Biophys. J. -- Collected Papers

NUCLEIC ACIDS

From the Current Issue: January 15 2007; 92 (2) [Table of Contents]

There are no NUCLEIC ACIDS articles in the current issue.

From Past Issues:

Haijia Yu, Jinsong Ren, and Xiaogang Qu: Time-Dependent DNA Condensation Induced by Amyloid ß-Peptide
Biophys. J. 2007. 92:185-191. [Abstract] [Full Text] [PDF]

Satoshi Yamasaki, Shugo Nakamura, Tohru Terada, and Kentaro Shimizu: Mechanism of the Difference in the Binding Affinity of E. coli tRNA^Gln to Glutaminyl-tRNA Synthetase Caused by Noninterface Nucleotides in Variable Loop
Biophys. J. 2007. 92:192-200. [Abstract] [Full Text] [PDF]

Alexey K. Mazur: Evaluation of Elastic Properties of Atomistic DNA Models
Biophys. J. 2006. 91:4507-4518. [Abstract] [Full Text] [PDF]

Jory Z. Ruscio and Alexey Onufriev: A Computational Study of Nucleosomal DNA Flexibility
Biophys. J. 2006. 91:4121-4132. [Abstract] [Full Text] [PDF]

M. T. Horne, D. J. Fish, and A. S. Benight: Statistical Thermodynamics and Kinetics of DNA Multiplex Hybridization Reactions
Biophys. J. 2006. 91:4133-4153. [Abstract] [Full Text] [PDF]

Gregory J. Gemmen, Rachel Millin, and Douglas E. Smith: Dynamics of Single DNA Looping and Cleavage by Sau3AI and Effect of Tension Applied to the DNA
Biophys. J. 2006. 91:4154-4165. [Abstract] [Full Text] [PDF]

Bryant S. Fujimoto, Gregory P. Brewood, and J. Michael Schurr: Torsional Rigidities of Weakly Strained DNAs
Biophys. J. 2006. 91:4166-4179. [Abstract] [Full Text] [PDF]

Jaime M. Ferreira and Richard D. Sheardy: Enthalpy of the B-to-Z Conformational Transition of a DNA Oligonucleotide Determined by Isothermal Titration Calorimetry
Biophys. J. 2006. 91:3383-3389. [Abstract] [Full Text] [PDF]

Srinivasaraghavan Kannan, Kai Kohlhoff, and Martin Zacharias: B-DNA Under Stress: Over- and Untwisting of DNA during Molecular Dynamics Simulations
Biophys. J. 2006. 91:2956-2965. [Abstract] [Full Text] [PDF]

Simon J. Green, Daniel Lubrich, and Andrew J. Turberfield: DNA Hairpins: Fuel for Autonomous DNA Devices
Biophys. J. 2006. 91:2966-2975. [Abstract] [Full Text] [PDF]

Mika A. Kastenholz, Thomas U. Schwartz, and Philippe H. Hunenberger: The Transition between the B and Z Conformations of DNA Investigated by Targeted Molecular Dynamics Simulations with Explicit Solvation
Biophys. J. 2006. 91:2976-2990. [Abstract] [Full Text] [PDF]

Lou-sing Kan, Laura Pasternack, Ming-Tsair Wey, Yu-Yu Tseng, and Dee-Hua Huang: The Paperclip Triplex: Understanding the Role of Apex Residues in Tight Turns
Biophys. J. 2006. 91:2552-2563. [Abstract] [Full Text] [PDF]

Arthi Jayaraman, Carol K. Hall, and Jan Genzer: Computer Simulation Study of Molecular Recognition in Model DNA Microarrays
Biophys. J. 2006. 91:2227-2236. [Abstract] [Full Text] [PDF]

Boualem Hammouda and David Worcester: The Denaturation Transition of DNA in Mixed Solvents
Biophys. J. 2006. 91:2237-2242. [Abstract] [Full Text] [PDF]

