-
1
-
-
0025308916
-
Ion distributions around DNA and other cylindrical polyions: Theoretical descriptions and physical implications.
-
Anderson, C.F. and Record, M.T. Jr. 1990. Ion distributions around DNA and other cylindrical polyions: Theoretical descriptions and physical implications. Annu. Rev. Biophys. Biophys. Chem. 19:423-465.
-
(1990)
Annu. Rev. Biophys. Biophys. Chem.
, vol.19
, pp. 423-465
-
-
Anderson, C.F.1
Record Jr., M.T.2
-
3
-
-
0035793219
-
Water and ion binding around r(UpA)12 and d(TpA)12 oligomers-Comparison with RNA and DNA (CpG)12 duplexes.
-
Auffinger, P. and Westhof, E. 2001. Water and ion binding around r(UpA)12 and d(TpA)12 oligomers-Comparison with RNA and DNA (CpG)12 duplexes. J. Mol. Biol. 305:1057-1072.
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 1057-1072
-
-
Auffinger, P.1
Westhof, E.2
-
4
-
-
0003803285
-
Nucleic Acids: Structures, Properties, and Functions.
-
University Science Books, Sausalito, California.
-
Bloomfield, V.A., Crothers, D.M., and Tinoco, I. Jr. 2000. Nucleic Acids: Structures, Properties, and Functions. University Science Books, Sausalito, California.
-
(2000)
-
-
Bloomfield, V.A.1
Crothers, D.M.2
Tinoco Jr., I.3
-
5
-
-
0001550068
-
Predicting DNA duplex stability from the base sequence.
-
Breslauer, K.J., Frank, R., Blocker, H., and Marky, L.A. 1986. Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. U.S.A. 83:3746-3750.
-
(1986)
Proc. Natl. Acad. Sci. U.S.A.
, vol.83
, pp. 3746-3750
-
-
Breslauer, K.J.1
Frank, R.2
Blocker, H.3
Marky, L.A.4
-
6
-
-
0041822089
-
Cell biology: Join the crowd.
-
Ellis, R.J. and Minton, A.P. 2003. Cell biology: Join the crowd. Nature 425:27-28.
-
(2003)
Nature
, vol.425
, pp. 27-28
-
-
Ellis, R.J.1
Minton, A.P.2
-
7
-
-
0006627150
-
A molecular simulation picture of DNA hydration around A- and B-DNA
-
Feig, M. and Pettitt, B.M. 1998. A molecular simulation picture of DNA hydration around A- and B-DNA. Biopolymers 48:199-209.
-
(1998)
Biopolymers
, vol.48
, pp. 199-209
-
-
Feig, M.1
Pettitt, B.M.2
-
8
-
-
0020184671
-
How crowded is the cytoplasm?
-
Fulton, A.B. 1982. How crowded is the cytoplasm? Cell 30:345-347.
-
(1982)
Cell
, vol.30
, pp. 345-347
-
-
Fulton, A.B.1
-
9
-
-
0037418563
-
Metabolic buffering exerted by macromolecular crowding onDNA-DNAinteractions: Origin and physiological significance
-
Goobes, R., Kahana, N., Cohen, O., and Minsky, A. 2003. Metabolic buffering exerted by macromolecular crowding onDNA-DNAinteractions: Origin and physiological significance. Biochemistry 42:2431-2440.
-
(2003)
Biochemistry
, vol.42
, pp. 2431-2440
-
-
Goobes, R.1
Kahana, N.2
Cohen, O.3
Minsky, A.4
-
10
-
-
0028959686
-
Analyses of thermodynamic data for concentrated hemoglobin solutions using scaled particle theory: Implications for a simple twostate model of water in thermodynamic analyses of crowding in vitro and in vivo
-
Guttman, H.J., Anderson, C.F., and Record, M.T. Jr. 1995. Analyses of thermodynamic data for concentrated hemoglobin solutions using scaled particle theory: Implications for a simple twostate model of water in thermodynamic analyses of crowding in vitro and in vivo. Biophys. J. 68:835-846.
-
(1995)
Biophys. J.
, vol.68
, pp. 835-846
-
-
Guttman, H.J.1
Anderson, C.F.2
Record Jr., M.T.3
-
11
-
-
0041931122
-
Macromolecular crowding: Qualitative and semiquantitative successes, quantitative challenges
-
Hall, D. and Minton, A.P. 2003. Macromolecular crowding: Qualitative and semiquantitative successes, quantitative challenges. Biochim. Biophys. Acta 1649:127-139.
