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Volumn 111, Issue 43, 2014, Pages 15408-15413

Double-stranded RNA under force and torque: Similarities to and striking differences from double-stranded DNA

Author keywords

Force; Magnetic tweezers; Nucleic acids; RNA; Torque

Indexed keywords

BIOTIN; DIGOXIGENIN; DOUBLE STRANDED DNA; DOUBLE STRANDED RNA; STREPTAVIDIN; DNA;

EID: 84908583733     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1407197111     Document Type: Article
Times cited : (153)

References (59)
  • 1
    • 0042424707 scopus 로고    scopus 로고
    • Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
    • Tama F, Valle M, Frank J, Brooks CL III (2003) Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc Natl Acad Sci USA 100(16):9319-9323.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.16 , pp. 9319-9323
    • Tama, F.1    Valle, M.2    Frank, J.3    Brooks, C.L.4
  • 2
    • 27644491082 scopus 로고    scopus 로고
    • Structures of the bacterial ribosome at 3.5 Å resolution
    • Schuwirth BS, et al. (2005) Structures of the bacterial ribosome at 3.5 Å resolution. Science 310(5749):827-834.
    • (2005) Science , vol.310 , Issue.5749 , pp. 827-834
    • Schuwirth, B.S.1
  • 3
    • 71549156528 scopus 로고    scopus 로고
    • Experimental and computational determination of tRNA dynamics
    • Alexander RW, Eargle J, Luthey-Schulten Z (2010) Experimental and computational determination of tRNA dynamics. FEBS Lett 584(2):376-386.
    • (2010) FEBS Lett , vol.584 , Issue.2 , pp. 376-386
    • Alexander, R.W.1    Eargle, J.2    Luthey-Schulten, Z.3
  • 4
    • 84862991581 scopus 로고    scopus 로고
    • Elastic coupling between RNA degradation and unwinding by an exoribonuclease
    • Lee G, Bratkowski MA, Ding F, Ke A, Ha T (2012) Elastic coupling between RNA degradation and unwinding by an exoribonuclease. Science 336(6089):1726-1729.
    • (2012) Science , vol.336 , Issue.6089 , pp. 1726-1729
    • Lee, G.1    Bratkowski, M.A.2    Ding, F.3    Ke, A.4    Ha, T.5
  • 5
    • 78649985789 scopus 로고    scopus 로고
    • The emerging field of RNA nanotechnology
    • Guo P (2010) The emerging field of RNA nanotechnology. Nat Nanotechnol 5(12):833-842.
    • (2010) Nat Nanotechnol , vol.5 , Issue.12 , pp. 833-842
    • Guo, P.1
  • 6
    • 79960697001 scopus 로고    scopus 로고
    • Organization of intracellular reactions with rationally designed RNA assemblies
    • Delebecque CJ, Lindner AB, Silver PA, Aldaye FA (2011) Organization of intracellular reactions with rationally designed RNA assemblies. Science 333(6041):470-474.
    • (2011) Science , vol.333 , Issue.6041 , pp. 470-474
    • Delebecque, C.J.1    Lindner, A.B.2    Silver, P.A.3    Aldaye, F.A.4
  • 7
    • 85015087906 scopus 로고    scopus 로고
    • Ten years of tension: Single-molecule DNA mechanics
    • Bustamante C, Bryant Z, Smith SB (2003) Ten years of tension: Single-molecule DNA mechanics. Nature 421(6921):423-427.
    • (2003) Nature , vol.421 , Issue.6921 , pp. 423-427
    • Bustamante, C.1    Bryant, Z.2    Smith, S.B.3
  • 8
    • 0037277427 scopus 로고    scopus 로고
    • Stretching of macromolecules and proteins
    • Strick TR, et al. (2003) Stretching of macromolecules and proteins. Rep Prog Phys 66(1):1-45.
