Bibliography

1
Watson J.D. and Crick F.H.C.
A structure for deoxyribose nucleic acid.
Nature, 171(4356):737-738, 1953.

2
Ritort F.
Single-molecule experiments in biological physics: methods and applications.
J. Phys. (Cond. Matt.), 18:R531-R583, 2006.

3
Mossa A., Huguet J.M., and Ritort F.
Investigating the thermodynamics of small biosystems with optical tweezers.
Physica E: Low-dimensional Systems and Nanostructures, 42:666-671, 2010.

4
Crooks G.E.
Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences.
Phys. Rev. E, 60:2721-2726, 1999.

5
Jarzynski C.
Nonequilibrium equality for free energy differences.
Phys. Rev. Lett., 78:2690, 1997.

6
Maxwell J.C.
A Treatise on Electricity and Magnetism, Vol. II.
Clarendon Press, Oxford, 1873.

7
Ashkin A.
Acceleration and trapping of particles by radiation pressure.
Phys. Rev. Lett., 24(4):156-159, 1970.

8
Ashkin A., Dziedzic J.M., Bjorkholm J.E., and Chu S.
Observation of single-beam gradient force optical trap for dielectric particles.
Opt. Lett., 11(5):288, 290 1986.

9
Svoboda K., Schmidt C.F., Schnapp B.J., and Block S.M.
Direct observation of kinesin stepping by optical trapping interferometry.
Nature, 365:721-727, 1993.

10
Kuo S.C. and Sheetz M.P.
Force of single kinesin molecules measured with optical tweezers.
Science, 260:232-234, 1993.

11
Ghislain L.P., Switz N.A., and Webb W.W.
Measurement of small forces using an optical trap.
Rev. Sci. Instrum., 65(9):2762-2768, 1994.

12
Moffitt J.R., Chemla Y.R., Smith S.B., and Bustamante C.
Recent advances in optical tweezers.
Annu. Rev. Biochem., 77:205-228, 2008.

13
Moffitt J.R., Chemla Y.R., Izhaky D., and Bustamante C.
Differential detection of dual traps improves the spatial resolution of optical tweezers.
Proc. Natl. Acad. Sci. USA, 103:9006-11, 2006.

14
Grier D.G.
A revolution in optical manipulation.
Nature, 424:810-16, 2003.

15
Gouesbet G., Grehan G., and Maheu B.
Scattering of a Gaussian beam by a Mie scatter center using a Bromwich formalism.
J. Optics (Paris), 16(2):83-93, 1985.

16
Smith S.B., Cui Y., and Bustamante C.
Optical-trap force transducer that operates by direct measurement of light momentum.
Methods Enzymol., 361:134-160, 2003.

17
Smith S.B. and Bustamante C.
Light-force sensor and method for measuring axial optical-trap forces from changes in light momentum along an optical axis.
U.S. Patent, 7,133,132 B2, 2006.

18
Smith S.B. and Bustamante C.
Optical beam translation device and method using a pivoting optical fiber.
U.S. Patent, 7,274,451 B2, 2006.

19
Smith S.B. and Rivetti C.
http://tweezerslab.unipr.it.
2010.

20
Crick F.H.C.
The biological replication of macromolecules.
Symp. Soc. Exp. Biol., XII:138-163, 1958.

21
Bockelmann U., Essevaz-Roulet B., and Heslot F.
Molecular Stick-Slip Motion Revealed by Opening DNA with Piconewton Forces.
Phys. Rev. Lett., 79(22):4489-4492, 1997.

22
Rief M., Clausen-Schaumann H., and Gaub H.E.
Sequence-dependent mechanics of single DNA molecules.
Nat. Struct. Biol., 6(4):346-349, 1999.

23
Danilowicz C., Coljee V.W., Bouzigues C., Lubensky D.K., Nelson D.R., and Prentiss M.
DNA unzipped under a constant force exhibits multiple metastable intermediates.
Proc. Natl. Acad. Sci. USA, 100(4):1694-1699, 2003.

24
Bockelmann U., Ph. Thomen, Essevaz-Roulet B., Viasnoff V., and Heslot F.
Unzipping DNA with optical tweezers: high sequence sensitivity and force flips.
Biophys. J., 82(3):1537-1553, 2002.

