-
3
-
-
1842479316
-
Linear free energy correlations for enzymatic base flipping: How do damaged basepairs facilitate specific recognition?
-
Krosky, D. J., F. P. Schwarz, and J. T. Stivers. 2004. Linear free energy correlations for enzymatic base flipping: how do damaged basepairs facilitate specific recognition? Biochemistry. 43:4188-4195.
-
(2004)
Biochemistry.
, vol.43
, pp. 4188-4195
-
-
Krosky, D.J.1
Schwarz, F.P.2
Stivers, J.T.3
-
4
-
-
9644255719
-
Specificity in protein-DNA interactions: Energetic recognition by the (cytosine-5-)-methyltransferase from HhaI
-
Huang, N., and A. D. MacKerell, Jr. 2005. Specificity in protein-DNA interactions: energetic recognition by the (cytosine-5-)-methyltransferase from HhaI. J. Mol. Biol. 345:265-274.
-
(2005)
J. Mol. Biol.
, vol.345
, pp. 265-274
-
-
Huang, N.1
MacKerell Jr., A.D.2
-
5
-
-
0035915260
-
Energetic and conformational aspects of A:T basepair opening within the DNA double helix
-
Giudice, E., P. Varnai, and R. Lavery. 2001. Energetic and conformational aspects of A:T basepair opening within the DNA double helix. Chem. Phys. Chem. 2:673-677.
-
(2001)
Chem. Phys. Chem.
, vol.2
, pp. 673-677
-
-
Giudice, E.1
Varnai, P.2
Lavery, R.3
-
6
-
-
0036306053
-
Free energy and structural pathways of base flipping in a DNA GCGC containing sequence
-
Banavali, N. K., and A. D. MacKerell, Jr. 2002. Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. J. Mol. Biol. 319:141-160.
-
(2002)
J. Mol. Biol.
, vol.319
, pp. 141-160
-
-
Banavali, N.K.1
MacKerell Jr., A.D.2
-
7
-
-
0037178070
-
Base flipping in DNA: Pathways and energetics studied with molecular dynamics simulations
-
Varnai, P., and R. Lavery. 2002. Base flipping in DNA: pathways and energetics studied with molecular dynamics simulations. J. Am. Chem. Soc. 124:7272-7273.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 7272-7273
-
-
Varnai, P.1
Lavery, R.2
-
8
-
-
0000777707
-
Energetic coupling between DNA bending and basepair opening
-
Ramstein, J., and R. Lavery. 1988. Energetic coupling between DNA bending and basepair opening. Proc. Natl. Acad. Sci. USA. 85:7231-7235.
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 7231-7235
-
-
Ramstein, J.1
Lavery, R.2
-
9
-
-
0036431531
-
Role of base flipping in specific recognition of damaged DNA by repair enzymes
-
Fuxreiter, M., N. Luo, P. Jedlovszky, I. Simon, and R. Osman. 2002. Role of base flipping in specific recognition of damaged DNA by repair enzymes. J. Mol. Biol. 323:823-834.
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 823-834
-
-
Fuxreiter, M.1
Luo, N.2
Jedlovszky, P.3
Simon, I.4
Osman, R.5
-
10
-
-
0037473575
-
Nucleic acid basepair dynamics: The impact of sequence and structure using free-energy calculations
-
Giudice, E., and R. Lavery. 2003. Nucleic acid basepair dynamics: the impact of sequence and structure using free-energy calculations. J. Am. Chem. Soc. 125:4998-4999.
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 4998-4999
-
-
Giudice, E.1
Lavery, R.2
-
11
-
-
0037335588
-
Basepair opening within B-DNA: Free energy pathways for GC and at basepairs from umbrella sampling simulations
-
Giudice, E., P. Varnai, and R. Lavery. 2003. Basepair opening within B-DNA: free energy pathways for GC and AT basepairs from umbrella sampling simulations. Nucleic Acids Res. 31:1434-1443.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 1434-1443
-
-
Giudice, E.1
Varnai, P.2
Lavery, R.3
-
12
-
-
0037422594
-
Protein facilitated base flipping in DNA by cytosine-5-methyltransferase
-
Huang, N., N. K. Banavali, and A. D. MacKerell, Jr. 2003. Protein facilitated base flipping in DNA by cytosine-5-methyltransferase. Proc. Natl. Acad. Sci. USA. 100:68-73.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 68-73
-
-
Huang, N.1
Banavali, N.K.2
MacKerell Jr., A.D.3
-
13
-
-
0028864424
-
Studies of basepair kinetics by NMR measurement of proton exchange
-
Gueron, M., and J. L. Leroy. 1995. Studies of basepair kinetics by NMR measurement of proton exchange. Methods Enzymol. 261:383-413.
-
(1995)
Methods Enzymol.
, vol.261
, pp. 383-413
-
-
Gueron, M.1
Leroy, J.L.2
-
14
-
-
1542269098
-
Probing site-specific energetics in proteins and nucleic acids by hydrogen exchange and NMR spectroscopy
-
Russu, I. M. 2004. Probing site-specific energetics in proteins and nucleic acids by hydrogen exchange and NMR spectroscopy. Methods Enzymol. 379:152-175.
