-
4
-
-
0346037281
-
Differential helix stabilities and sites pre-organized for tertiary interactions revealed by monitoring local nucleotide flexibility in the bI5 group I intron RNA
-
Chamberlin S., and Weeks K. Differential helix stabilities and sites pre-organized for tertiary interactions revealed by monitoring local nucleotide flexibility in the bI5 group I intron RNA. Biochemistry 42 (2003) 901-909
-
(2003)
Biochemistry
, vol.42
, pp. 901-909
-
-
Chamberlin, S.1
Weeks, K.2
-
5
-
-
0037452797
-
Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme
-
Rangan P., Masquida B., Westhof E., and Woodson S. Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme. Proc. Natl Acad. Sci. USA 100 (2003) 1574-1579
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 1574-1579
-
-
Rangan, P.1
Masquida, B.2
Westhof, E.3
Woodson, S.4
-
7
-
-
0344844493
-
Near native structure in an RNA collapsed state
-
Buchmueller K.L., and Weeks K.M. Near native structure in an RNA collapsed state. Biochemistry 42 (2003) 13869-13878
-
(2003)
Biochemistry
, vol.42
, pp. 13869-13878
-
-
Buchmueller, K.L.1
Weeks, K.M.2
-
9
-
-
0034100560
-
Small angle X-ray scattering reveals a compact intermediate in RNA folding
-
Russell R., Millett I.S., Doniach S., and Herschlag D. Small angle X-ray scattering reveals a compact intermediate in RNA folding. Nature Struct. Biol. 7 (2000) 367-370
-
(2000)
Nature Struct. Biol.
, vol.7
, pp. 367-370
-
-
Russell, R.1
Millett, I.S.2
Doniach, S.3
Herschlag, D.4
-
10
-
-
0037007009
-
Rapid compaction during RNA folding
-
Russell R., Millett I.S., Tate M.W., Kwok L.W., Nakatani B., Gruner S.M., et al. Rapid compaction during RNA folding. Proc. Natl Acad. Sci. USA 99 (2002) 4266-4271
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 4266-4271
-
-
Russell, R.1
Millett, I.S.2
Tate, M.W.3
Kwok, L.W.4
Nakatani, B.5
Gruner, S.M.6
-
11
-
-
0037039464
-
Exploring the folding landscape of a structured RNA
-
Russell R., Zhuang X., Babcock H.P., Millett I.S., Doniach S., Chu S., and Herschlag D. Exploring the folding landscape of a structured RNA. Proc. Natl Acad. Sci. USA 99 (2002) 155-160
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 155-160
-
-
Russell, R.1
Zhuang, X.2
Babcock, H.P.3
Millett, I.S.4
Doniach, S.5
Chu, S.6
Herschlag, D.7
-
12
-
-
0033605081
-
Pathway modulation, circular permutation and rapid rna folding under kinetic control
-
Pan T., Fang X.-W., and Sosnick T. Pathway modulation, circular permutation and rapid rna folding under kinetic control. J. Mol. Biol. 286 (1999) 721-731
-
(1999)
J. Mol. Biol.
, vol.286
, pp. 721-731
-
-
Pan, T.1
Fang, X.-W.2
Sosnick, T.3
-
13
-
-
29244449617
-
An obligate intermediate along the slow folding pathway of a group II intron ribozyme
-
Su L.J., Waldsich C., and Pyle A.M. An obligate intermediate along the slow folding pathway of a group II intron ribozyme. Nucleic Acids Res. 33 (2005) 6674-6687
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 6674-6687
-
-
Su, L.J.1
Waldsich, C.2
Pyle, A.M.3
-
14
-
-
0043009768
-
A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate
-
Tan E., Wilson T.J., Nahas M.K., Clegg R.M., Lilley D.M.J., and Ha T. A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate. Proc. Natl Acad. Sci. USA 100 (2003) 9308-9313
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 9308-9313
-
-
Tan, E.1
Wilson, T.J.2
Nahas, M.K.3
Clegg, R.M.4
Lilley, D.M.J.5
Ha, T.6
-
15
-
-
7544225920
-
Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic
-
Okumus B., Wilson T.J., Lilley D.M.J., and Ha T. Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic. Biophys. J. 87 (2004) 2798-2806
-
(2004)
Biophys. J.