-
(2003)
Biochim. Biophys. Acta
, vol.1649
, pp. 127-139
-
-
Hall, D.1
Minton, A.P.2
-
12
-
-
43949083779
-
Effects of polyethylene glycol on DNA duplex stability at different NaCl concentrations
-
Karimata, H., Nakano, S., and Sugimoto, N. 2007. Effects of polyethylene glycol on DNA duplex stability at different NaCl concentrations. Bull. Chem. Soc. Jpn. 80:1987-1994.
-
(2007)
Bull. Chem. Soc. Jpn.
, vol.80
, pp. 1987-1994
-
-
Karimata, H.1
Nakano, S.2
Sugimoto, N.3
-
13
-
-
77953900637
-
Molecular crowding stabilizes folded RNA structure by the excluded volume effect
-
Kilburn, D., Roh, J.H., Guo, L., Briber, R.M., and Woodson, S.A. 2010. Molecular crowding stabilizes folded RNA structure by the excluded volume effect. J. Am. Chem. Soc. 132:8690-8696.
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 8690-8696
-
-
Kilburn, D.1
Roh, J.H.2
Guo, L.3
Briber, R.M.4
Woodson, S.A.5
-
14
-
-
0015274187
-
On the application of polyelectrolyte "limiting laws" to the helix-coil transition of DNA. I. Excess univalent cations
-
Manning, G.S. 1972. On the application of polyelectrolyte "limiting laws" to the helix-coil transition of DNA. I. Excess univalent cations. Biopolymers 11:937-949.
-
(1972)
Biopolymers
, vol.11
, pp. 937-949
-
-
Manning, G.S.1
-
15
-
-
45849086552
-
Molecular crowding effects on structure and stability of DNA
-
Miyoshi, D. and Sugimoto, N. 2008. Molecular crowding effects on structure and stability of DNA. Biochimie 90:1040-1051.
-
(2008)
Biochimie
, vol.90
, pp. 1040-1051
-
-
Miyoshi, D.1
Sugimoto, N.2
-
16
-
-
33745374520
-
Hydration regulates thermodynamics of Gquadruplex formation under molecular crowding conditions
-
Miyoshi, D., Karimata, H., and Sugimoto, N. 2006. Hydration regulates thermodynamics of Gquadruplex formation under molecular crowding conditions. J. Am. Chem. Soc. 128:7957-7963.
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 7957-7963
-
-
Miyoshi, D.1
Karimata, H.2
Sugimoto, N.3
-
17
-
-
67749110113
-
Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions
-
Miyoshi, D., Nakamura, K., Tateishi-Karimata, H., Ohmichi, T., and Sugimoto, N. 2009. Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions. J. Am. Chem. Soc. 131:3522-3531.
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 3522-3531
-
-
Miyoshi, D.1
Nakamura, K.2
Tateishi-Karimata, H.3
Ohmichi, T.4
Sugimoto, N.5
-
18
-
-
79961123973
-
Hydration is required in DNA G-quadruplex-protein binding
-
Nagatoishi, S., Isono, N., Tsumoto, K., and Sugimoto, N. 2011. Hydration is required in DNA G-quadruplex-protein binding. Chembiochem 12:1822-1826.
-
(2011)
Chembiochem
, vol.12
, pp. 1822-1826
-
-
Nagatoishi, S.1
Isono, N.2
Tsumoto, K.3
Sugimoto, N.4
-
19
-
-
0033565267
-
Nucleic acid duplex stability: Influence of base composition on cation effects
-
Nakano, S., Fujimoto, M., Hara, H., and Sugimoto, N. 1999. Nucleic acid duplex stability: Influence of base composition on cation effects. Nucleic Acids Res. 27:2957-2965.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 2957-2965
-
-
Nakano, S.1
Fujimoto, M.2
Hara, H.3
Sugimoto, N.4
-
20
-
-
7744221005
-
The effect of molecular crowdingwith nucleotide length and cosolute structure on DNA duplex stability
-
Nakano, S., Karimata, H., Ohmichi, T., Kawakami, J., and Sugimoto, N. 2004. The effect of molecular crowdingwith nucleotide length and cosolute structure on DNA duplex stability. J. Am. Chem. Soc. 126:14330-14331.
