-
1
-
-
78651345914
-
Assembly of complex RNAs by splinted ligation
-
Akiyama BM, Stone MD. 2009. Assembly of complex RNAs by splinted ligation. Methods Enzymol 469:27-46. doi: 10.1016/S0076-6879(09)69002-9.
-
(2009)
Methods Enzymol
, vol.469
, pp. 27-46
-
-
Akiyama, B.M.1
Stone, M.D.2
-
3
-
-
80053979296
-
MSMBuilder2: Modeling conformational dynamics on the picosecond to millisecond scale
-
Beauchamp KA, Bowman GR, Lane TJ, Maibaum L, Haque IS, Pande VS. 2011. MSMBuilder2: modeling conformational dynamics on the picosecond to millisecond scale. Journal of Chemical Theory and Computation 7:3412-3419. doi: 10.1021/ct200463m.
-
(2011)
Journal of Chemical Theory and Computation
, vol.7
, pp. 3412-3419
-
-
Beauchamp, K.A.1
Bowman, G.R.2
Lane, T.J.3
Maibaum, L.4
Haque, I.S.5
Pande, V.S.6
-
4
-
-
84925512079
-
A DNA-based molecular probe for optically reporting cellular traction forces
-
Blakely BL, Dumelin CE, Trappmann B, McGregor LM, Choi CK, Anthony PC, Duesterberg VK, Baker BM, Block SM, Liu DR, Chen CS. 2014. A DNA-based molecular probe for optically reporting cellular traction forces. Nature Methods 11:1229-1232. doi: 10.1038/nmeth.3145.
-
(2014)
Nature Methods
, vol.11
, pp. 1229-1232
-
-
Blakely, B.L.1
Dumelin, C.E.2
Trappmann, B.3
McGregor, L.M.4
Choi, C.K.5
Anthony, P.C.6
Duesterberg, V.K.7
Baker, B.M.8
Block, S.M.9
Liu, D.R.10
Chen, C.S.11
-
5
-
-
79953873168
-
Combining optical trapping, fluorescence microscopy and micro- fluidics for single molecule studies of DNA-protein interactions
-
Candelli A, Wuite GJL, Peterman EJG. 2011. Combining optical trapping, fluorescence microscopy and micro- fluidics for single molecule studies of DNA-protein interactions. Physical Chemistry Chemical Physics 13:7263-7272. doi: 10.1039/c0cp02844d.
-
(2011)
Physical Chemistry Chemical Physics
, vol.13
, pp. 7263-7272
-
-
Candelli, A.1
Wuite, G.2
Peterman, E.3
-
6
-
-
34249278470
-
Control of alternative RNA splicing and gene expression by eukaryotic riboswitches
-
Cheah MT, Wachter A, Sudarsan N, Breaker RR. 2007. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447:497-500. doi: 10.1038/nature05769.
-
(2007)
Nature
, vol.447
, pp. 497-500
-
-
Cheah, M.T.1
Wachter, A.2
Sudarsan, N.3
Breaker, R.R.4
-
7
-
-
79953292607
-
Ultrahigh-resolution optical trap with single-fluorophore sensitivity
-
Comstock MJ, Ha T, Chemla YR. 2011. Ultrahigh-resolution optical trap with single-fluorophore sensitivity. Nature Methods 8:335-340. doi: 10.1038/nmeth.1574.
-
(2011)
Nature Methods
, vol.8
, pp. 335-340
-
-
Comstock, M.J.1
Ha, T.2
Chemla, Y.R.3
-
8
-
-
84927716904
-
Direct observation of structure-function relationship in a nucleic acid-processing enzyme
-
Comstock MJ, Whitley KD, Jia H, Sokoloski J, Lohman TM, Ha T, Chemla YR. 2015. Direct observation of structure-function relationship in a nucleic acid-processing enzyme. Science 348:352-354. doi: 10.1126/science.aaa0130.