Anan B. Copty, Yair Neve-Oz, Itai Barak, Michael Golosovsky, and Dan Davidov: Evidence for a Specific Microwave Radiation Effect on the Green Fluorescent Protein
Biophys. J. 2006. 91:1413-1423. [Abstract] [Full Text] [PDF]

Yaowu Xiao, Mingsheng Guo, Kevin Parker, and M. Shane Hutson: Wavelength-Dependent Collagen Fragmentation during Mid-IR Laser Ablation
Biophys. J. 2006. 91:1424-1432. [Abstract] [Full Text] [PDF]

Jakub Psencik, Juan B. Arellano, Teemu P. Ikonen, Carles M. Borrego, Pasi A. Laurinmaki, Sarah J. Butcher, Ritva E. Serimaa, and Roman Tuma: Internal Structure of Chlorosomes from Brown-Colored Chlorobium Species and the Role of Carotenoids in Their Assembly
Biophys. J. 2006. 91:1433-1440. [Abstract] [Full Text] [PDF]

R. Efremov, V. I. Gordeliy, J. Heberle, and G. Buldt: Time-Resolved Microspectroscopy on a Single Crystal of Bacteriorhodopsin Reveals Lattice-Induced Differences in the Photocycle Kinetics
Biophys. J. 2006. 91:1441-1451. [Abstract] [Full Text] [PDF]

Jurgen Baier, Tim Maisch, Max Maier, Eva Engel, Michael Landthaler, and Wolfgang Baumler: Singlet Oxygen Generation by UVA Light Exposure of Endogenous Photosensitizers
Biophys. J. 2006. 91:1452-1459. [Abstract] [Full Text] [PDF]

Jozica Dolenc, Riccardo Baron, Chris Oostenbrink, Joze Koller, and Wilfred F. van Gunsteren: Configurational Entropy Change of Netropsin and Distamycin upon DNA Minor-Groove Binding
Biophys. J. 2006. 91:1460-1470. [Abstract] [Full Text] [PDF]

Martin Zacharias: Minor Groove Deformability of DNA: A Molecular Dynamics Free Energy Simulation Study
Biophys. J. 2006. 91:882-891. [Abstract] [Full Text] [PDF]

Lourdes Campos, Nuria Valls, Lourdes Urpi, Catherine Gouyette, Trinidad Sanmartin, Michael Richter, Elida Alechaga, Alicia Santaolalla, Roberto Baldini, Marc Creixell, Ruth Ciurans, Petr Skokan, Joan Pous, and Juan A. Subirana: Overview of the Structure of All-AT Oligonucleotides: Organization in Helices and Packing Interactions
Biophys. J. 2006. 91:892-903. [Abstract] [Full Text] [PDF]

Christina E. B. Caesar, Richard Johnsson, Ulf Ellervik, Keith R. Fox, Per Lincoln, and Bengt Norden: A Polarized-Light Spectroscopy Study of Interactions of a Hairpin Polyamide with DNA
Biophys. J. 2006. 91:904-911. [Abstract] [Full Text] [PDF]

Christopher Stanley and Donald C. Rau: Preferential Hydration of DNA: The Magnitude and Distance Dependence of Alcohol and Polyol Interactions
Biophys. J. 2006. 91:912-920. [Abstract] [Full Text] [PDF]

Maryna V. Krasovska, Jana Sefcikova, Kamila Reblova, Bohdan Schneider, Nils G. Walter, and Jiri Sponer: Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme
Biophys. J. 2006. 91:626-638. [Abstract] [Full Text] [PDF]

Hong Shen, Yueyue Hu, and W. M. Saltzman: DNA Diffusion in Mucus: Effect of Size, Topology of DNAs, and Transfection Reagents
Biophys. J. 2006. 91:639-644. [Abstract] [Full Text] [PDF]