    • (2003) Rep Prog Phys , vol.66 , Issue.1 , pp. 1-45
    • Strick, T.R.1
  • 9
    • 34548403896 scopus 로고    scopus 로고
    • Torque and dynamics of linking number relaxation in stretched supercoiled DNA
    • Marko JF (2007) Torque and dynamics of linking number relaxation in stretched supercoiled DNA. Phys Rev E Stat Nonlin Soft Matter Phys 76(2 Pt 1):021926.
    • (2007) Phys Rev E Stat Nonlin Soft Matter Phys , vol.76 , Issue.2 , pp. 021926
    • Marko, J.F.1
  • 10
    • 84862615458 scopus 로고    scopus 로고
    • Recent developments in single-molecule DNA mechanics
    • Bryant Z, Oberstrass FC, Basu A (2012) Recent developments in single-molecule DNA mechanics. Curr Opin Struct Biol 22(3):304-312.
    • (2012) Curr Opin Struct Biol , vol.22 , Issue.3 , pp. 304-312
    • Bryant, Z.1    Oberstrass, F.C.2    Basu, A.3
  • 11
    • 80052387844 scopus 로고    scopus 로고
    • Underwound DNA under tension: Structure, elasticity, and sequence-dependent behaviors
    • Sheinin MY, Forth S, Marko JF, Wang MD (2011) Underwound DNA under tension: Structure, elasticity, and sequence-dependent behaviors. Phys Rev Lett 107(10):108102.
    • (2011) Phys Rev Lett , vol.107 , Issue.10 , pp. 108102
    • Sheinin, M.Y.1    Forth, S.2    Marko, J.F.3    Wang, M.D.4
  • 12
    • 33749132605 scopus 로고    scopus 로고
    • DNA mechanics as a tool to probe helicase and translocase activity
    • Lionnet T, et al. (2006) DNA mechanics as a tool to probe helicase and translocase activity. Nucleic Acids Res 34(15):4232-4244.
    • (2006) Nucleic Acids Res , vol.34 , Issue.15 , pp. 4232-4244
    • Lionnet, T.1
  • 13
    • 77950519937 scopus 로고    scopus 로고
    • Origins of specificity in protein-dna recognition
    • Rohs R, et al. (2010) Origins of specificity in protein-DNA recognition. Annu Rev Biochem 79:233-269.
    • (2010) Annu Rev Biochem , vol.79 , pp. 233-269
    • Rohs, R.1
  • 14
    • 84860171099 scopus 로고    scopus 로고
    • Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures
    • Kim DN, Kilchherr F, Dietz H, Bathe M (2012) Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures. Nucleic Acids Res 40(7):2862-2868.
    • (2012) Nucleic Acids Res , vol.40 , Issue.7 , pp. 2862-2868
    • Kim, D.N.1    Kilchherr, F.2    Dietz, H.3    Bathe, M.4
  • 15
  • 16
    • 84872103235 scopus 로고    scopus 로고
    • Mechanical identities of RNA and DNA double helices unveiled at the single-molecule level
    • Herrero-Galán E, et al. (2013) Mechanical identities of RNA and DNA double helices unveiled at the single-molecule level. J Am Chem Soc 135(1):122-131.
    • (2013) J Am Chem Soc , vol.135 , Issue.1 , pp. 122-131
    • Herrero-Galán, E.1
  • 17
    • 0037102249 scopus 로고    scopus 로고
    • Analysis of RNA flexibility by scanning force spectroscopy
    • Bonin M, et al. (2002) Analysis of RNA flexibility by scanning force spectroscopy. Nucleic Acids Res 30(16):e81.
    • (2002) Nucleic Acids Res , vol.30 , Issue.16 , pp. e81
    • Bonin, M.1
  • 19
    • 77958197520 scopus 로고    scopus 로고
    • Quantitative guidelines for force calibration through spectral analysis of magnetic tweezers data
    • te Velthuis AJ, Kerssemakers JWJ, Lipfert J, Dekker NH (2010) Quantitative guidelines for force calibration through spectral analysis of magnetic tweezers data. Biophys J 99(4):1292-1302.