25
Huguet J.M., Bizarro C.V., Forns N., Smith S.B., Bustamante C., and Ritort F.
Single-molecule derivation of salt dependent base-pair free energies in DNA.
Proc. Natl. Acad. Sci. USA, 107:15431-15436, 2010.

26
Devoe H. and Tinoco Jr. I.
The stability of helical polynucleotides: base contributions.
J. Mol. Biol., 4:500-517, 1962.

27
Crothers D.M. and Zimm B.H.
Theory of the melting transition of synthetic polynucleotides: evaluation of the stacking free energy.
J. Mol. Biol., 9:1-9, 1964.

28
SantaLucia Jr. J.
A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics.
Proc. Natl. Acad. Sci. USA, 95(4):1460-1465, 1998.

29
Lubensky D.K. and Nelson D.R.
Single molecule statistics and the polynucleotide unzipping transition.
Phys. Rev. E, 65:031917, 2002.

30
Sanger F. and Coulson A.R.
A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase.
J. Mol. Biol., 94:441-446, 1975.

31
Bischof M.
Some remarks on the history of biophysics and its future.
Proceedings of the 1st Hombroich Symposium of Biophysics, Oct.3-6, 1995, Neuss, Germany, pages 10-21, 1995.

32
Schrödinger E.
What is life?
Cambridge University Press., 1992.

33
Strick T., Allemand J.-F., Croquette V., and Bensimon D.
The manipulation of single biomolecules.
Phys. Today, 54:46-51, 2001.

34
Biophysical Society.
http://www.biophysics.org/.

35
Daune M.
Molecular Biophysics.
Oxford University Press, Oxford, 1999.

36
Eom S.H. and Wang J. Steitz T.A.
Structure of Taq polymerase with DNA at the polymerase active site.
Nature, 382:278-81, 1996.

37
Several authors. Edited by French A.P.
Physics in a Technological World.
AIP, New York, 1988.

38
Kratky O. and Porod G.
Röntgenuntersuchung gelöster Fadenmoleküle.
Rec. Trav. Chim. Pays-Bas, 68:1106-1123, 1949.

39
Smith S.B., Finzi L., and Bustamante C.
Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads.
Science, 258(5085):1122-1126, 1992.

40
Bustamante C., Marko J.F., Siggia E.D., and Smith S.B.
Entropic elasticity of lambda-phage DNA.
Science, 265(5178):1599-1600, 1994.

41
Glaser R.
Biophysics.
Springer-Verlag, Berlin, 5th ed., 2001.

42
Bai C., Wang C. Xie X.S., and Wolynes P.G.
Single molecule phyisics and chemistry.
Proc. Natl. Acad. Sci. USA, 96:11075, 1999.

43
Mehta A.D., Rief M., Spudich J.A., Smith D.A., and Simmons R.M.
Single-Molecule Biomechanics with Optical Methods.
Science, 283:1689-1695, 1999.

44
Block S.M., Goldstein L.S.B., and Schnapp B.J.
Bead movement by single kinesin molecules studied with optical tweezers.
Nature, 348(348-352), 1990.

45
Finer J.T., Simmons R.M., and Spudich J.A.
Single myosin molecule mechanics: piconewton forces and nanometre steps.
Nature, 368:113-119, 1994.

46
Noji H., Yasuda R., Yoshida M., and Kinosita Jr K.
Direct observation of the rotation of F$ _1$-ATPase.
Nature, 386:299-302, 1997.

47
Yin H., Wang M.D., Svoboda K., Landick R., Block S.M., and Gelles J.
Transcription against an applied force.
Science, 270:1653 - 1657, 1995.

48
Smith S.B., Cui Y., and Bustamante C.
Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules.
Science, 271:795-799, 1996.

49
Liphardt J., Onoa B., Smith S.B., Tinoco Jr. I., and Bustamante C.
Reversible unfolding of single rna molecules by mechanical force.
Science, 292:733-737, 2001.

50
Carrion-Vazquez M., Oberhauser A.F., Fowler S.B., Marszalek P.E., Broedel S.E., Clarke J., and Fernandez J.M.
Mechanical and chemical unfolding of a single protein: a comparison.
Proc. Natl. Acad. Sci. USA, 96:3694-9, 1999.

