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For: Hochstrasser RA, Chen SM, Millar DP. Distance distribution in a dye-linked oligonucleotide determined by time-resolved fluorescence energy transfer. Biophys Chem 1992;45:133-41. [PMID: 1286148 DOI: 10.1016/0301-4622(92)87005-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Number Cited by Other Article(s)
1
Zagotta WN, Evans EGB, Eggan P, Tessmer MH, Shaffer KD, Petersson EJ, Stoll S, Gordon SE. Measuring conformational equilibria in allosteric proteins with time-resolved tmFRET. Biophys J 2024;123:2050-2062. [PMID: 38303511 PMCID: PMC11309986 DOI: 10.1016/j.bpj.2024.01.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]  Open
2
Zagotta WN, Evans EGB, Eggan P, Tessmer MH, Shaffer KD, Petersson EJ, Stoll S, Gordon SE. Measuring conformational equilibria in allosteric proteins with time-resolved tmFRET. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.09.561594. [PMID: 37873384 PMCID: PMC10592786 DOI: 10.1101/2023.10.09.561594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
3
Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CAM, Weiss S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife 2021;10:e60416. [PMID: 33779550 PMCID: PMC8007216 DOI: 10.7554/elife.60416] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022]  Open
4
Arjmand F, Afsan Z, Sharma S, Parveen S, Yousuf I, Sartaj S, Siddique HR, Tabassum S. Recent advances in metallodrug-like molecules targeting non-coding RNAs in cancer chemotherapy. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.02.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
5
Shi X, Walker P, Harbury PB, Herschlag D. Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry. Nucleic Acids Res 2017;45:e64. [PMID: 28108663 PMCID: PMC5416899 DOI: 10.1093/nar/gkw1352] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 01/05/2017] [Indexed: 12/03/2022]  Open
6
Peulen TO, Opanasyuk O, Seidel CAM. Combining Graphical and Analytical Methods with Molecular Simulations To Analyze Time-Resolved FRET Measurements of Labeled Macromolecules Accurately. J Phys Chem B 2017;121:8211-8241. [PMID: 28709377 PMCID: PMC5592652 DOI: 10.1021/acs.jpcb.7b03441] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
7
Aissaoui N, Moth-Poulsen K, Käll M, Johansson P, Wilhelmsson LM, Albinsson B. FRET enhancement close to gold nanoparticles positioned in DNA origami constructs. NANOSCALE 2017;9:673-683. [PMID: 27942672 DOI: 10.1039/c6nr04852h] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
8
Toptygin D, Chin AF, Hilser VJ. Effect of Diffusion on Resonance Energy Transfer Rate Distributions: Implications for Distance Measurements. J Phys Chem B 2015;119:12603-22. [PMID: 26358033 DOI: 10.1021/acs.jpcb.5b06567] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
9
From a structural average to the conformational ensemble of a DNA bulge. Proc Natl Acad Sci U S A 2014;111:E1473-80. [PMID: 24706812 DOI: 10.1073/pnas.1317032111] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
10
RUEDAS-RAMA MJ, ALVAREZ-PEZ JM, ORTE A. SOLVING SINGLE BIOMOLECULES BY ADVANCED FRET-BASED SINGLE-MOLECULE FLUORESCENCE TECHNIQUES. ACTA ACUST UNITED AC 2014. [DOI: 10.1142/s1793048013300041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
11
Preus S, Wilhelmsson LM. Advances in quantitative FRET-based methods for studying nucleic acids. Chembiochem 2012;13:1990-2001. [PMID: 22936620 DOI: 10.1002/cbic.201200400] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Indexed: 01/02/2023]
12
Scholes CA, Millar DP, Gee ML, Smith TA. Resonance energy-transfer studies of the conformational change on the adsorption of oligonucleotides to a silica interface. J Phys Chem B 2011;115:6329-39. [PMID: 21500794 DOI: 10.1021/jp201332w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
13
Rindermann JJ, Akhtman Y, Richardson J, Brown T, Lagoudakis PG. Gauging the Flexibility of Fluorescent Markers for the Interpretation of Fluorescence Resonance Energy Transfer. J Am Chem Soc 2010;133:279-85. [DOI: 10.1021/ja105720j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
