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For: Pörchke D. The nature of stacking interations in polynucleotides. Molecular states in Oligo- and polyribocytidylic acids by relaxation analysis. Biochemistry 1976;15:1495-9. [PMID: 1259951 DOI: 10.1021/bi00652a021] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.0] [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
Kinetic Mechanism of RNA Helix-Terminal Basepairing-A Kinetic Minima Network Analysis. Biophys J 2019;117:1674-1683. [PMID: 31590890 DOI: 10.1016/j.bpj.2019.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 11/22/2022]  Open
2
Smith LG, Zhao J, Mathews DH, Turner DH. Physics-based all-atom modeling of RNA energetics and structure. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018;8. [PMID: 28815951 DOI: 10.1002/wrna.1422] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 02/03/2017] [Accepted: 03/08/2017] [Indexed: 12/31/2022]
3
Porschke D. Kinetics of the B-A transition of DNA: analysis of potential contributions to a reaction barrier. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018;47:325-332. [PMID: 29404661 PMCID: PMC5982448 DOI: 10.1007/s00249-018-1276-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 11/21/2017] [Accepted: 01/02/2018] [Indexed: 11/28/2022]
4
Xu X, Yu T, Chen SJ. Understanding the kinetic mechanism of RNA single base pair formation. Proc Natl Acad Sci U S A 2016;113:116-21. [PMID: 26699466 PMCID: PMC4711849 DOI: 10.1073/pnas.1517511113] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
5
Tubbs J, Condon DE, Kennedy S, Hauser M, Bevilacqua P, Turner DH. The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics. Biochemistry 2013;52:996-1010. [PMID: 23286901 PMCID: PMC3571207 DOI: 10.1021/bi3010347] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 12/27/2012] [Indexed: 12/29/2022]
6
Ouldridge TE, Louis AA, Doye JPK. Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. J Chem Phys 2011;134:085101. [PMID: 21361556 DOI: 10.1063/1.3552946] [Citation(s) in RCA: 312] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
7
Porschke D. Analysis of chemical and physical relaxation processes of polyelectrolytes by electric field pulse methods: A comparison of critical comments with facts. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19961000606] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
8
Zhao L, Xia T. Probing RNA conformational dynamics and heterogeneity using femtosecond time-resolved fluorescence spectroscopy. Methods 2009;49:128-35. [DOI: 10.1016/j.ymeth.2009.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 03/26/2009] [Accepted: 04/02/2009] [Indexed: 01/16/2023]  Open
9
Porschke D. Unique Physical Signature of DNA Curvature and Its Implications for Structure and Dynamics. J Phys Chem B 2007;111:12004-11. [PMID: 17887666 DOI: 10.1021/jp073965e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
10
Porschke D. The nature of "unusual" electro-optical transients observed for DNA. Colloids Surf B Biointerfaces 2007;56:44-9. [PMID: 17188466 DOI: 10.1016/j.colsurfb.2006.11.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Accepted: 11/15/2006] [Indexed: 11/18/2022]
11
Ma H, Wan C, Wu A, Zewail AH. DNA folding and melting observed in real time redefine the energy landscape. Proc Natl Acad Sci U S A 2007;104:712-6. [PMID: 17215374 PMCID: PMC1766338 DOI: 10.1073/pnas.0610028104] [Citation(s) in RCA: 88] [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
12
Pörchke D. Molecular states in single-stranded adenylate chains by relaxation analysis. Biopolymers 2004. [DOI: 10.1002/bip.1978.360170205] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
13
Jezewska MJ, Galletto R, Bujalowski W. Dynamics of gapped DNA recognition by human polymerase beta. J Biol Chem 2002;277:20316-27. [PMID: 11912205 DOI: 10.1074/jbc.m200918200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
14