Yan Zeng and Giovanni Zocchi: Mismatches and Bubbles in DNA
Biophys. J. 2006. 90:4522-4529. [Abstract] [Full Text] [PDF]

Se Bok Jang, Li-Wei Hung, Mi Suk Jeong, Elizabeth L. Holbrook, Xiaoying Chen, Douglas H. Turner, and Stephen R. Holbrook: The Crystal Structure at 1.5 Å Resolution of an RNA Octamer Duplex Containing Tandem G·U Basepairs
Biophys. J. 2006. 90:4530-4537. [Abstract] [Full Text] [PDF]

J. T. Mannion, C. H. Reccius, J. D. Cross, and H. G. Craighead: Conformational Analysis of Single DNA Molecules Undergoing Entropically Induced Motion in Nanochannels
Biophys. J. 2006. 90:4538-4545. [Abstract] [Full Text] [PDF]

William B. Sherman and Nadrian C. Seeman: Design of Minimally Strained Nucleic Acid Nanotubes
Biophys. J. 2006. 90:4546-4557. [Abstract] [Full Text] [PDF]

Ying Zhang, Valeria T. Milam, David J. Graves, and Daniel A. Hammer: Differential Adhesion of Microspheres Mediated by DNA Hybridization I: Experiment
Biophys. J. 2006. 90:4128-4136. [Abstract] [Full Text] [PDF]

Ulrich Rant, Kenji Arinaga, Marc Tornow, Yong Woon Kim, Roland R. Netz, Shozo Fujita, Naoki Yokoyama, and Gerhard Abstreiter: Dissimilar Kinetic Behavior of Electrically Manipulated Single- and Double-Stranded DNA Tethered to a Gold Surface
Biophys. J. 2006. 90:3666-3671. [Abstract] [Full Text] [PDF]

Meredith Newby Lambert, Eva Vocker, Seth Blumberg, Stefanie Redemann, Arivalagan Gajraj, Jens-Christian Meiners, and Nils G. Walter: Mg²⁺-Induced Compaction of Single RNA Molecules Monitored by Tethered Particle Microscopy
Biophys. J. 2006. 90:3672-3685. [Abstract] [Full Text] [PDF]

Haiyuan Zhang, Haijia Yu, Jinsong Ren, and Xiaogang Qu: Reversible B/Z-DNA Transition under the Low Salt Condition and Non-B-Form PolydApolydT Selectivity by a Cubane-Like Europium-L-Aspartic Acid Complex
Biophys. J. 2006. 90:3203-3207. [Abstract] [Full Text] [PDF]

Gerald S. Manning: The Contribution of Transient Counterion Imbalances to DNA Bending Fluctuations
Biophys. J. 2006. 90:3208-3215. [Abstract] [Full Text] [PDF]

Xingguo Liang, Heiko Kuhn, and Maxim D. Frank-Kamenetskii: Monitoring Single-Stranded DNA Secondary Structure Formation by Determining the Topological State of DNA Catenanes
Biophys. J. 2006. 90:2877-2889. [Abstract] [Full Text] [PDF]

Andre Barthel and Martin Zacharias: Conformational Transitions in RNA Single Uridine and Adenosine Bulge Structures: A Molecular Dynamics Free Energy Simulation Study
Biophys. J. 2006. 90:2450-2462. [Abstract] [Full Text] [PDF]

Xuesong Shi and Robert B. Macgregor Jr.: Temperature Dependence of the Volumetric Parameters of Drug Binding to Poly[d(A-T)]·Poly[d(A-T)] and Poly(dA)·Poly(dT)
Biophys. J. 2006. 90:1729-1738. [Abstract] [Full Text] [PDF]

Binh Nguyen, Jaroslav Stanek, and W. David Wilson: Binding-Linked Protonation of a DNA Minor-Groove Agent
Biophys. J. 2006. 90:1319-1328. [Abstract] [Full Text] [PDF]