    • (2010) Biophys J , vol.99 , Issue.4 , pp. 1292-1302
    • Te Velthuis, A.J.1    Kerssemakers, J.W.J.2    Lipfert, J.3    Dekker, N.H.4
  • 20
    • 0028071373 scopus 로고
    • Entropic elasticity of lambdaphage dna
    • Bustamante C, Marko JF, Siggia ED, Smith S (1994) Entropic elasticity of lambdaphage DNA. Science 265(5178):1599-1600.
    • (1994) Science , vol.265 , Issue.5178 , pp. 1599-1600
    • Bustamante, C.1    Marko, J.F.2    Siggia, E.D.3    Smith, S.4
  • 21
    • 0032937079 scopus 로고    scopus 로고
    • Estimating the persistence length of a worm-like chain molecule from force-extension measurements
    • Bouchiat C, et al. (1999) Estimating the persistence length of a worm-like chain molecule from force-extension measurements. Biophys J 76(1 Pt 1):409-413.
    • (1999) Biophys J , vol.76 , Issue.1 , pp. 409-413
    • Bouchiat, C.1
  • 22
    • 0014408016 scopus 로고
    • Molecular conformations and structure transitions of RNA complementary helices and their possible biological significance
    • Arnott S, Fuller W, Hodgson A, Prutton I (1968) Molecular conformations and structure transitions of RNA complementary helices and their possible biological significance. Nature 220(5167):561-564.
    • (1968) Nature , vol.220 , Issue.5167 , pp. 561-564
    • Arnott, S.1    Fuller, W.2    Hodgson, A.3    Prutton, I.4
  • 23
    • 0025906148 scopus 로고
    • Electrophoretic and hydrodynamic properties of duplex ribonucleic acid molecules transcribed in vitro: Evidence that a-tracts do not generate curvature in RNA
    • Gast FU, Hagerman PJ (1991) Electrophoretic and hydrodynamic properties of duplex ribonucleic acid molecules transcribed in vitro: Evidence that A-tracts do not generate curvature in RNA. Biochemistry 30(17):4268-4277.
    • (1991) Biochemistry , vol.30 , Issue.17 , pp. 4268-4277
    • Gast, F.U.1    Hagerman, P.J.2
  • 24
    • 33751156715 scopus 로고
    • Stiff chains and filaments under tension
    • Odijk T (1995) Stiff chains and filaments under tension. Macromolecules 28(20):7016-7018.
    • (1995) Macromolecules , vol.28 , Issue.20 , pp. 7016-7018
    • Odijk, T.1
  • 25
    • 84872103235 scopus 로고    scopus 로고
    • Mechanical identities of RNA and DNA double helices unveiled at the single-molecule level
    • Herrero-Galan E, et al. (2013) Mechanical identities of RNA and DNA double helices unveiled at the single-molecule level. J Am Chem Soc 135(1):122-131.
    • (2013) J Am Chem Soc , vol.135 , Issue.1 , pp. 122-131
    • Herrero-Galan, E.1
  • 26
    • 18344386476 scopus 로고    scopus 로고
    • Structural transitions of a twisted and stretched DNA molecule
    • Léger JF, et al. (1999) Structural transitions of a twisted and stretched DNA molecule. Phys Rev Lett 83(5):1066-1069.
    • (1999) Phys Rev Lett , vol.83 , Issue.5 , pp. 1066-1069
    • Léger, J.F.1
  • 27
    • 70849086477 scopus 로고    scopus 로고
    • Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging
    • van Mameren J, et al. (2009) Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging. Proc Natl Acad Sci USA 106(43):18231-18236.
    • (2009) Proc Natl Acad Sci USA , vol.106 , Issue.43 , pp. 18231-18236
    • Van Mameren, J.1
  • 28
    • 79952602216 scopus 로고    scopus 로고
    • Overstretching DNA at 65 pN does not require peeling from free ends or nicks
    • Paik DH, Perkins TT (2011) Overstretching DNA at 65 pN does not require peeling from free ends or nicks. J Am Chem Soc 133(10):3219-3221.