, vol.87
, pp. 2798-2806
-
-
Okumus, B.1
Wilson, T.J.2
Lilley, D.M.J.3
Ha, T.4
-
16
-
-
23044431628
-
Docking kinetics and equilibrium of a GAAA tetraloop-receptor motif probed by single-molecule FRET
-
Hodak J.H., Downey C.D., Fiore J.L., Pardi A., and Nesbitt D.J. Docking kinetics and equilibrium of a GAAA tetraloop-receptor motif probed by single-molecule FRET. Proc. Natl Acad. Sci. USA 102 (2005) 10505-10510
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 10505-10510
-
-
Hodak, J.H.1
Downey, C.D.2
Fiore, J.L.3
Pardi, A.4
Nesbitt, D.J.5
-
17
-
-
0037165996
-
Correlating structural dynamics and function in single ribozyme molecules
-
Zhuang X., Kim H., Pereira M.J.B., Babcock H.P., Walter N.G., and Chu S. Correlating structural dynamics and function in single ribozyme molecules. Science 296 (2002) 1473-1476
-
(2002)
Science
, vol.296
, pp. 1473-1476
-
-
Zhuang, X.1
Kim, H.2
Pereira, M.J.B.3
Babcock, H.P.4
Walter, N.G.5
Chu, S.6
-
18
-
-
0042925420
-
Single-molecule transition-state analysis of RNA folding
-
Bokinsky G., Rueda D., Misra V.K., Rhodes M.M., Gordus A., Babcock H.P., et al. Single-molecule transition-state analysis of RNA folding. Proc. Natl Acad. Sci. USA 100 (2003) 9302-9307
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 9302-9307
-
-
Bokinsky, G.1
Rueda, D.2
Misra, V.K.3
Rhodes, M.M.4
Gordus, A.5
Babcock, H.P.6
-
19
-
-
3042709638
-
Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance
-
Rueda D., Bokinsky G., Rhodes M.M., Rust M.J., Zhuang X., and Walter N. Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance. Proc. Natl Acad. Sci. USA 101 (2004) 10066-10071
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 10066-10071
-
-
Rueda, D.1
Bokinsky, G.2
Rhodes, M.M.3
Rust, M.J.4
Zhuang, X.5
Walter, N.6
-
20
-
-
0242500997
-
Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA
-
Bartley L.E., Zhuang X., Das R., Chu S., and Herschlag D. Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA. J. Mol. Biol. 328 (2003) 1011-1026
-
(2003)
J. Mol. Biol.
, vol.328
, pp. 1011-1026
-
-
Bartley, L.E.1
Zhuang, X.2
Das, R.3
Chu, S.4
Herschlag, D.5
-
21
-
-
23744470902
-
Single-molecule RNA folding
-
Bokinsky G., and Zhuang X. Single-molecule RNA folding. Accts Chem. Res. 38 (2005) 566-573
-
(2005)
Accts Chem. Res.