51
Dame R.T., Noom M.C., and Wuite G.J.L.
Bacterial chromatin organization by H-NS protein.
Nature, 444:387-390, 2006.

52
Pathria R.K.
Statistical Mechanics.
Butterworth-Heinemann, Oxford, 1996.

53
Liphardt J., Dumont S., Smith S.B., Tinoco Jr I., and Bustamante C.
Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality.
Science, 296:1832-5, 2002.

54
Collin D., Ritort F., Jarzynsk C., Smith S.B., Tinoco Jr. I., and Bustamante C.
Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies.
Nature, 437:231-234, 2005.

55
Junier I., Mossa A., and Manosas M. Ritort F.
Recovery of free energy branches in single molecule experiments.
Phys. Rev. Let., 102:070602, 2009.

56
Ritort F.
Nonequilibrium fluctuations in small systems: from physics to biology.
Advances in Chemical Physics (Ed. Stuart. A. Rice, Wiley publications), 137:31-123, 2007.

57
Mie G.
Beiträge zur Optik trüber Medien, speziell kolloidaler Metallösungen.
Ann. der Phys., 25:377-445, 1908.

58
Debye P.
Der Lichtdruck auf Kugeln von beliebigem Material.
Ann. der Phys., 335:57-136, 1909.

59
Ashkin A.
Optical levitation by radiation pressure.
Appl. Phys. Lett., 19(8):283-285, 1971.

60
Block S.M., Blair D.F., and Berg H.C.
Compliance of bacterial flagella measured with optical tweezers.
Nature, 338:514-518, 1989.

61
Ashkin A., Schütze K., Dziedzic J.M., Euteneuer U., and Schliwa M.
Force generation of organelle transport measured in vivo by an infrared laser trap.
Nature, 348:346-348, 1990.

62
Denk W. and Webb W.W.
Optical measurement of picometer displacements of transparent microscopic objects.
Appl. Opt., 29(16):2382-2391, 1990.

63
Ghislain L.P. and Webb W.W.
Scanning-force microscope based on an optical trap.
Opt. Lett., 18(19):1678-1680, 1993.

64
Simmons R.M., Finer J.T., Chu S., and Spudich J.A.
Quantitative measurements of force and displacement using an optical trap.
Biophys. J., 70(4):1813-1822, 1996.

65
Tolic-Nørrelykke S.F., Schäffer E., Howard J., Pavone F.S., Jülicher F., and Flyvbjerg H.
Calibration of optical tweezers with positional detection in the back focal plane.
Rev. Sci. Instrum., 77:103101, 2006.

66
Visscher K., Gross S.P., and Block S.M.
Construction of multiple-beam optical traps with nanometer-level position sensing.
IEEE J. Sel. Top. Quantum Electron. 2, pages 1066-1076, 1996.

67
Montes-Usategui M., Pleguezuelos E., Andilla J., and Martín-Badosa E.
Fast generation of holographic optical tweezers by random mask encoding of Fourier components.
Optics Express, 14:2101-2107, 2006.

68
Pleguezuelos E., Carnicer A., Andilla J., Martín-Badosa E., and Montes-Usategui M.
Holotrap: Interactive hologram design for multiple dynamic optical trapping.
Comp. Phys. Commun., 176:701-709, 2007.

69
Bryant Z., Stone M.D., Gore J., Smith S.B., Cozzarelli N.R., and Bustamante C.
Structural transitions and elasticity from torque measurements on DNA.
Nature, 424:338-341, 2003.

70
Sacconi L., Romano G., Ballerini R., Capitanio M., De Pas M., Giuntini M, Dunlap D., Finzi L., and Pavone F.S.
Three-dimensional magneto-optic trap for micro-object manipulation.
Opt. Lett., 26:1359-61, 2001.

71
Barnett S.M. and Allen L.
Orbital angular momentum and nonparaxial light beams.
Opt. Commun., 110:670, 1994.

72
He H., Friese M.E.J., Heckenberg N.R., and Rubinsztein-Dunlop H.
Direct observation of transfer of angular momentum to absorptive particles from a laser beam with a phase singularity.
Phys. Rev. Lett., 75:826-829, 1995.

73
La Porta A. and Wang M.D.
Optical torque wrench: Angular trapping, rotation, and torque detection of quartz microparticles.
Phys. Rev. Lett., 92:190801, 2004.

74
Keyser U.F., van der Does J., Dekker C., and Dekker N.H.
Optical tweezers for force measurements on DNA in nanopores.
Rev. Sci. Instrum., 77:105105, 2006.