    • (2011) J Am Chem Soc , vol.133 , Issue.10 , pp. 3219-3221
    • Paik, D.H.1    Perkins, T.T.2
  • 29
    • 0032168371 scopus 로고    scopus 로고
    • Homologous pairing in stretched supercoiled dna
    • Strick TR, Croquette V, Bensimon D (1998) Homologous pairing in stretched supercoiled DNA. Proc Natl Acad Sci USA 95(18):10579-10583.
    • (1998) Proc Natl Acad Sci USA , vol.95 , Issue.18 , pp. 10579-10583
    • Strick, T.R.1    Croquette, V.2    Bensimon, D.3
  • 30
    • 3843130804 scopus 로고    scopus 로고
    • High salt solution structure of a lefthanded RNA double helix
    • Popenda M, Milecki J, Adamiak RW (2004) High salt solution structure of a lefthanded RNA double helix. Nucleic Acids Res 32(13):4044-4054.
    • (2004) Nucleic Acids Res , vol.32 , Issue.13 , pp. 4044-4054
    • Popenda, M.1    Milecki, J.2    Adamiak, R.W.3
  • 31
    • 0032564447 scopus 로고    scopus 로고
    • Stretched and overwound DNA forms a pauling-like structure with exposed bases
    • Allemand JF, Bensimon D, Lavery R, Croquette V (1998) Stretched and overwound DNA forms a Pauling-like structure with exposed bases. Proc Natl Acad Sci USA 95(24): 14152-14157.
    • (1998) Proc Natl Acad Sci USA , vol.95 , Issue.24 , pp. 14152-14157
    • Allemand, J.F.1    Bensimon, D.2    Lavery, R.3    Croquette, V.4
  • 32
    • 33750829427 scopus 로고    scopus 로고
    • On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension
    • Wereszczynski J, Andricioaei I (2006) On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension. Proc Natl Acad Sci USA 103(44):16200-16205.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.44 , pp. 16200-16205
    • Wereszczynski, J.1    Andricioaei, I.2
  • 33
    • 65249161305 scopus 로고    scopus 로고
    • Magnetic tweezers measurement of single molecule torque
    • Celedon A, et al. (2009) Magnetic tweezers measurement of single molecule torque. Nano Lett 9(4):1720-1725.
    • (2009) Nano Lett , vol.9 , Issue.4 , pp. 1720-1725
    • Celedon, A.1
  • 34
    • 78649709362 scopus 로고    scopus 로고
    • Magnetic torque tweezers: Measuring torsional stiffness in DNA and reca-dna filaments
    • Lipfert J, Kerssemakers JW, Jager T, Dekker NH (2010) Magnetic torque tweezers: Measuring torsional stiffness in DNA and RecA-DNA filaments. Nat Methods 7(12):977-980.
    • (2010) Nat Methods , vol.7 , Issue.12 , pp. 977-980
    • Lipfert, J.1    Kerssemakers, J.W.2    Jager, T.3    Dekker, N.H.4
  • 35
    • 84863856881 scopus 로고    scopus 로고
    • Electromagnetic torque tweezers: A versatile approach for measurement of single-molecule twist and torque
    • Janssen XJ, et al. (2012) Electromagnetic torque tweezers: A versatile approach for measurement of single-molecule twist and torque. Nano Lett 12(7):3634-3639.
    • (2012) Nano Lett , vol.12 , Issue.7 , pp. 3634-3639
    • Janssen, X.J.1
  • 36
    • 84860012641 scopus 로고    scopus 로고
    • Torque measurements reveal sequencespecific cooperative transitions in supercoiled dna
    • Oberstrass FC, Fernandes LE, Bryant Z (2012) Torque measurements reveal sequencespecific cooperative transitions in supercoiled DNA. Proc Natl Acad Sci USA 109(16): 6106-6111.