, vol.38
, pp. 566-573
-
-
Bokinsky, G.1
Zhuang, X.2
-
22
-
-
0033529972
-
Ligand-induced conformational changes observed in single RNA molecules
-
Ha T., Zhuang X., Kim H., Orr J.W., Williamson J.R., and Chu S. Ligand-induced conformational changes observed in single RNA molecules. Proc. Natl Acad. Sci. USA 96 (1999) 9077-9082
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, pp. 9077-9082
-
-
Ha, T.1
Zhuang, X.2
Kim, H.3
Orr, J.W.4
Williamson, J.R.5
Chu, S.6
-
25
-
-
17644373802
-
Observing spontaneous branch migration of Holliday junctions one step at a time
-
McKinney S.A., Freeman A.D., Lilley D.M., and Ha T. Observing spontaneous branch migration of Holliday junctions one step at a time. Proc. Natl Acad. Sci. USA 102 (2005) 5715-5720
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 5715-5720
-
-
McKinney, S.A.1
Freeman, A.D.2
Lilley, D.M.3
Ha, T.4
-
26
-
-
30044448463
-
Extreme conformational diversity in human telomeric DNA
-
Lee J.Y., Okumus B., Kim D.D., and Ha T. Extreme conformational diversity in human telomeric DNA. Proc. Natl Acad. Sci. USA 102 (2005) 18938-18943
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 18938-18943
-
-
Lee, J.Y.1
Okumus, B.2
Kim, D.D.3
Ha, T.4
-
27
-
-
0347004715
-
Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme
-
Xie Z., Srividya N., Sosnick T.R., Pan T., and Scherer N.F. Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme. Proc. Natl Acad. Sci. USA 101 (2004) 534-539
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 534-539
-
-
Xie, Z.1
Srividya, N.2
Sosnick, T.R.3
Pan, T.4
Scherer, N.F.5
-
28
-
-
0035836722
-
The thermodynamic origin of the stability of a thermophilic ribozyme
-
Fang X.-W., Golden B.L., Littrell K., Shelton V., Thiyagarajan P., Pan T., and Sosnick T.R. The thermodynamic origin of the stability of a thermophilic ribozyme. Proc. Natl Acad. Sci. USA 98 (2001) 4355-4360
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 4355-4360
-
-
Fang, X.-W.1
Golden, B.L.2
Littrell, K.3
Shelton, V.4
Thiyagarajan, P.5
Pan, T.6
Sosnick, T.R.7
-
29
-
-
0032590020
-
2+-dependent folding of a large ribozyme without kinetic traps
-
2+-dependent folding of a large ribozyme without kinetic traps. Nauret Struct. Biol. 6 (1999) 1091-1095
-
(1999)
Nauret Struct. Biol.
, vol.6
, pp. 1091-1095
-
-
Fang, X.-W.1
Pan, T.2
Sosnick, T.3
-
30
-
-
0037173087
-
The rate-limiting step in the folding of a large ribozyme without kinetic traps
-
Fang X.-W., Thiyagarajan P., Sosnick T.R., and Pan T. The rate-limiting step in the folding of a large ribozyme without kinetic traps. Proc. Natl Acad. Sci. USA 99 (2002) 8518-8523
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 8518-8523
-
-
Fang, X.-W.1
Thiyagarajan, P.2
Sosnick, T.R.3
Pan, T.4
-
31
-
-
12844274892
-
Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization
-
Smith G.J., Sosnick T.R., Scherer N.F., and Pan T. Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization. RNA 11 (2005) 234-239
-
(2005)
RNA
, vol.11
, pp. 234-239
-
-
Smith, G.J.1
Sosnick, T.R.2
Scherer, N.F.3
Pan, T.4
-
32
-
-
26444490660
-
Crystal structure of a bacterial ribonuclease P RNA
-
Kazantsev A., Krivenko A., Harrington D., Holbrook S., Adams P., and Pace N. Crystal structure of a bacterial ribonuclease P RNA. Proc. Natl Acad. Sci. USA 102 (2005) 13392-13397
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 13392-13397
-
-
Kazantsev, A.1
Krivenko, A.2
Harrington, D.3
Holbrook, S.4
Adams, P.5
Pace, N.6
-
33
-
-
44349144363
-
-
2+-concentration jump experiments reveal details of the early folding pathways of a large RNA. Proc. Natl Acad. Sci. USA, In press, doi:10.1073/PNAS.0801436105.