14
Flehr R, Kienzler A, Bannwarth W, Kumke MU. Photophysical characterization of a FRET system using tailor-made DNA oligonucleotide sequences. Bioconjug Chem 2010;21:2347-54. [PMID: 21114283 DOI: 10.1021/bc100389k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
15
Jockusch S, Li Z, Ju J, Turro NJ. Two-photon Excitation Induced Fluorescence of a Trifluorophore-labeled DNA¶. Photochem Photobiol 2007. [DOI: 10.1111/j.1751-1097.2005.tb00180.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
16
VanBeek DB, Zwier MC, Shorb JM, Krueger BP. Fretting about FRET: correlation between kappa and R. Biophys J 2007;92:4168-78. [PMID: 17384068 PMCID: PMC1877789 DOI: 10.1529/biophysj.106.092650] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
17
Jockusch S, Martí AA, Turro NJ, Li Z, Li X, Ju J, Stevens N, Akins DL. Spectroscopic investigation of a FRET molecular beacon containing two fluorophores for probing DNA/RNA sequences. Photochem Photobiol Sci 2006;5:493-8. [PMID: 16685327 DOI: 10.1039/b600213g] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
18
Laurence TA, Kong X, Jäger M, Weiss S. Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins. Proc Natl Acad Sci U S A 2005;102:17348-53. [PMID: 16287971 PMCID: PMC1297681 DOI: 10.1073/pnas.0508584102] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
19
Jockusch S, Li Z, Ju J, Turro NJ. Two-photon Excitation Induced Fluorescence of a Trifluorophore-labeled DNA¶. Photochem Photobiol 2005. [DOI: 10.1562/2004-09-27-ra-329.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
20
Gu YS, Whang CW. Capillary electrophoresis of baclofen with argon-ion laser-induced fluorescence detection. J Chromatogr A 2002;972:289-93. [PMID: 12416888 DOI: 10.1016/s0021-9673(02)01083-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
21
Klostermeier D, Millar DP. Time-resolved fluorescence resonance energy transfer: a versatile tool for the analysis of nucleic acids. Biopolymers 2002;61:159-79. [PMID: 11987179 DOI: 10.1002/bip.10146] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
22
Parkhurst LJ, Parkhurst KM, Powell R, Wu J, Williams S. Time-resolved fluorescence resonance energy transfer studies of DNA bending in double-stranded oligonucleotides and in DNA-protein complexes. Biopolymers 2002;61:180-200. [PMID: 11987180 DOI: 10.1002/bip.10138] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
23
Malicka J, Groth M, Czaplewski C, Karolczak J, Liwo A, Wiczk W. Influence of solvent and configuration of residues at positions 2 and 3 on distance and mobility of pharmacophore groups at positions 1 and 4 in cyclic enkephalin analogues. Biopolymers 2001;59:180-90. [PMID: 11391567 DOI: 10.1002/1097-0282(200109)59:3<180::aid-bip1017>3.0.co;2-j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
24
Rueping M, Dietrich A, Buschmann V, Fritz MG, Sauer M, Seebach D. On the Structure of Poly(3-hydroxybutanoic acid) in Solution and in Phospholipid Bilayers. Circular Dichroism and Fluorescence Spectroscopy with Oligo(3-hydroxybutanoic acid) Derivatives. Macromolecules 2001. [DOI: 10.1021/ma010520u] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
25
Klostermeier D, Millar DP. RNA conformation and folding studied with fluorescence resonance energy transfer. Methods 2001;23:240-54. [PMID: 11243837 DOI: 10.1006/meth.2000.1135] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]  Open
26
Lakowicz JR, Piszczek G, Kang JS. On the possibility of long-wavelength long-lifetime high-quantum-yield luminophores. Anal Biochem 2001;288:62-75. [PMID: 11141307 PMCID: PMC6818246 DOI: 10.1006/abio.2000.4860] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
27
Torimura M, Kurata S, Yamada K, Yokomaku T, Kamagata Y, Kanagawa T, Kurane R. Fluorescence-quenching phenomenon by photoinduced electron transfer between a fluorescent dye and a nucleotide base. ANAL SCI 2001;17:155-60. [PMID: 11993654 DOI: 10.2116/analsci.17.155] [Citation(s) in RCA: 299] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