-
(2004)
Methods Enzymol.
, vol.379
, pp. 152-175
-
-
Russu, I.M.1
-
15
-
-
0025325784
-
Processes of basepair opening and proton exchange in Z-DNA
-
Kochoyan, M., J. L. Leroy, and M. Gueron. 1990. Processes of basepair opening and proton exchange in Z-DNA. Biochemistry. 29:4799-4805.
-
(1990)
Biochemistry.
, vol.29
, pp. 4799-4805
-
-
Kochoyan, M.1
Leroy, J.L.2
Gueron, M.3
-
16
-
-
0024285807
-
Evidence from basepair kinetics for two types of adenine tract structures in solution: Their relation to DNA curvature
-
Leroy, J. L., E. Charretier, M. Kochoyan, and M. Gueron. 1988. Evidence from basepair kinetics for two types of adenine tract structures in solution: their relation to DNA curvature. Biochemistry. 27:8894-8898.
-
(1988)
Biochemistry.
, vol.27
, pp. 8894-8898
-
-
Leroy, J.L.1
Charretier, E.2
Kochoyan, M.3
Gueron, M.4
-
17
-
-
0026737976
-
Kinetics and energetics of basepair opening in 5′- D(CGCGAATTCGCG)-3′ and a substituted dodecamer containing G-T mismatches
-
Moe, J. G., and I. M. Russu. 1992. Kinetics and energetics of basepair opening in 5′- d(CGCGAATTCGCG)-3′ and a substituted dodecamer containing G-T mismatches. Biochemistry. 31:8421-8428.
-
(1992)
Biochemistry.
, vol.31
, pp. 8421-8428
-
-
Moe, J.G.1
Russu, I.M.2
-
18
-
-
0027934143
-
Sequence-dependence of basepair opening in a DNA dodecamer containing the CACA/GTGT sequence motif
-
Folta-Stogniew, E. J., and I. M. Russu. 1994. Sequence-dependence of basepair opening in a DNA dodecamer containing the CACA/GTGT sequence motif. Biochemistry. 33:11016-11024.
-
(1994)
Biochemistry.
, vol.33
, pp. 11016-11024
-
-
Folta-Stogniew, E.J.1
Russu, I.M.2
-
19
-
-
0033548682
-
High basepair opening rates in tracts of GC basepairs
-
Dornberger, U., M. Leijon, and H. Fritzsche. 1999. High basepair opening rates in tracts of GC basepairs. J. Biol. Chem. 274:6957-6962.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 6957-6962
-
-
Dornberger, U.1
Leijon, M.2
Fritzsche, H.3
-
20
-
-
16644365966
-
Sequence-dependence of the energetics of opening of at basepairs in DNA
-
Chen, C., and I. M. Russu. 2004. Sequence-dependence of the energetics of opening of AT basepairs in DNA. Biophys. J. 87:1-7.
-
(2004)
Biophys. J.
, vol.87
, pp. 1-7
-
-
Chen, C.1
Russu, I.M.2
-
23
-
-
0037006984
-
Site-resolved energetics in DNA triple helices containing G-TA and T-CG triads
-
Coman, D., and I. M. Russu. 2002. Site-resolved energetics in DNA triple helices containing G-TA and T-CG triads. Biochemistry. 41: 4407-4414.
-
(2002)
Biochemistry.
, vol.41
, pp. 4407-4414
-
-
Coman, D.1
Russu, I.M.2
-
24
-
-
0014725117
-
Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxyoligonucleotides
-
Cantor, C. R., M. M. Warshaw, and H. Shapiro. 1970. Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxyoligonucleotides. Biopolymers. 9:1059-1077.
-
(1970)
Biopolymers.
, vol.9
, pp. 1059-1077
-
-
Cantor, C.R.1
Warshaw, M.M.2
Shapiro, H.3
-
26
-
-
33845555707
-
Exchangeable proton NMR without base-line distortion, using new strong-pulse sequences
-
Plateau, P., and M. Gueron. 1982. Exchangeable proton NMR without base-line distortion, using new strong-pulse sequences. J. Am. Chem. Soc. 104:7310-7311.
-
(1982)
J. Am. Chem. Soc.
, vol.104
, pp. 7310-7311
-
-
Plateau, P.1
Gueron, M.2
-
27
-
-
0035957144
-
A signature of the T→R transition in human hemoglobin
-
Mihailescu, M. R., and I. M. Russu. 2001. A signature of the T→R transition in human hemoglobin. Proc. Natl. Acad. Sci. USA. 98:3773-3777.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 3773-3777
-
-
Mihailescu, M.R.1
Russu, I.M.2
-
28
-
-
0020855355
-
Hydrogen exchange and structural dynamics of proteins and nucleic acids
-
Englander, S. W., and N. R. Kallenbach. 1984. Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q. Rev. Biophys. 16:521-655.