-
(2015)
Science
, vol.348
, pp. 352-354
-
-
Comstock, M.J.1
Whitley, K.D.2
Jia, H.3
Sokoloski, J.4
Lohman, T.M.5
Ha, T.6
Chemla, Y.R.7
-
9
-
-
79952941746
-
Mechanisms and advancement of antifading agents for fluorescence microscopy and single-molecule spectroscopy
-
Cordes T, Maiser A, Steinhauer C, Schermelleh L, Tinnefeld P. 2011. Mechanisms and advancement of antifading agents for fluorescence microscopy and single-molecule spectroscopy. Physical Chemistry Chemical Physics 13: 6699-6709. doi: 10.1039/c0cp01919d.
-
(2011)
Physical Chemistry Chemical Physics
, vol.13
, pp. 6699-6709
-
-
Cordes, T.1
Maiser, A.2
Steinhauer, C.3
Schermelleh, L.4
Tinnefeld, P.5
-
11
-
-
77956642214
-
The effect of dye-dye interactions on the spatial resolution of single-molecule FRET measurements in nucleic acids
-
Di Fiori N, Meller A. 2010. The effect of dye-dye interactions on the spatial resolution of single-molecule FRET measurements in nucleic acids. Biophysical Journal 98:2265-2272. doi: 10.1016/j.bpj.2010.02.008.
-
(2010)
Biophysical Journal
, vol.98
, pp. 2265-2272
-
-
Di Fiori, N.1
Meller, A.2
-
12
-
-
33748300801
-
Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition
-
Edwards TE, Ferré-D’Amaré AR. 2006. Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. Structure 14:1459-1468. doi: 10.1016/j.str.2006.07.008.
-
(2006)
Structure
, vol.14
, pp. 1459-1468
-
-
Edwards, T.E.1
Ferré-D’amaré, A.R.2
-
13
-
-
38849204944
-
Direct observation of hierarchical folding in single riboswitch aptamers
-
Greenleaf WJ, Frieda KL, Foster DAN, Woodside MT, Block SM. 2008. Direct observation of hierarchical folding in single riboswitch aptamers. Science 319:630-633. doi: 10.1126/science.1151298.
-
(2008)
Science
, vol.319
, pp. 630-633
-
-
Greenleaf, W.J.1
Frieda, K.L.2
Foster, D.3
Woodside, M.T.4
Block, S.M.5
-
14
-
-
84875043544
-
Folding and ligand recognition of the TPP riboswitch aptamer at single-molecule resolution
-
Haller A, Altman RB, Souliere MF, Blanchard SC, Micura R. 2013. Folding and ligand recognition of the TPP riboswitch aptamer at single-molecule resolution. Proceedings of the National Academy of Sciences of the United States of America 110:4188-4193. doi: 10.1073/pnas.1218062110.
-
(2013)
Proceedings of the National Academy of Sciences of the United States of America
, vol.110
, pp. 4188-4193
-
-
Haller, A.1
Altman, R.B.2
Souliere, M.F.3
Blanchard, S.C.4
Micura, R.5
-
15
-
-
0033021362
-
Single-molecule imaging of RNA polymerase-DNA interactions in real time
-
Harada Y, Funatsu T, Murakami K, Nonoyama Y, Ishihama A, Yanagida T. 1999. Single-molecule imaging of RNA polymerase-DNA interactions in real time. Biophysical Journal 76:709-715. doi: 10.1016/S0006-3495(99)77237-1.
-
(1999)
Biophysical Journal
, vol.76
, pp. 709-715
-
-
Harada, Y.1
Funatsu, T.2
Murakami, K.3
Nonoyama, Y.4
Ishihama, A.5
Yanagida, T.6
-
16
-
-
0036188531
-
Stains, labels and detection strategies for nucleic acids assays
-
Kricka LJ. 2002. Stains, labels and detection strategies for nucleic acids assays. Annals of Clinical Biochemistry 39:114-129. doi: 10.1258/0004563021901865.