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 14330-14331
-
-
Nakano, S.1
Karimata, H.2
Ohmichi, T.3
Kawakami, J.4
Sugimoto, N.5
-
21
-
-
38649086365
-
Capture of cationic ligands bound diffusely to base pairs during DNA refolding
-
Nakano, S., Kirihata, T., and Sugimoto, N. 2008a. Capture of cationic ligands bound diffusely to base pairs during DNA refolding. Chem. Commun. 6:700-702.
-
(2008)
Chem. Commun.
, vol.6
, pp. 700-702
-
-
Nakano, S.1
Kirihata, T.2
Sugimoto, N.3
-
22
-
-
43949109260
-
Conformation and the sodium ion condensation on DNA and RNA structures in the presence of a neutral cosolute as a mimic of the intracellular media
-
Nakano, S., Wu, L., Oka, H., Karimata, H.T., Kirihata, T., Sato, Y., Fujii, S., Sakai, H., Kuwahara, M., Sawai, H., and Sugimoto, N. 2008b. Conformation and the sodium ion condensation on DNA and RNA structures in the presence of a neutral cosolute as a mimic of the intracellular media. Mol. Biosyst. 4:579-588.
-
(2008)
Mol. Biosyst
, vol.4
, pp. 579-588
-
-
Nakano, S.1
Wu, L.2
Oka, H.3
Karimata, H.T.4
Kirihata, T.5
Sato, Y.6
Fujii, S.7
Sakai, H.8
Kuwahara, M.9
Sawai, H.10
Sugimoto, N.11
-
23
-
-
70450159038
-
Facilitation of RNA enzyme activity in the molecular crowding media of cosolutes
-
Nakano, S., Karimata-Tateishi, H., Kitagawa, Y., and Sugimoto, N. 2009. Facilitation of RNA enzyme activity in the molecular crowding media of cosolutes. J. Am. Chem. Soc. 131:16881-16888.
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 16881-16888
-
-
Nakano, S.1
Karimata-Tateishi, H.2
Kitagawa, Y.3
Sugimoto, N.4
-
24
-
-
84862702987
-
Hydration changes upon DNA folding studied by osmotic stress experiments
-
Nakano, S., Yamaguchi, D., Tateishi-Karimata, H., Miyoshi, D., and Sugimoto, N. 2012. Hydration changes upon DNA folding studied by osmotic stress experiments. Biophys. J. 102:2808-2817.
-
(2012)
Biophys. J.
, vol.102
, pp. 2808-2817
-
-
Nakano, S.1
Yamaguchi, D.2
Tateishi-Karimata, H.3
Miyoshi, D.4
Sugimoto, N.5
-
25
-
-
33747144250
-
Effect of ethylene glycol, urea, and N-methylated glycines on DNA thermal stability: The role of DNA base pair composition and hydration
-
Nordstrom, L.J., Clark, C.A., Andersen, B., Champlin, S.M., and Schwinefus, J.J. 2006. Effect of ethylene glycol, urea, and N-methylated glycines on DNA thermal stability: The role of DNA base pair composition and hydration. Biochemistry 45:9604-9614.
-
(2006)
Biochemistry
, vol.45
, pp. 9604-9614
-
-
Nordstrom, L.J.1
Clark, C.A.2
Andersen, B.3
Champlin, S.M.4
Schwinefus, J.J.5
-
26
-
-
79951889910
-
Thermodynamic stability of Hoogsteen and Watson-Crick base pairs in the presence of histone H3-mimicking peptide
-
Pramanik, S., Nakamura, K., Usui, K., Nakano, S., Saxena, S., Matsui, J., Miyoshi, D., and Sugimoto, N. 2011. Thermodynamic stability of Hoogsteen and Watson-Crick base pairs in the presence of histone H3-mimicking peptide. Chem. Commun. 47:2790-2792.
-
(2011)
Chem. Commun.
, vol.47
, pp. 2790-2792
-
-
Pramanik, S.1
Nakamura, K.2
Usui, K.3
Nakano, S.4
Saxena, S.5
Matsui, J.6
Miyoshi, D.7
Sugimoto, N.8
-
27
-
-
0035835086
-
Hydration changes for DNA intercalation reactions
-
Qu, X. and Chaires, J.B. 2001. Hydration changes for DNA intercalation reactions. J. Am. Chem. Soc. 123:1-7.