75
Ishijima A., Kojima H., Funatsu T., Tokunaga M., Higuchi H., Tanaka H., and Yanagida T.
Simultaneous observation of individual ATPase and mechanical events by a single myosin molecule during interaction with actin.
Cell, 92:161-171, 1998.

76
Mameren J., Modesti M., Kanaar R., Wyman C., Wuite G.J., and Peterman E.J.
Dissecting elastic heterogeneity along DNA molecules coated partly with Rad51 using concurrent fluorescence microscopy and optical tweezers.
Biophys. J., 91:L78-80, 2006.

77
Ashkin A. and Dziedzic J. M.
Optical trapping and manipulation of viruses and bacteria.
Science, 235:1517-1520, 1987.

78
Ashkin A.
Forces of a single-beam gradient laser trap on a dielectric sphere in the ray optics regime.
Biophys. J., 61:569-582, 1992.

79
Neuman K.C. and Block S.M.
Optical trapping.
Rev. Sci. Instrum., 75(9):2787-2809, 2004.

80
Born M. and Wolf E.
Principles of optics: electromagnetic theory of propagation, interference and diffraction of light.
Cambridge University Press., 7th expanded ed. edition, 1999.

81
Harada Y. and Asakura T.
Radiation forces on a dielectric sphere in the Rayleigh scattering regime.
Opt. Commun., 124:529-541, 1996.

82
Bazhan V.
http://www.scatlab.org.
2003.

83
Barton J.P., Alexander D.R., and Schaub S.A.
Internal and near-surface elecromagnetic fields for a spherical particle irradiated by a focused laser beam.
J. Appl. Phys., 64:1632-1639, 1988.

84
Maheu B., Gouesbet G., and Grehan G.
A concise presentation of the generalized Lorenz-Mie theory for arbitrary location of the scatterer in an arbitrary incident profile.
J. Optics (Paris), 19:59-67, 1988.

85
Barton J.P., Alexander D.R., and Schaub S.A.
Theoretical determination of net radiation force and torque for a spherical particle illuminated by a focused laser beam.
J. Appl. Phys., 66(10):4594-4602, 1989.

86
Grange W., Husale S., GÃ14ntherodt H.-J., and Hegner M.
Optical tweezers system measuring the change in light momentum flux.
Rev. Sci. Instrum., 73(6):2308-2316, 2002.

87
Future Technology Devices International Ltd.
http://www.ftdichip.com/drivers/vcp.htm.
2010.

88
Hayashi K., Forns N., Manosas M., Huguet J.M., and Ritort F.
Stochastic resonance in the mechanical folding/unfolding of single DNA hairpins.
Submitted for publication, 2010.

89
Crick F.
Central dogma of molecular biology.
Nature, 227:561-563, 1970.

90
Cantor C. and Schimmel P.R.
Biophysical chemistry.
Freeman, cop, New York, 1980.

91
Calladine C.R. and Drew H.R.
Understanding DNA: the molecule and how it works.
Academic Press, San Diego, 1997.

92
Saenger W.
Principles of Nucleic Acid Structure.
Springer-Verlag, New York, 1988.

93
Cluzel P., Lebrun A., Heller C., Lavery R., Viovy J.-L., Chatenay D., and Caron F.
DNA: An Extensible Molecule.
Science, 271:792-794, 1996.

94
van Mameren J., Gross P., Farge G., Hooijman P., Modesti M., Falkenberg M., Wuite G.J., and Peterman E.J.
Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging.
Proc. Natl. Acad. Sci. USA, 106:18231-6, 2009.

95
Premilat S. and Albiser G.
Conformations of A-DNA ad B-DNA in agreemet with fiber X-ray and infrared dichroism.
Nucl. Acids Res., 11(6):1897-1908, 1983.

96
Watson J.D., Baker T.A., Bell S.P., Gann A., Levine M., and Losick R.
Molecular Biology of the Gene.
Benjamin Cummings, 5th. ed., San Francisco., 2004.

97
Cui Y. and Bustamante C.
Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure.
Proc. Nat. Acad. Sci. USA, 97:127-132, 2000.

98
Darwin C.
On the origin of species.
Oxford University Press, London, 1951.

99
Wagensberg J.
La rebelión de las formas.
Ed. Tusquets, Barcelona, 2004.

100
Modrich P. and Richardson C.C.
Bacteriophage T7 deoxyribonucleic acid replication in vitro. A protein of Escherichia coli required for bacteriophage T7 DNA polymerase activity.
J. Biol. Chem., 250:5508-5514, 1975.