-
(1984)
Q. Rev. Biophys.
, vol.16
, pp. 521-655
-
-
Englander, S.W.1
Kallenbach, N.R.2
-
29
-
-
0000269878
-
-
R.H. Sarma, and M. H. Sarma, editors. Adenine Press, Schenectady, NY
-
Gueron, M., E. Charretier, J. Hagerhorst, M. Kochoyan, J. L. Leroy, and A. Moraillon. 1990. Structure and Methods. R.H. Sarma, and M. H. Sarma, editors. Adenine Press, Schenectady, NY. 113-137.
-
(1990)
Structure and Methods
, pp. 113-137
-
-
Gueron, M.1
Charretier, E.2
Hagerhorst, J.3
Kochoyan, M.4
Leroy, J.L.5
Moraillon, A.6
-
30
-
-
0025743423
-
Proton exchange and internal motions in two chromomycin dimer-DNA oligomer complexes
-
Leroy, J. L., X. Gao, M. Gueron, and D. J. Patel. 1991. Proton exchange and internal motions in two chromomycin dimer-DNA oligomer complexes. Biochemistry. 30:5653-5661.
-
(1991)
Biochemistry.
, vol.30
, pp. 5653-5661
-
-
Leroy, J.L.1
Gao, X.2
Gueron, M.3
Patel, D.J.4
-
32
-
-
20144368711
-
Basepair opening in three DNA unwinding elements
-
Coman, D., and I. M. Russu. 2005. Basepair opening in three DNA unwinding elements. J. Biol. Chem. 280:20216-20221.
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 20216-20221
-
-
Coman, D.1
Russu, I.M.2
-
33
-
-
0025194337
-
Proton exchange and basepair opening kinetics in 5′-d(CGCGAATTCGCG) -3′ and related dodecamers
-
Moe, J. G., and I. M. Russu. 1990. Proton exchange and basepair opening kinetics in 5′-d(CGCGAATTCGCG)-3′ and related dodecamers. Nucleic Acids Res. 18:821-827.
-
(1990)
Nucleic Acids Res.
, vol.18
, pp. 821-827
-
-
Moe, J.G.1
Russu, I.M.2
-
34
-
-
0003617193
-
The theory of rate processes
-
McGraw-Hill, New York and London
-
Glasstone, S., K. J. Laidler, and H. Eyring. 1941. The theory of rate processes. In The Kinetics of Chemical Reactions, Viscosity, Diffusion, and Electrochemical Phenomena. McGraw-Hill, New York and London.
-
(1941)
The Kinetics of Chemical Reactions, Viscosity, Diffusion, and Electrochemical Phenomena
-
-
Glasstone, S.1
Laidler, K.J.2
Eyring, H.3
-
35
-
-
33847798413
-
Enthalpy-entropy compensation. II. Separation of the chemical from the statistical effect
-
Krug, R. R., W. G. Hunter, and R. A. Grieger. 1976. Enthalpy-entropy compensation. II. Separation of the chemical from the statistical effect. J. Phys. Chem. 80:2341-2351.
-
(1976)
J. Phys. Chem.
, vol.80
, pp. 2341-2351
-
-
Krug, R.R.1
Hunter, W.G.2
Grieger, R.A.3
-
36
-
-
0344270866
-
Atomistic understanding of kinetic pathways for single basepair binding and unbinding in DNA
-
Hagan, M. F., A. R. Dinner, D. Chandler, and A. K. Chakraborty. 2003. Atomistic understanding of kinetic pathways for single basepair binding and unbinding in DNA. Proc. Natl. Acad. Sci. USA. 100: 13922-13927.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 13922-13927
-
-
Hagan, M.F.1
Dinner, A.R.2
Chandler, D.3
Chakraborty, A.K.4
-
39
-
-
0000288714
-
Parameters for the description of transition states
-
Leffler, J. E. 1953. Parameters for the description of transition states. Science. 117:340-341.
-
(1953)
Science.
, vol.117
, pp. 340-341
-
-
Leffler, J.E.1
-
40
-
-
0027171034
-
Application of physical organic chemistry to engineered mutants of proteins: Hammond postulate behavior in the transition state of protein folding
-
Matouschek, A., and A. R. Fersht. 1993. Application of physical organic chemistry to engineered mutants of proteins: Hammond postulate behavior in the transition state of protein folding. Proc. Natl. Acad. Sci. USA. 90:7814-7818.
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 7814-7818
-
-
Matouschek, A.1
Fersht, A.R.2
-
41
-
-
0037418635
-
Hammond behavior versus ground state effects in protein folding: Evidence for narrow free energy barriers and residual structure in the unfolded state
-
Sanchez, I. E., and T. Kiefhaber. 2003. Hammond behavior versus ground state effects in protein folding: evidence for narrow free energy barriers and residual structure in the unfolded state. J. Mol. Biol. 327:867-884.
-
(2003)
J. Mol. Biol.
, vol.327
, pp. 867-884
-
-
Sanchez, I.E.1
Kiefhaber, T.2
|