28
Stühmeier F, Hillisch A, Clegg RM, Diekman S. Fluorescence energy transfer analysis of DNA structures containing several bulges and their interaction with CAP. J Mol Biol 2000;302:1081-100. [PMID: 11183776 DOI: 10.1006/jmbi.2000.4089] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
29
Lilley DM, Wilson TJ. Fluorescence resonance energy transfer as a structural tool for nucleic acids. Curr Opin Chem Biol 2000;4:507-17. [PMID: 11006537 DOI: 10.1016/s1367-5931(00)00124-1] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
30
Murata SI, Kuśba J, Piszczek G, Gryczynski I, Lakowicz JR. Donor fluorescence decay analysis for energy transfer in double-helical DNA with various acceptor concentrations. Biopolymers 2000;57:306-15. [PMID: 10958322 PMCID: PMC6902054 DOI: 10.1002/1097-0282(2000)57:5<306::aid-bip70>3.0.co;2-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
31
Jacob J, Baker B, Bryant RG, Cafiso DS. Distance estimates from paramagnetic enhancements of nuclear relaxation in linear and flexible model peptides. Biophys J 1999;77:1086-92. [PMID: 10423452 PMCID: PMC1300398 DOI: 10.1016/s0006-3495(99)76958-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
32
Winter S, Kirschstein S, Miller DP. Molecular dynamics of labeled oligonucleotide probes used for the detection of point mutations in DNA. NUCLEOSIDES & NUCLEOTIDES 1999;18:411-23. [PMID: 10408923 DOI: 10.1080/15257779908043086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
33
Chan B, Weidemaier K, Yip WT, Barbara PF, Musier-Forsyth K. Intra-tRNA distance measurements for nucleocapsid proteindependent tRNA unwinding during priming of HIV reverse transcription. Proc Natl Acad Sci U S A 1999;96:459-64. [PMID: 9892655 PMCID: PMC15158 DOI: 10.1073/pnas.96.2.459] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
34
Yang M, Millar DP. Fluorescence resonance energy transfer as a probe of DNA structure and function. Methods Enzymol 1997;278:417-44. [PMID: 9170325 DOI: 10.1016/s0076-6879(97)78022-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
35
Réfrégiers M, Laigle A, Jollès B, Chinsky L. Fluorescence resonance energy transfer analysis of the degradation of an oligonucleotide protected by a very stable hairpin. J Biomol Struct Dyn 1996;14:365-71. [PMID: 9016413 DOI: 10.1080/07391102.1996.10508131] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
36
Vámosi G, Gohlke C, Clegg RM. Fluorescence characteristics of 5-carboxytetramethylrhodamine linked covalently to the 5' end of oligonucleotides: multiple conformers of single-stranded and double-stranded dye-DNA complexes. Biophys J 1996;71:972-94. [PMID: 8842236 PMCID: PMC1233554 DOI: 10.1016/s0006-3495(96)79300-1] [Citation(s) in RCA: 121] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]  Open
37
Millar DP. Fluorescence studies of DNA and RNA structure and dynamics. Curr Opin Struct Biol 1996;6:322-6. [PMID: 8804835 DOI: 10.1016/s0959-440x(96)80050-9] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
38
Ghosh SS, Eis PS, Blumeyer K, Fearon K, Millar DP. Real time kinetics of restriction endonuclease cleavage monitored by fluorescence resonance energy transfer. Nucleic Acids Res 1994;22:3155-9. [PMID: 8065930 PMCID: PMC310290 DOI: 10.1093/nar/22.15.3155] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]  Open
39
Clegg RM, Murchie AI, Lilley DM. The solution structure of the four-way DNA junction at low-salt conditions: a fluorescence resonance energy transfer analysis. Biophys J 1994;66:99-109. [PMID: 8130350 PMCID: PMC1275668 DOI: 10.1016/s0006-3495(94)80765-9] [Citation(s) in RCA: 143] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]  Open
40
Lilley DM, Clegg RM. The structure of branched DNA species. Q Rev Biophys 1993;26:131-75. [PMID: 8284349 DOI: 10.1017/s0033583500004054] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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