Jezewska MJ, Rajendran S, Galletto R, Bujalowski W. Kinetic mechanisms of rat polymerase beta-ssDNA interactions. Quantitative fluorescence stopped-flow analysis of the formation of the (Pol beta)(16) and (Pol beta)(5) ssDNA binding mode. J Mol Biol 2001;313:977-1002. [PMID: 11700054 DOI: 10.1006/jmbi.2001.5042] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
15
Bujalowski W, Jezewska MJ. Kinetic mechanism of the single-stranded DNA recognition by Escherichia coli replicative helicase DnaB protein. Application of the matrix projection operator technique to analyze stopped-flow kinetics. J Mol Biol 2000;295:831-52. [PMID: 10656794 DOI: 10.1006/jmbi.1999.3378] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
16
Florián J, Šponer J, Warshel A. Thermodynamic Parameters for Stacking and Hydrogen Bonding of Nucleic Acid Bases in Aqueous Solution:  Ab Initio/Langevin Dipoles Study. J Phys Chem B 1999. [DOI: 10.1021/jp983699s] [Citation(s) in RCA: 137] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
17
Searle MS, Williams DH. On the stability of nucleic acid structures in solution: enthalpy-entropy compensations, internal rotations and reversibility. Nucleic Acids Res 1993;21:2051-6. [PMID: 7684832 PMCID: PMC309464 DOI: 10.1093/nar/21.9.2051] [Citation(s) in RCA: 107] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]  Open
18
Chapter 7 Codon Recognition: Evaluation of the Effects of Modified Bases in the Anticodon Loop of Trna Using the Temperature-Jump Relaxation Method. ACTA ACUST UNITED AC 1990. [DOI: 10.1016/s0301-4770(08)61473-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
19
Ménard R, Zador M. Kinetic and thermodynamic investigation of the (dien)Pd(II)-polycytidylic acid system. Biophys Chem 1988;29:263-70. [PMID: 3390526 DOI: 10.1016/0301-4622(88)85047-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
20
Bujalowski W, Graeser E, McLaughlin LW, Proschke D. Anticodon loop of tRNAPhe: structure, dynamics, and Mg2+ binding. Biochemistry 1986;25:6365-71. [PMID: 3539189 DOI: 10.1021/bi00369a004] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
21
Hobza P, Mehlhorn A, Čársky P, Zahradník R. Stacking interactions: Ab initio SCF and MP2 study on (H2O)2, (H2S)2, (HCN)2, (CH2O)2 and (C2H4)2. ACTA ACUST UNITED AC 1986. [DOI: 10.1016/0166-1280(86)80030-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
22
Romby P, Giegé R, Houssier C, Grosjean H. Anticodon-anticodon interactions in solution. Studies of the self-association of yeast or Escherichia coli tRNAAsp and of their interactions with Escherichia coli tRNAVal. J Mol Biol 1985;184:107-118. [PMID: 2411934 DOI: 10.1016/0022-2836(85)90047-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
23
Vacher J, Grosjean H, Houssier C, Buckingham RH. The effect of point mutations affecting Escherichia coli tryptophan tRNA on anticodon-anticodon interactions and on UGA suppression. J Mol Biol 1984;177:329-42. [PMID: 6379198 DOI: 10.1016/0022-2836(84)90460-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
24
Freier SM, Petersheim M, Hickey DR, Turner DH. Thermodynamic studies of RNA stability. J Biomol Struct Dyn 1984;1:1229-42. [PMID: 6086053 DOI: 10.1080/07391102.1984.10507514] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
25
Hirota K, Igarashi M, Inoue Y, Chûjô R. Effects of Lysine and Arginine Derivatives on the Base Stacking Association of 2′-Deoxyguanosine 5′-Monophosphate. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1983. [DOI: 10.1246/bcsj.56.3796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
26
Freier SM, Albergo DD, Turner DH. Solvent effects on the dynamics of (dG-dC)3. Biopolymers 1983;22:1107-31. [PMID: 6850059 DOI: 10.1002/bip.360220408] [Citation(s) in RCA: 76] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
27
pH-Dependent Raman spectra and thermal melting profiles for polycytidylic acid. Biopolymers 1981. [DOI: 10.1002/bip.1981.360201106] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
