
(1991)
Biochemistry
, vol.30
, pp. 8018-8026
-
-
Zieba, K.1
Chu, T.M.2
Kupke, D.W.3
Marky, L.A.4
-
43
-
-
0000754002
-
"Theory of melting" of the helical form in double chains of the DNA type
-
Zimm, B. H. 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
-
44
-
-
0024806949
-
Computer prediction of RNA structure
-
Zuker, M. 1989a. Computer prediction of RNA structure. Methods Enzymol. 180:262-288.
-
(1989)
Methods Enzymol.
, vol.180
, pp. 262-288
-
-
Zuker, M.1
-
45
-
-
0024477261
-
On finding all suboptimal foldings of an RNA molecule
-
Zuker, M. 1989b. On finding all suboptimal foldings of an RNA molecule. Science. 244:48-52.
-
(1989)
Science
, vol.244
, pp. 48-52
-
-
Zuker, M.1
-
46
-
-
0000616205
-
RNA secondary structures and their prediction
-
Zuker, M., and D. Sankoff. 1984. RNA secondary structures and their prediction. Bull. Math. Biol. 46:591-621.
-
(1984)
Bull. Math. Biol.
, vol.46
, pp. 591-621
-
-
Zuker, M.1
Sankoff, D.2
-
47
-
-
0019876473
-
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
-
Zuker, M., and P. Stiegler. 1981. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9:133-148.
-
(1981)
Nucleic Acids Res.
, vol.9
, pp. 133-148
-
-
Zuker, M.1
Stiegler, P.2
-
48
-
-
0002287019
-
Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide
-
J. Barciszewski, and B. F. C. Clark, editors. NATO ASI Series. Kluwer Academic Publishers. Dordrecht, the Netherlands
-
Zuker, M., D. H. Mathews, and D. H. Turner. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In RNA Biochemistry and Biotechnology. J. Barciszewski, and B. F. C. Clark, editors. NATO ASI Series. Kluwer Academic Publishers. Dordrecht, the Netherlands. 11-43.
-
(1999)
RNA Biochemistry and Biotechnology
, pp. 11-43
-
-
Zuker, M.1
Mathews, D.H.2
Turner, D.H.3
|