Anjana Sen and Peter E. Nielsen: Unique Properties of Purine/Pyrimidine Asymmetric PNA·DNA Duplexes: Differential Stabilization of PNA·DNA Duplexes by Purines in the PNA Strand
Biophys. J. 2006. 90:1329-1337. [Abstract] [Full Text] [PDF]

Christopher M. Barbieri and Daniel S. Pilch: Complete Thermodynamic Characterization of the Multiple Protonation Equilibria of the Aminoglycoside Antibiotic Paromomycin: A Calorimetric and Natural Abundance ¹⁵N NMR Study
Biophys. J. 2006. 90:1338-1349. [Abstract] [Full Text] [PDF]

Yuko Yoshikawa, Kohji Hizume, Yoshiko Oda, Kunio Takeyasu, Sumiko Araki, and Kenichi Yoshikawa: Protective Effect of Vitamin C against Double-Strand Breaks in Reconstituted Chromatin Visualized by Single-Molecule Observation
Biophys. J. 2006. 90:993-999. [Abstract] [Full Text] [PDF]

Elena Cubero, F. Javier Luque, and Modesto Orozco: Theoretical Study of the Hoogsteen–Watson-Crick Junctions in DNA
Biophys. J. 2006. 90:1000-1008. [Abstract] [Full Text] [PDF]

J. Zhou, S. K. Gregurick, S. Krueger, and F. P. Schwarz: Conformational Changes in Single-Strand DNA as a Function of Temperature by SANS
Biophys. J. 2006. 90:544-551. [Abstract] [Full Text] [PDF]

Pan T. X. Li, Delphine Collin, Steven B. Smith, Carlos Bustamante, and Ignacio Tinoco Jr.: Probing the Mechanical Folding Kinetics of TAR RNA by Hopping, Force-Jump, and Force-Ramp Methods
Biophys. J. 2006. 90:250-260. [Abstract] [Full Text] [PDF]

Takashi Sakamoto, Atsushi Mahara, Koichi Yamagata, Reiko Iwase, Tetsuji Yamaoka, and Akira Murakami: Evaluation of Dynamic Features of Escherichia coli 16S Ribosomal RNA in Homogeneous Physiological Solution
Biophys. J. 2005. 89:4122-4128. [Abstract] [Full Text] [PDF]

Sobhan Sen, Nicole A. Paraggio, Latha A. Gearheart, Ellen E. Connor, Ala Issa, Robert S. Coleman, David M. Wilson 3rd, Michael D. Wyatt, and Mark A. Berg: Effect of Protein Binding on Ultrafast DNA Dynamics: Characterization of a DNA:APE1 Complex
Biophys. J. 2005. 89:4129-4138. [Abstract] [Full Text] [PDF]

Jacob R. Borden, Carlos J. Paredes, and Eleftherios Terry Papoutsakis: Diffusion, Mixing, and Associated Dye Effects in DNA-Microarray Hybridizations
Biophys. J. 2005. 89:3277-3284. [Abstract] [Full Text] [PDF]

Daniel Coman and Irina M. Russu: A Nuclear Magnetic Resonance Investigation of the Energetics of Basepair Opening Pathways in DNA
Biophys. J. 2005. 89:3285-3292. [Abstract] [Full Text] [PDF]

D. Djuranovic and B. Hartmann: Molecular Dynamics Studies on Free and Bound Targets of the Bovine Papillomavirus Type I E2 Protein: The Protein Binding Effect on DNA and the Recognition Mechanism
Biophys. J. 2005. 89:2542-2551. [Abstract] [Full Text] [PDF]

Christopher B. Stanley, Helen Hong, and Helmut H. Strey: DNA Cholesteric Pitch as a Function of Density and Ionic Strength
Biophys. J. 2005. 89:2552-2557. [Abstract] [Full Text] [PDF]