-
(2002)
Annals of Clinical Biochemistry
, vol.39
, pp. 114-129
-
-
Kricka, L.J.1
-
17
-
-
0036284131
-
An automated two-dimensional optical force clamp for single molecule studies
-
Lang MJ, Asbury CL, Shaevitz JW, Block SM. 2002. An automated two-dimensional optical force clamp for single molecule studies. Biophysical Journal 83:491-501. doi: 10.1016/S0006-3495(02)75185-0.
-
(2002)
Biophysical Journal
, vol.83
, pp. 491-501
-
-
Lang, M.J.1
Asbury, C.L.2
Shaevitz, J.W.3
Block, S.M.4
-
18
-
-
17444366080
-
Simultaneous, coincident optical trapping and single-molecule fluorescence
-
Lang MJ, Fordyce PM, Engh AM, Neuman KC, Block SM. 2004. Simultaneous, coincident optical trapping and single-molecule fluorescence. Nature Methods 1:133-139. doi: 10.1038/nmeth714.
-
(2004)
Nature Methods
, vol.1
, pp. 133-139
-
-
Lang, M.J.1
Fordyce, P.M.2
Engh, A.M.3
Neuman, K.C.4
Block, S.M.5
-
19
-
-
33646131832
-
Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods
-
Li PTX, Collin D, Smith SB, Bustamante C, Tinoco I. 2006. Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods. Biophysical Journal 90:250-260. doi: 10.1529/biophysj.105.068049.
-
(2006)
Biophysical Journal
, vol.90
, pp. 250-260
-
-
Li, P.1
Collin, D.2
Smith, S.B.3
Bustamante, C.4
Tinoco, I.5
-
20
-
-
0035957720
-
Reversible unfolding of single RNA molecules by mechanical force
-
Liphardt J, Onoa B, Smith SB, Tinoco I, Bustamante C. 2001. Reversible unfolding of single RNA molecules by mechanical force. Science 292:733-737. doi: 10.1126/science.1058498.
-
(2001)
Science
, vol.292
, pp. 733-737
-
-
Liphardt, J.1
Onoa, B.2
Smith, S.B.3
Tinoco, I.4
Bustamante, C.5
-
21
-
-
33749522198
-
Dissecting elastic heterogeneity along DNA molecules coated partly with Rad51 using concurrent fluorescence microscopy and optical tweezers
-
Mameren J, Modesti M, Kanaar R, Wyman C, Wuite GJ, Peterman EJ. 2006. Dissecting elastic heterogeneity along DNA molecules coated partly with Rad51 using concurrent fluorescence microscopy and optical tweezers. Biophysical Journal 91:L78-L80. doi: 10.1529/biophysj.106.089466.
-
(2006)
Biophysical Journal
, vol.91
-
-
Mameren, J.1
Modesti, M.2
Kanaar, R.3
Wyman, C.4
Wuite, G.J.5
Peterman, E.J.6
-
22
-
-
77955700423
-
Optimizing methods to recover absolute FRET efficiency from immobilized single molecules
-
McCann JJ, Choi UB, Zheng L, Weninger K, Bowen ME. 2010. Optimizing methods to recover absolute FRET efficiency from immobilized single molecules. Biophysical Journal 99:961-970. doi: 10.1016/j.bpj.2010.04.063.
-
(2010)
Biophysical Journal
, vol.99
, pp. 961-970
-
-
McCann, J.J.1
Choi, U.B.2
Zheng, L.3
Weninger, K.4
Bowen, M.E.5
-
23
-
-
84924589156
-
Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility
-
Ngo TTM, Zhang Q, Zhou R, Yodh JG, Ha T. 2015. Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility. Cell 160:1135-1144. doi: 10.1016/j.cell.2015.02.001.
-
(2015)
Cell
, vol.160
, pp. 1135-1144
-
-
Ngo, T.1
Zhang, Q.2
Zhou, R.3
Yodh, J.G.4
Ha, T.5
-
24
-
-
33748551022
-
Phosphate-group recognition by the aptamer domain of the thiamine pyrophosphate sensing riboswitch
-
Noeske J, Richter C, Stirnal E, Schwalbe H, Wo¨ hnert J. 2006. Phosphate-group recognition by the aptamer domain of the thiamine pyrophosphate sensing riboswitch. ChemBioChem 7:1451-1456. doi: 10.1002/cbic.200600151.