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.16 , pp. 6106-6111
    • Oberstrass, F.C.1    Fernandes, L.E.2    Bryant, Z.3
  • 37
    • 0031474159 scopus 로고    scopus 로고
    • Torsional directed walks, entropic elasticity, and DNA twist stiffness
    • Moroz JD, Nelson P (1997) Torsional directed walks, entropic elasticity, and DNA twist stiffness. Proc Natl Acad Sci USA 94(26):14418-14422.
    • (1997) Proc Natl Acad Sci USA , vol.94 , Issue.26 , pp. 14418-14422
    • Moroz, J.D.1    Nelson, P.2
  • 39
    • 33747461393 scopus 로고    scopus 로고
    • DNA overwinds when stretched
    • Gore J, et al. (2006) DNA overwinds when stretched. Nature 442(7104):836-839.
    • (2006) Nature , vol.442 , Issue.7104 , pp. 836-839
    • Gore, J.1
  • 40
    • 68849118253 scopus 로고    scopus 로고
    • Twist-stretch coupling and phase transition during DNA supercoiling
    • Sheinin MY, Wang MD (2009) Twist-stretch coupling and phase transition during DNA supercoiling. Phys Chem Chem Phys 11(24):4800-4803.
    • (2009) Phys Chem Chem Phys , vol.11 , Issue.24 , pp. 4800-4803
    • Sheinin, M.Y.1    Wang, M.D.2
  • 41
    • 84897954099 scopus 로고    scopus 로고
    • Gold rotor bead tracking for high-speed measurements of DNA twist, torque and extension
    • Lebel P, Basu A, Oberstrass FC, Tretter EM, Bryant Z (2014) Gold rotor bead tracking for high-speed measurements of DNA twist, torque and extension. Nat Methods 11(4):456-462.
    • (2014) Nat Methods , vol.11 , Issue.4 , pp. 456-462
    • Lebel, P.1    Basu, A.2    Oberstrass, F.C.3    Tretter, E.M.4    Bryant, Z.5
  • 42
    • 77950659882 scopus 로고    scopus 로고
    • Energetics at the DNA supercoiling transition
    • Brutzer H, Luzzietti N, Klaue D, Seidel R (2010) Energetics at the DNA supercoiling transition. Biophys J 98(7):1267-1276.
    • (2010) Biophys J , vol.98 , Issue.7 , pp. 1267-1276
    • Brutzer, H.1    Luzzietti, N.2    Klaue, D.3    Seidel, R.4
  • 43
    • 84908586687 scopus 로고    scopus 로고
    • Blind predictions of DNA and RNA tweezers experiments with force and torque
    • Chou FC, Lipfert J, Das R (2014) Blind predictions of DNA and RNA tweezers experiments with force and torque. PLoS Computat Biol 10(8):e1003756.
    • (2014) PLoS Computat Biol , vol.10 , Issue.8 , pp. e1003756
    • Chou, F.C.1    Lipfert, J.2    Das, R.3
  • 45
    • 0031579785 scopus 로고    scopus 로고
    • Stretching must twist dna
    • Marko JF (1997) Stretching must twist DNA. Europhys Lett 38(3):183-188.
    • (1997) Europhys Lett , vol.38 , Issue.3 , pp. 183-188
    • Marko, J.F.1
  • 46
    • 80052825120 scopus 로고    scopus 로고
    • The geometrical origin of the strain-twist coupling in double helices
    • Olsen K, Bohr J (2011) The geometrical origin of the strain-twist coupling in double helices. AIP Adv 1(1):012108.
    • (2011) AIP Adv , vol.1 , Issue.1 , pp. 012108
    • Olsen, K.1    Bohr, J.2
  • 47
    • 0033603393 scopus 로고    scopus 로고
    • DNA stretching and compression: Large-scale simulations of double helical structures
    • Kosikov KM, Gorin AA, Zhurkin VB, Olson WK (1999) DNA stretching and compression: Large-scale simulations of double helical structures. J Mol Biol 289(5):1301-1326.