Alessandro Podesta, Marco Indrieri, Doriano Brogioli, Gerald S. Manning, Paolo Milani, Rosalinda Guerra, Laura Finzi, and David Dunlap: Positively Charged Surfaces Increase the Flexibility of DNA
Biophys. J. 2005. 89:2558-2563. [Abstract] [Full Text] [PDF]

Chongli Yuan, Elizabeth Rhoades, Daniel M. Heuer, and Lynden A. Archer: Mismatch-Induced DNA Unbending upon Duplex Opening
Biophys. J. 2005. 89:2564-2573. [Abstract] [Full Text] [PDF]

Vladimir B. Teif: Ligand-Induced DNA Condensation: Choosing the Model
Biophys. J. 2005. 89:2574-2587. [Abstract] [Full Text] [PDF]

Michael A. Morgan, Kenji Okamoto, Jason D. Kahn, and Douglas S. English: Single-Molecule Spectroscopic Determination of Lac Repressor-DNA Loop Conformation
Biophys. J. 2005. 89:2588-2596. [Abstract] [Full Text] [PDF]

Francesco Vanzi, Yasuharu Takagi, Henry Shuman, Barry S. Cooperman, and Yale E. Goldman: Mechanical Studies of Single Ribosome/mRNA Complexes
Biophys. J. 2005. 89:1909-1919. [Abstract] [Full Text] [PDF]

Marcelo Nollmann, Olwyn Byron, and W. Marshall Stark: Behavior of Tn3 Resolvase in Solution and Its Interaction with res
Biophys. J. 2005. 89:1920-1931. [Abstract] [Full Text] [PDF]

Jie Yang and Donald C. Rau: Incomplete Ion Dissociation Underlies the Weakened Attraction between DNA Helices at High Spermidine Concentrations
Biophys. J. 2005. 89:1932-1940. [Abstract] [Full Text] [PDF]

Ioulia Rouzina, Kiran Pant, Richard L. Karpel, and Mark C. Williams: Theory of Electrostatically Regulated Binding of T4 Gene 32 Protein to Single- and Double-Stranded DNA
Biophys. J. 2005. 89:1941-1956. [Abstract] [Full Text] [PDF]

Hans Binder and Stephan Preibisch: Specific and Nonspecific Hybridization of Oligonucleotide Probes on Microarrays
Biophys. J. 2005. 89:337-352. [Abstract] [Full Text] [PDF]

Micah McCauley, Philip R. Hardwidge, L. James Maher III, and Mark C. Williams: Dual Binding Modes for an HMG Domain from Human HMGB2 on DNA
Biophys. J. 2005. 89:353-364. [Abstract] [Full Text] [PDF]

Elena E. Merkina and Keith R. Fox: Kinetic Stability of Intermolecular DNA Quadruplexes
Biophys. J. 2005. 89:365-373. [Abstract] [Full Text] [PDF]

Tarita Biver, Angela De Biasi, Fernando Secco, Marcella Venturini, and Sergiy Yarmoluk: Cyanine Dyes as Intercalating Agents: Kinetic and Thermodynamic Studies on the DNA/Cyan40 and DNA/CCyan2 Systems
Biophys. J. 2005. 89:374-383. [Abstract] [Full Text] [PDF]

G. Charvin, T. R. Strick, D. Bensimon, and V. Croquette: Topoisomerase IV Bends and Overtwists DNA upon Binding
Biophys. J. 2005. 89:384-392. [Abstract] [Full Text] [PDF]

Anatoly A. Zinchenko and Kenichi Yoshikawa: Na⁺ Shows a Markedly Higher Potential than K⁺ in DNA Compaction in a Crowded Environment
Biophys. J. 2005. 88:4118-4123. [Abstract] [Full Text] [PDF]

G. Charvin, A. Vologodskii, D. Bensimon, and V. Croquette: Braiding DNA: Experiments, Simulations, and Models
Biophys. J. 2005. 88:4124-4136. [Abstract] [Full Text] [PDF]