-
2+-concentration jump experiments reveal details of the early folding pathways of a large RNA. Proc. Natl Acad. Sci. USA, In press, doi:10.1073/PNAS.0801436105.
-
-
-
-
34
-
-
0020490146
-
On the stochastic properties of bursts of single ion channel openings and of clusters of bursts
-
Colquhoun D., and Hawkes A.G. On the stochastic properties of bursts of single ion channel openings and of clusters of bursts. Philos. Trans. R. Soc. Ser. B 300 (1982) 1-59
-
(1982)
Philos. Trans. R. Soc. Ser. B
, vol.300
, pp. 1-59
-
-
Colquhoun, D.1
Hawkes, A.G.2
-
36
-
-
0035913536
-
Two-event echos in single-molecule kinetics: a signature of conformational fluctuations
-
Yang S., and Cao J. Two-event echos in single-molecule kinetics: a signature of conformational fluctuations. J. Phys. Chem. B 105 (2001) 6536-6549
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 6536-6549
-
-
Yang, S.1
Cao, J.2
-
37
-
-
7044253170
-
Single molecule kinetics. I. Theoretical analysis of indicators
-
Witkoskie J., and Cao J. Single molecule kinetics. I. Theoretical analysis of indicators. J. Chem. Phys. 121 (2004) 6373-6379
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 6373-6379
-
-
Witkoskie, J.1
Cao, J.2
-
38
-
-
0028913136
-
Fluorescence Resonance Energy Transfer
-
Selvin P. Fluorescence Resonance Energy Transfer. Methods Enzymol. 246 (1995) 300-334
-
(1995)
Methods Enzymol.
, vol.246
, pp. 300-334
-
-
Selvin, P.1
-
39
-
-
41949142023
-
-
Callen, H. B. (1985). A Polymer Model: The Rubber Band Revisited. In Thermodynamics; an Introduction to the Physical Theories of Equilibrium Thermostatics and Irreversible Thermodynamics, 2nd edit., pp. 339-342. John Wiley and Sons, Inc., New York.
-
Callen, H. B. (1985). A Polymer Model: The Rubber Band Revisited. In Thermodynamics; an Introduction to the Physical Theories of Equilibrium Thermostatics and Irreversible Thermodynamics, 2nd edit., pp. 339-342. John Wiley and Sons, Inc., New York.
-
-
-
-
40
-
-
1942423138
-
Probing Single-stranded DNA conformational flexibility using fluorescence spectroscopy
-
Murphy M.C., Rasnik I., Cheng W., Lohman T.M., and Ha T. Probing Single-stranded DNA conformational flexibility using fluorescence spectroscopy. Biophys. J. 86 (2004) 2530-2537
-
(2004)
Biophys. J.
, vol.86
, pp. 2530-2537
-
-
Murphy, M.C.1
Rasnik, I.2
Cheng, W.3
Lohman, T.M.4
Ha, T.5
-
41
-
-
0026495432
-
Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads
-
Smith S.B., Finzi L., and Bustamante C. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258 (1992) 1122-1126
-
(1992)
Science
, vol.258
, pp. 1122-1126
-
-
Smith, S.B.1
Finzi, L.2
Bustamante, C.3
-
42
-
-
0034045782
-
Application of circular dichroism to study RNA folding transitions
-
Sosnick T.R., Fang X.W., and Shelton V.M. Application of circular dichroism to study RNA folding transitions. Methods Enzymol. 317 (2000) 393-409
-
(2000)
Methods Enzymol.