-
(2006)
Chembiochem
, vol.7
, pp. 1451-1456
-
-
Noeske, J.1
Richter, C.2
Stirnal, E.3
Schwalbe, H.4
Hnert, W.5
-
25
-
-
67650713931
-
The structural and functional diversity of metabolite-binding riboswitches
-
Roth A, Breaker RR. 2009. The structural and functional diversity of metabolite-binding riboswitches. Annual Review of Biochemistry 78:305-334. doi: 10.1146/annurev.biochem.78.070507.135656.
-
(2009)
Annual Review of Biochemistry
, vol.78
, pp. 305-334
-
-
Roth, A.1
Breaker, R.R.2
-
26
-
-
84872543206
-
A decade of riboswitches
-
Serganov A, Nudler E. 2013. A decade of riboswitches. Cell 152:17-24. doi: 10.1016/j.cell.2012.12.024.
-
(2013)
Cell
, vol.152
, pp. 17-24
-
-
Serganov, A.1
Nudler, E.2
-
27
-
-
84861405805
-
Metabolite recognition principles and molecular mechanisms underlying riboswitch function
-
Serganov A, Patel DJ. 2012. Metabolite recognition principles and molecular mechanisms underlying riboswitch function. Annual Review of Biophysics 41:343-370. doi: 10.1146/annurev-biophys-101211-113224.
-
(2012)
Annual Review of Biophysics
, vol.41
, pp. 343-370
-
-
Serganov, A.1
Patel, D.J.2
-
28
-
-
33745635350
-
Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch
-
Serganov A, Polonskaia A, Phan AT, Breaker RR, Patel DJ. 2006. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature 441:1167-1171. doi: 10.1038/nature04740.
-
(2006)
Nature
, vol.441
, pp. 1167-1171
-
-
Serganov, A.1
Polonskaia, A.2
Phan, A.T.3
Breaker, R.R.4
Patel, D.J.5
-
29
-
-
84867012109
-
Combined versatile high-resolution optical tweezers and single- molecule fluorescence microscopy
-
Sirinakis G, Ren Y, Gao Y, Xi Z, Zhang Y. 2012. Combined versatile high-resolution optical tweezers and single- molecule fluorescence microscopy. Review of Scientific Instruments 83:093708. doi: 10.1063/1.4752190.
-
(2012)
Review of Scientific Instruments
, vol.83
, pp. 093708
-
-
Sirinakis, G.1
Ren, Y.2
Gao, Y.3
Xi, Z.4
Zhang, Y.5
-
30
-
-
78650006466
-
Methods of site-specific labeling of RNA with fluorescent dyes
-
Solomatin S, Herschlag D. 2009. Methods of site-specific labeling of RNA with fluorescent dyes. Methods Enzymol 469:47-68. doi: 10.1016/S0076-6879(09)69003-0.
-
(2009)
Methods Enzymol
, vol.469
, pp. 47-68
-
-
Solomatin, S.1
Herschlag, D.2
-
31
-
-
0038136962
-
Metabolite-binding RNA domains are present in the genes of eukaryotes
-
Sudarsan N, Barrick JE, Breaker RR. 2003. Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA 9:644-647. doi: 10.1261/rna.5090103.
-
(2003)
RNA
, vol.9
, pp. 644-647
-
-
Sudarsan, N.1
Barrick, J.E.2
Breaker, R.R.3
-
32
-
-
84943742317
-
Structural dynamics of e. Coli single- stranded DNA binding protein reveal DNA wrapping and unwrapping pathways
-
Suksombat S, Khafizov R, Kozlov AG, Lohman TM, Chemla YR. 2015. Structural dynamics of e. coli single- stranded DNA binding protein reveal DNA wrapping and unwrapping pathways. eLife 4. doi: 10.7554/eLife.08193.