101
Dumont S., Cheng W., Serebrov V., Beran R.K., Tinoco Jr. I., Pyle A.M., and Bustamante C.
RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP.
Nature, 439(7072):105-108, 2006.

102
Johnson D.S., Bai L., Smith B.Y., Patel S.S., and Wang M.D.
Single molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase.
Cell, 29:1299-1309, 2007.

103
Lionnet T., Spiering M.M., Benkovic S.J., Bensimon D., and Croquette V.
Real-time observation of bacteriophage t4 gp41 helicase reveals an unwinding mechanism.
Proc. Natl. Acad. Sci. USA, 104(50):19790-19795, 2007.

104
Lee G.U., Chrisey L.A., and Colton R.J.
Direct measurement of the forces between complementary strands of DNA.
Science, 266:771 - 773, 1994.

105
Boland T. and Ratner D.
Direct measurement of hydrogen bonding in DNA nucleotide bases by atomic force microscopy.
Proc. Natl. Acad. Sci. USA, 92:5297-5301, 1995.

106
Essevaz-Roulet B., Bockelmann U., and Heslot F.
Mechanical separation of the complementary strands of DNA.
Proc. Natl. Acad. Sci. USA, 94:11935-11940, 1997.

107
Bockelmann U., Essevaz-Roulet B., and Heslot F.
DNA strand separation studied by single molecule force measurements.
Phys. Rev. E, 58(2):2386-2394, 1998.

108
Kishino A. and Yanagida T.
Force measurements by micromanipulation of a single actin filament by glass needles.
Nature., 334:74-76, 1988.

109
Breslauer K.J., Frank R., Blöcker H., and Marky L.A.
Predicting DNA duplex stability from the base sequence.
Proc. Natl. Acad. Sci. USA, 83:3746-3750, 1986.

110
Clausen-Schaumann H., Rief M., Tolksdorf C., and Gaub H.E.
Mechanical stability of single DNA molecules.
Biophys. J., 78:1997-2007, 2000.

111
Thomen P., Bockelmann U., and Heslot F.
Rotational drag on DNA: A single molecule experiment.
Phys. Rev. Lett., 88(24):248102, 2002.

112
Manosas M. and Ritort F.
Thermodynamic and kinetic aspects of RNA pulling experiments.
Biophys. J., 88(5):3224-3242, 2005.

113
Woodside M.T., Anthony P.C., Behnke-Parks W.M., Larizadeh K., Herschlag D., and Block S.M.
Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid.
Science, 314(5801):1001-1004, 2006.

114
Koch S.J., Shundrovsky A., Jantzen B.C., and Wang M.D.
Probing protein-DNA interactions by unzipping a single DNA double helix.
Biophys. J., 83:1098, 2002.

115
Wen J.-D., Lancaster L., Hodges C., Zeri A.-C., Yoshimura S.H., Noller H.F., Bustamante C., and Tinoco Jr. I.
Following translation by single ribosomes one codon at a time.
Nature, 452:598-603, 2008.

116
Cocco S., Marko J.F., and Monasson R.
Theoretical models for single-molecule DNA and RNA experiments: from elasticity to unzipping.
arXiv:cond-mat/0206238v1, 2002.

117
Voulgarakis N.K, Redondo A., Bishop A.R., and Rasmussen K.Ø.
Sequencing DNA by dynamic force spectroscopy: Limitations and prospects.
Nano Lett., 6:1483-1486, 2006.

118
Peyret N.
Prediction of nucleic acid hybridization: Parameters and algorithms.
PhD thesis, Wayne State University, Department of Chemistry, Detroit, MI., 2000.

119
Zuker M.
Mfold web server for nucleic acid folding and hybridization prediction.
Nucl. Acids Res., 31:3406-3415, 2003.

120
Marky L.A. and Breslauer K.J.
Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves.
Biopolymers, 26:1601-1620, 1987.

121
Erie D., Sinha N., Olson W., Jones R., and Breslauer K.
A dumbbell-shaped, double-hairpin structure of DNA: a thermodynamic investigation.
Biochemistry, 26:7150-7159, 1987.