, vol.317
, pp. 393-409
-
-
Sosnick, T.R.1
Fang, X.W.2
Shelton, V.M.3
-
43
-
-
0033065083
-
Magnesium-dependent folding of self-splicing RNA: Exploring the link between cooperativity, thermodynamics, and kinetics
-
Pan J., Thirumalai D., and Woodson S.A. Magnesium-dependent folding of self-splicing RNA: Exploring the link between cooperativity, thermodynamics, and kinetics. Proc. Natl Acad. Sci. USA 96 (1999) 6149-6154
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, pp. 6149-6154
-
-
Pan, J.1
Thirumalai, D.2
Woodson, S.A.3
-
46
-
-
0036440985
-
Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding
-
Krantz B.A., Mayne L., Rumbley J., Englander S.W., and Sosnick T.R. Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding. J. Mol. Biol. 324 (2002) 359-371
-
(2002)
J. Mol. Biol.
, vol.324
, pp. 359-371
-
-
Krantz, B.A.1
Mayne, L.2
Rumbley, J.3
Englander, S.W.4
Sosnick, T.R.5
-
47
-
-
13744257300
-
Site-specific labeling of the ribosome for single-molecule spectroscopy
-
Dorywalska M., Blanchard S.C., Gonzalez Jr. R.L., Kim H.D., Chu S., and Puglisi J.D. Site-specific labeling of the ribosome for single-molecule spectroscopy. Nucleic Acids Res. 33 (2005) 182-189
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 182-189
-
-
Dorywalska, M.1
Blanchard, S.C.2
Gonzalez Jr., R.L.3
Kim, H.D.4
Chu, S.5
Puglisi, J.D.6
-
49
-
-
0742324525
-
DNA-binding orientation and domain conformation of the E. coli Rep helicase monomer bound to a partial duplex junction: single-molecule studies of fluorescently labeled enzymes
-
Rasnik I., Myong S., Cheng W., Lohman T.M., and Ha T. DNA-binding orientation and domain conformation of the E. coli Rep helicase monomer bound to a partial duplex junction: single-molecule studies of fluorescently labeled enzymes. J. Mol. Biol. 336 (2004) 395-408
-
(2004)
J. Mol. Biol.
, vol.336
, pp. 395-408
-
-
Rasnik, I.1
Myong, S.2
Cheng, W.3
Lohman, T.M.4
Ha, T.5
-
50
-
-
30344473311
-
Organized arrays of individual DNA molecules tethered to supported lipid bilayers
-
Graneli A., Yeykal C., Prasad T.K., and Greene E.C. Organized arrays of individual DNA molecules tethered to supported lipid bilayers. Langmuir 22 (2006) 292-299
-
(2006)
Langmuir
, vol.22
, pp. 292-299
-
-
Graneli, A.1
Yeykal, C.2
Prasad, T.K.3
Greene, E.C.4
-
51
-
-
0034807927
-
Single molecule fluorescence resonance transfer
-
Ha T. Single molecule fluorescence resonance transfer. Methods 25 (2001) 78-86
-
(2001)
Methods
, vol.25
, pp. 78-86
-
-
Ha, T.1
-
52
-
-
3843104585
-
Nanometer-localized multiple single-molecule fluorescence microscopy
-
Qu X.W., Wu D., Mets L., and Scherer N.F. Nanometer-localized multiple single-molecule fluorescence microscopy. Proc. Natl Acad. Sci. USA 101 (2004) 11298-11303
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 11298-11303
-
-
Qu, X.W.1
Wu, D.2
Mets, L.3
Scherer, N.F.4
-
53
-
-
8644274165
-
Noise reduction in single-molecule fluorescence trajectories of folding proteins
-
Haran G. Noise reduction in single-molecule fluorescence trajectories of folding proteins. Chem. Phys. 307 (2004) 137-145
-
(2004)
Chem. Phys.
, vol.307
, pp. 137-145
-
-
Haran, G.1
-
54
-
-
33847085308
-
Variational transition state theory
-
Truhlar D., and Garrett B. Variational transition state theory. Accts Chem. Res. 13 (1980) 440-448
-
(1980)
Accts Chem. Res.
, vol.13
, pp. 440-448
-
-
Truhlar, D.1
Garrett, B.2
|