-
(2015)
Elife
, vol.4
-
-
Suksombat, S.1
Khafizov, R.2
Kozlov, A.G.3
Lohman, T.M.4
Chemla, Y.R.5
-
33
-
-
33744469562
-
Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand
-
Thore S, Leibundgut M, Ban N. 2006. Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science 312:1208-1211. doi: 10.1126/science.1128451.
-
(2006)
Science
, vol.312
, pp. 1208-1211
-
-
Thore, S.1
Leibundgut, M.2
Ban, N.3
-
34
-
-
79953853888
-
Identifying molecular dynamics in single- molecule FRET experiments with burst variance analysis
-
Torella JP, Holden SJ, Santoso Y, Hohlbein J, Kapanidis AN. 2011. Identifying molecular dynamics in single- molecule FRET experiments with burst variance analysis. Biophysical Journal 100:1568-1577. doi: 10.1016/j.bpj.2011.01.066.
-
(2011)
Biophysical Journal
, vol.100
, pp. 1568-1577
-
-
Torella, J.P.1
Holden, S.J.2
Santoso, Y.3
Hohlbein, J.4
Kapanidis, A.N.5
-
35
-
-
59649116344
-
Counting RAD51 proteins disassembling from nucleoprotein filaments under tension
-
van Mameren J, Modesti M, Kanaar R, Wyman C, Peterman EJG, Wuite GJL. 2009. Counting RAD51 proteins disassembling from nucleoprotein filaments under tension. Nature 457:745-748. doi: 10.1038/nature07581.
-
(2009)
Nature
, vol.457
, pp. 745-748
-
-
Van Mameren, J.1
Modesti, M.2
Kanaar, R.3
Wyman, C.4
Peterman, E.5
Wuite, G.6
-
36
-
-
48349090299
-
See me, feel me: Methods to concurrently visualize and manipulate single DNA molecules and associated proteins
-
van Mameren J, Peterman EJG, Wuite GJL. 2008. See me, feel me: methods to concurrently visualize and manipulate single DNA molecules and associated proteins. Nucleic Acids Research 36:4381-4389. doi: 10.1093/nar/gkn412.
-
(2008)
Nucleic Acids Research
, vol.36
, pp. 4381-4389
-
-
Van Mameren, J.1
Peterman, E.2
Wuite, G.3
-
37
-
-
37849045636
-
Riboswitch control of gene expression in plants by splicing and alternative 3’ end processing of mRNAs
-
Wachter A, Tunc-Ozdemir M, Grove BC, Green PJ, Shintani DK, Breaker RR. 2007. Riboswitch control of gene expression in plants by splicing and alternative 3’ end processing of mRNAs. The Plant Cell Online 19:3437-3450. doi: 10.1105/tpc.107.053645.
-
(2007)
The Plant Cell Online
, vol.19
, pp. 3437-3450
-
-
Wachter, A.1
Tunc-Ozdemir, M.2
Grove, B.C.3
Green, P.J.4
Shintani, D.K.5
Breaker, R.R.6
-
38
-
-
0037206833
-
Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression
-
Winkler W, Nahvi A, Breaker RR. 2002. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419:952-956. doi: 10.1038/nature01145.
-
(2002)
Nature
, vol.419
, pp. 952-956
-
-
Winkler, W.1
Nahvi, A.2
Breaker, R.R.3
-
39
-
-
33646587736
-
Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins
-
Woodside MT, Behnke-Parks WM, Larizadeh K, Travers K, Herschlag D, Block SM. 2006. Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins. Proceedings of the National Academy of Sciences of the United States of America 103:6190-6195. doi: 10.1073/pnas.0511048103.
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, pp. 6190-6195
-
-
Woodside, M.T.1
Behnke-Parks, W.M.2
Larizadeh, K.3
Travers, K.4
Herschlag, D.5
Block, S.M.6
|