122
Gerland U., Bundschuh R., and Hwa T.
Force-induced denaturation of RNA.
Biophys. J., 81:1324-1332, 2001.

123
Süzen M., Sega M., and Holm C.
Ensemble inequivalence in single-molecule experiments.
Phys. Rev. E, 79:051118, 2009.

124
Garcimartín A., Guarino A., Bellon L., and Ciliberto S.
Statistical properties of fracture precursors.
Phys. Rev. Lett., 79:3202, 1997.

125
Bonnot E. Romero R., Illa X. Mañosa L., Planes A., and Vives E.
Hysteresis in a system driven by either generalized force or displacement variables: Martensitic phase transition in single-crystalline Cu-Zn-Al.
Phys. Rev. B, 76:064105, 2007.

126
Rubio-Bollinger G., Bahn S.R., Agraït N., Jacobsen K.W., and Vieira S.
Mechanical properties of formation mechanisms of a wire of single gold atoms.
Phys. Rev. Lett., 87:026101, 2001.

127
Socoliuc A., Bennewitz R., Gnecco E., and Meyer E.
Transition from stick-slip to continuous sliding in atomic friction: Entering a new regime of ultralow friction.
Phys. Rev. Lett., 92:134301, 2004.

128
Rothemund P.W.K.
Folding dna to create nanoscale shapes and patterns.
Nature, 440:297-302, 2006.

129
Douglas S.M., Dietz H., Liedl T., Hogberg B., Graf F., and Shih W.M.
Self-assembly of dna into nanoscale three-dimensional shapes.
Nature, 459:414-418, 2009.

130
Shoemaker D.D., Schadt E.E., Armour C.D., He Y.D., Garrett-Engele P., McDonagh P.D., Loerch P.M., Leonardson A., Lum P.Y., Cavet G., Wu L.F., Altschuler S.J., Edwards S., King J., Tsang J.S., Schimmack G., Schelter J.M., Koch J., Ziman M., Marton M.J., Li B., Cundiff P., Ward T., Castle J., Krolewski M., Meyer M.R., Mao M., Burchard J., Kidd M.J., Dai H., Phillips J.W., Linsley P.S., Stoughton R., Scherer S., and Boguski M.S.
Experimental annotation of the human genome using microarray technology.
Nature, 409:922-927, 2010.

131
Dorsett Y. and Tuschl T.
siRNAs: Applications in functional genomics and potential as therapeutics.
Nat. Rev. Drug Discovery, 3:318-329, 2004.

132
Russel R.
RNA misfolding and the action of chaperones.
Front. Biosci., 13:1-20, 2008.

133
Nykypanchuk D., Maye M.M., van der Lelie D., and Gang O.
DNA-guided crystallization of colloidal nanoparticles.
Nature, 451:549-552, 2008.

134
Gotoh O. and Tagashira Y.
Stabilities of nearest-neighbor doublets in double-helical DNA determined by fitting calculated melting profiles to observed profiles.
Biopolymers, 20:1033-1042, 1981.

135
Vologodskii A.V., Amirikyan B.R., Lyubchenko Y.L., and Frank-Kamenetskii M.D.
Allowance for heterogeneous stacking in the DNA helix-coil transition theory.
J. Biomol. Struct. Dyn., 2:131-48, 1984.

136
Manosas M., Collin D., and Ritort F.
Force dependent fragility in RNA hairpins.
Phys. Rev. Lett., 96:218301, 2006.

137
Bornschlögl T. and Rief M.
Single molecule unzipping of coiled coils: sequence resolved stability profiles.
Phys. Rev. Lett., 96:118102, 2006.

138
Seol Y., Skinner G.M., and Visscher K.
Stretching of homopolymeric RNA reveals single-stranded helices and base-stacking.
Phys. Rev. Lett., 98:158103, 2007.

139
Dessinges M.-N., Maier B., Zhang Y., Peliti M., Bensimon D., and Croquette V.
Stretching single stranded DNA, a model polyelectrolyte.
Phys. Rev. Lett., 89(24):248102, 2002.

140
Kirkpatrick S., Gelatt Jr. C.D., and Vecchi M.P.
Optimization by simulated annealing.
Science, 220:671-680, 1983.

141
Tan Z.-J. and Chen S.-J.
Nucleic acid helix stability: Effects of salt concentration, cation valence and size, and chain length.
Biophys. J., 90:1175-1190, 2006.