28
Weissenbach J, Grosjean H. Effect of threonylcarbamoyl modification (t6A) in yeast tRNA Arg III on codon-anticodon and anticodon-anticodon interactions. A thermodynamic and kinetic evaluation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981;116:207-13. [PMID: 6788546 DOI: 10.1111/j.1432-1033.1981.tb05320.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
29
Albergo DD, Turner DH. Solvent effects on thermodynamics of double-helix formation in (dG-dC)3. Biochemistry 1981;20:1413-8. [PMID: 7225339 DOI: 10.1021/bi00509a002] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
30
Freier SM, Hill KO, Dewey TG, Marky LA, Breslauer KJ, Turner DH. Solvent effects on the kinetics and thermodynamics of stacking in poly(cytidylic acid). Biochemistry 1981;20:1419-26. [PMID: 7225340 DOI: 10.1021/bi00509a003] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
31
Frechet D, Gabarro-Arpa J. Thermal perturbation differential spectra of ribonucleic acids. III. Chain length effect. BIOCHIMICA ET BIOPHYSICA ACTA 1980;609:1-13. [PMID: 6157416 DOI: 10.1016/0005-2787(80)90196-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
32
Tazawa I, Koike T, Inoue Y. Stacking properties of a highly hydrophobic dinucleotide sequence, N6, N6-dimethyladenylyl(3' leads to 5')N6, N6-dimethyladenosine, occurring in 16--18-S ribosomal RNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1980;109:33-8. [PMID: 7053060 DOI: 10.1111/j.1432-1033.1980.tb04764.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
33
Morgan JP, Daniels M. EXCITED STATES OF DNA AND ITS COMPONENTS AT ROOM TEMPERATURE—IV. SPECTRAL, POLARIZATION AND QUANTUM YIELD STUDIES OF EMISSIONS FROM CpC AND POLY rC. Photochem Photobiol 1980. [DOI: 10.1111/j.1751-1097.1980.tb03709.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
34
Dewey TG, Turner DH. Laser temperature-jump study of stacking in adenylic acid polymers. Biochemistry 1979;18:5757-62. [PMID: 518868 DOI: 10.1021/bi00593a002] [Citation(s) in RCA: 84] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
35
Kallenbach NR, Berman HM. RNA structure. Q Rev Biophys 1977;10:138-236. [PMID: 333501 DOI: 10.1017/s0033583500000202] [Citation(s) in RCA: 44] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
36
Pörschke D. Elementary steps of base recognition and helix-coil transitions in nucleic acids. MOLECULAR BIOLOGY, BIOCHEMISTRY, AND BIOPHYSICS 1977;24:191-218. [PMID: 904614 DOI: 10.1007/978-3-642-81117-3_5] [Citation(s) in RCA: 87] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
37
Henco K, Riesner D, Sanger HL. Conformation of viroids. Nucleic Acids Res 1977;4:177-94. [PMID: 866174 PMCID: PMC342418 DOI: 10.1093/nar/4.1.177] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
38
Lowdon M, Goddard JP. The kinetics of bisulphite modification of reactive residues in E. coli tRNA2Phe. Nucleic Acids Res 1976;3:3383-96. [PMID: 794838 PMCID: PMC343183 DOI: 10.1093/nar/3.12.3383] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
39
Pörschke D. Threshold effects observed in conformation changes induced by electric fields. Biopolymers 1976;15:1917-28. [PMID: 963236 DOI: 10.1002/bip.1976.360151004] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
40
Yoon K, Turner DH, Tinoco I, Haar F, Cramer F. The kinetics of binding of U-U-C-A to a dodecanucleotide anticodon fragment from yeast tRNA-Phe. Nucleic Acids Res 1976;3:2233-41. [PMID: 787934 PMCID: PMC343079 DOI: 10.1093/nar/3.9.2233] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
41
Pörschke D. Thermodynamic and kinetic parameters of ion condensation to polynucleotides. Outer sphere complex formed by Mg++ions. Biophys Chem 1976;4:383-94. [PMID: 953154 DOI: 10.1016/0301-4622(76)80018-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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