    • (1999) J Mol Biol , vol.289 , Issue.5 , pp. 1301-1326
    • Kosikov, K.M.1    Gorin, A.A.2    Zhurkin, V.B.3    Olson, W.K.4
  • 49
    • 84864758536 scopus 로고    scopus 로고
    • Probing the elasticity of DNA on short length scales by modeling supercoiling under tension
    • Schöpflin R, Brutzer H, Müller O, Seidel R, Wedemann G (2012) Probing the elasticity of DNA on short length scales by modeling supercoiling under tension. Biophys J 103(2):323-330.
    • (2012) Biophys J , vol.103 , Issue.2 , pp. 323-330
    • Schöpflin, R.1    Brutzer, H.2    Müller, O.3    Seidel, R.4    Wedemann, G.5
  • 52
    • 2342518189 scopus 로고    scopus 로고
    • Spontaneous sharp bending of double-stranded dna
    • Cloutier TE, Widom J (2004) Spontaneous sharp bending of double-stranded DNA. Mol Cell 14(3):355-362.
    • (2004) Mol Cell , vol.14 , Issue.3 , pp. 355-362
    • Cloutier, T.E.1    Widom, J.2
  • 53
    • 84865546608 scopus 로고    scopus 로고
    • Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization
    • Vafabakhsh R, Ha T (2012) Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization. Science 337(6098):1097-1101.
    • (2012) Science , vol.337 , Issue.6098 , pp. 1097-1101
    • Vafabakhsh, R.1    Ha, T.2
  • 54
    • 54249088052 scopus 로고    scopus 로고
    • Remeasuring the double helix
    • Mathew-Fenn RS, Das R, Harbury PA (2008) Remeasuring the double helix. Science 322(5900):446-449.
    • (2008) Science , vol.322 , Issue.5900 , pp. 446-449
    • Mathew-Fenn, R.S.1    Das, R.2    Harbury, P.A.3
  • 55
    • 33845810345 scopus 로고    scopus 로고
    • High flexibility of DNA on short length scales probed by atomic force microscopy
    • Wiggins PA, et al. (2006) High flexibility of DNA on short length scales probed by atomic force microscopy. Nat Nanotechnol 1(2):137-141.
    • (2006) Nat Nanotechnol , vol.1 , Issue.2 , pp. 137-141
    • Wiggins, P.A.1
  • 56
    • 46549085105 scopus 로고    scopus 로고
    • Unwinding RNA's secrets: Advances in the biology, physics, and modeling of complex RNAs
    • Chu VB, Herschlag D (2008) Unwinding RNA's secrets: Advances in the biology, physics, and modeling of complex RNAs. Curr Opin Struct Biol 18(3):305-314.
    • (2008) Curr Opin Struct Biol , vol.18 , Issue.3 , pp. 305-314
    • Chu, V.B.1    Herschlag, D.2
  • 57
    • 0024469851 scopus 로고
    • Crystallographic structure of an RNA helix: [U(UA)6A]2
    • Dock-Bregeon AC, et al. (1989) Crystallographic structure of an RNA helix: [U(UA)6A]2. J Mol Biol 209(3):459-474.
    • (1989) J Mol Biol , vol.209 , Issue.3 , pp. 459-474
    • Dock-Bregeon, A.C.1
  • 59
    • 61349129512 scopus 로고    scopus 로고
    • Measurement of the torque on a single stretched and twisted DNA using magnetic tweezers
    • Mosconi F, Allemand JF, Bensimon D, Croquette V (2009) Measurement of the torque on a single stretched and twisted DNA using magnetic tweezers. Phys Rev Lett 102(7): 078301.
    • (2009) Phys Rev Lett , vol.102 , Issue.7 , pp. 078301
    • Mosconi, F.1    Allemand, J.F.2    Bensimon, D.3    Croquette, V.4


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