142
Alemayehu S., Fish D.J., Brewood G.P., Horne M.T., Manyanga F., Dickman R., Yates I., and Benight A.S.
Influence of buffer species on the thermodynamics of short DNA duplex melting: Sodium phosphate versus sodium cacodylate.
J. Phys. Chem. B, 113:2578-2586, 2009.

143
Owczarzy R., You Y., Moreira B.G., Manthey J.A., Huang L., Behlke M.A., and Walder J.A.
Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures.
Biochemistry, 43:3537-3554, 2004.

144
Nakano S., Fujimoto M., Hara H., and Sugimoto N.
Nucleic acid duplex stability: influence of base composition on cation effects.
Nucleic Acids Res., 27:2957-2965, 1999.

145
Cheatham III T.E. and Kollman P.A.
Md simulations highlight the structural differences among DNA:DNA, RNA:RNA and DNA:RNA hybrid duplexes.
J. Am. Chem. Soc., 119:4805-4825, 1997.

146
Owczarzy R.
Melting temperatures of nucleic acids: Discrepancies in analysis.
Biophys. Chem., 117:207-215., 2005.

147
Hatch K., Danilowicz C., Coljee V., and Prentiss M.
Measurements of the hysteresis in unzipping and rezipping double-stranded DNA.
Phys. Rev. E, 75:051908, 2007.

148
Huguet J.M., Forns N., and Ritort F.
Statistical properties of metastable intermediates in DNA unzipping.
Phys. Rev. Lett., 103:248106, 2009.

149
Greenleaf W.J., Woodside M.T, Abbondanzieri E.A, and Block S.M.
Passive all-optical force clamp for high-resolution laser trapping.
Phys. Rev. Lett., 95:208102, 2005.

150
Meresman H., Wills J.B., Summers M., McGloin D., and Reid J.P.
Manipulation and characterisation of accumulation and coarse mode aerosol particles using a Bessel beam trap.
Phys. Chem. Chem. Phys., 11:11333-11339, 2009.

151
Evans E. and Williams P.
Physics of Biomolecules and Cells.
Proceedings of the Les Houches Summer School, Session LXXV, edited by H. Flyvberg and F. Julicher. Springer-Verlag, Berlin, 2002.

152
Zwanzig R.
Nonequilibrium Statistical Mechanics.
Oxford University Press, New York, 1st ed., 2001.

153
Ritort F., Bustamante C., and Tinoco Jr. I.
A two-state kinetic model for the unfolding of single molecules by mechanical force.
Proc. Nat. Acad. Sci., 99:13544, 2002.

154
Manosas M., Mossa A., Forns N., Huguet J.M, and Ritort F.
Dynamic force spectroscopy of DNA hairpins (II): Irreversibility and dissipation.
J. Stat. Mech (Theor. and Exp.), P02061, 2009.

155
Mao H., Arias-Gonzalez J.R., Smith S.B., Tinoco I., and Bustamante C.
Temperature control methods in a laser tweezers system.
Biophys J., 89:1308-1316, 2005.

156
Sanger F., Nicklen S., and Coulson A.R.
DNA sequencing with chain-terminating inhibitors.
Proc. Natl. Acad. Sci. USA, 74:5463-7, 1977.

157
Stout A.L.
Detection and characterization of individual intermolecular bonds using optical tweezers.
Biophys. J., 80:2976-2986, 2001.

158
Clarke J., Wu H.C., Jayasinghe L., Patel A., Reid A., and Bayley H.
Continuous base identification for single-molecule nanopore DNA sequencing.
Nature Nanotech., 4:265-270, 2009.

159
J.D. Jackson.
Classical electrodynamics.
Wiley, New York, 2d ed edition, 1975.

160
Bouchiat C., Wang M.D., Allemand J., Strick T., Block S.M., and Croquette V.
Estimating the persistence length of a worm-like chain molecule from force-extension measurements.
Biophys. J., 76:409-413, 1999.

161
Wang M.D., Yin H., Landick R., Gelles J., and Block S.M.
Stretching DNA with optical tweezers.
Biophys. J., 72:1335-1346, 1997.

162
Press W.H., Teukolsky S.A., Vetterling W.T., and Flannery B.P.
Numerical Recipes in C: The Art of Scientific Computing.
Cambridge University Press, New York, 2nd Ed., 1992.



Subsections

JM Huguet 2014-02-12