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 1-7
-
-
Qu, X.1
Chaires, J.B.2
-
28
-
-
0017820499
-
Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: The roles of ion association or release, screening, and ion effects on water activity
-
Record, M.T. Jr., Anderson, C.F., and Lohman, T.M. 1978. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: The roles of ion association or release, screening, and ion effects on water activity. Q. Rev. Biophys. 11:103-178.
-
(1978)
Q. Rev. Biophys.
, vol.11
, pp. 103-178
-
-
Record Jr., M.T.1
Anderson, C.F.2
Lohman, T.M.3
-
29
-
-
0000186216
-
Nucleic acids and polynucleotides
-
3rd ed., Vol. 1. (G.D. Fasman, ed.). CRC Press, Cleveland, Ohio.
-
Richards, E.G. 1975. Nucleic acids and polynucleotides. In Handbook of Biochemistry and Molecular Biology: Nucleic Acids, 3rd ed., Vol. 1. (G.D. Fasman, ed.) pp. 596-598. CRC Press, Cleveland, Ohio.
-
Handbook of Biochemistry and Molecular Biology: Nucleic Acids
, Issue.1975
, pp. 596-598
-
-
Richards, E.G.1
-
30
-
-
1242264497
-
Hydration of short DNA, RNA and 2'-OMe oligonucleotides determined by osmotic stressing
-
Rozners, E. and Moulder, J. 2004. Hydration of short DNA, RNA and 2'-OMe oligonucleotides determined by osmotic stressing. Nucleic Acids Res. 32:248-254.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 248-254
-
-
Rozners, E.1
Moulder, J.2
-
31
-
-
0033524401
-
Effects of hydration, ion release, and excluded volume on the melting of triplex and duplex DNA
-
Spink, C.H. and Chaires, J.B. 1999. Effects of hydration, ion release, and excluded volume on the melting of triplex and duplex DNA. Biochemistry 38:496-508.
-
(1999)
Biochemistry
, vol.38
, pp. 496-508
-
-
Spink, C.H.1
Chaires, J.B.2
-
32
-
-
33846649652
-
Enthalpies of DNA melting in the presence of osmolytes
-
Spink, C.H., Garbett, N., and Chaires, J.B. 2007 Enthalpies of DNA melting in the presence of osmolytes. Biophys. Chem. 126:176-185.
-
(2007)
Biophys. Chem.
, vol.126
, pp. 176-185
-
-
Spink, C.H.1
Garbett, N.2
Chaires, J.B.3
-
33
-
-
0023055766
-
Energetics of internal GU mismatches in ribooligonucleotide helixes
-
Sugimoto, N., Kierzek, R., Freier, S.M., and Turner, D.H. 1986. Energetics of internal GU mismatches in ribooligonucleotide helixes. Biochemistry 25:5755-5759.
-
(1986)
Biochemistry
, vol.25
, pp. 5755-5759
-
-
Sugimoto, N.1
Kierzek, R.2
Freier, S.M.3
Turner, D.H.4
-
34
-
-
84856473602
-
A-T base pairs are more stable than G-C base pairs in a hydrated ionic liquid
-
Tateishi-Karimata, H. and Sugimoto, N. 2012. A-T base pairs are more stable than G-C base pairs in a hydrated ionic liquid. Angew Chem. Int. Ed. 51:1416-1419.
-
(2012)
Angew Chem. Int. Ed.
, vol.51
, pp. 1416-1419
-
-
Tateishi-Karimata, H.1
Sugimoto, N.2
-
35
-
-
18744411284
-
The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure
-
Tobe, S., Heams, T., Vergne, J., Herve, G., andMaurel, M.C. 2005. The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure. Nucleic Acids Res. 33:2557-2564.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 2557-2564
-
-
Tobe, S.1
Heams, T.2
Vergne, J.3
Herve, G.4
Maurel, M.C.5
-
36
-
-
0032762645
-
Crowding effects on EcoRV kinetics and binding
-
Wenner, J.R. and Bloomfield, V.A. 1999. Crowding effects on EcoRV kinetics and binding. Biophys. J. 77:3234-3241.
-
(1999)
Biophys. J.
, vol.77
, pp. 3234-3241
-
-
Wenner, J.R.1
Bloomfield, V.A.2
|