Quan Du, Maria Vologodskaia, Heiko Kuhn, Maxim Frank-Kamenetskii, and Alexander Vologodskii: Gapped DNA and Cyclization of Short DNA Fragments
Biophys. J. 2005. 88:4137-4145. [Abstract] [Full Text] [PDF]

Chad S. Braun, Mark T. Fisher, Donald A. Tomalia, Gary S. Koe, Janet G. Koe, and C. Russell Middaugh: A Stopped-Flow Kinetic Study of the Assembly of Nonviral Gene Delivery Complexes
Biophys. J. 2005. 88:4146-4158. [Abstract] [Full Text] [PDF]

Olivier Delalande, Jaroslav Malina, Viktor Brabec, and Jiri Kozelka: Chiral Differentiation of DNA Adducts Formed by Enantiomeric Analogues of Antitumor Cisplatin Is Sequence-Dependent
Biophys. J. 2005. 88:4159-4169. [Abstract] [Full Text] [PDF]

Jay R. Unruh, Giridharan Gokulrangan, G. H. Lushington, Carey K. Johnson, and George S. Wilson: Orientational Dynamics and Dye-DNA Interactions in a Dye-Labeled DNA Aptamer
Biophys. J. 2005. 88:3455-3465. [Abstract] [Full Text] [PDF]

Filip Razga, Jaroslav Koca, Jiri Sponer, and Neocles B. Leontis: Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-Minor Motif and Nominally Unpaired Bases
Biophys. J. 2005. 88:3466-3485. [Abstract] [Full Text] [PDF]

Damien Baigl and Kenichi Yoshikawa: Dielectric Control of Counterion-Induced Single-Chain Folding Transition of DNA
Biophys. J. 2005. 88:3486-3493. [Abstract] [Full Text] [PDF]

J. A. Abels, F. Moreno-Herrero, T. van der Heijden, C. Dekker, and N. H. Dekker: Single-Molecule Measurements of the Persistence Length of Double-Stranded RNA
Biophys. J. 2005. 88:2737-2744. [Abstract] [Full Text] [PDF]

Danfeng Yao, Junyoung Kim, Fang Yu, Peter E. Nielsen, Eva-Kathrin Sinner, and Wolfgang Knoll: Surface Density Dependence of PCR Amplicon Hybridization on PNA/DNA Probe Layers
Biophys. J. 2005. 88:2745-2751. [Abstract] [Full Text] [PDF]

J. D. Weeks, J. B. Lucks, Y. Kafri, C. Danilowicz, D. R. Nelson, and M. Prentiss: Pause Point Spectra in DNA Constant-Force Unzipping
Biophys. J. 2005. 88:2752-2765. [Abstract] [Full Text] [PDF]

Wei Ge, Bohdan Schneider, and Wilma K. Olson: Knowledge-Based Elastic Potentials for Docking Drugs or Proteins with Nucleic Acids
Biophys. J. 2005. 88:1166-1190. [Abstract] [Full Text] [PDF]

Yongjun Lu, Brock D. Weers, and Nancy C. Stellwagen: Intrinsic Curvature in the VP1 Gene of SV40: Comparison of Solution and Gel Results
Biophys. J. 2005. 88:1191-1206. [Abstract] [Full Text] [PDF]

Vendula Bursova, Jana Kasparkova, Ctirad Hofr, and Viktor Brabec: Effects of Monofunctional Adducts of Platinum(II) Complexes on Thermodynamic Stability and Energetics of DNA Duplexes
Biophys. J. 2005. 88:1207-1214. [Abstract] [Full Text] [PDF]

E. Raspaud, D. Durand, and F. Livolant: Interhelical Spacing in Liquid Crystalline Spermine and Spermidine-DNA Precipitates
Biophys. J. 2005. 88:392-403. [Abstract] [Full Text] [PDF]

Andy Sischka, Katja Toensing, Rainer Eckel, Sven David Wilking, Norbert Sewald, Robert Ros, and Dario Anselmetti: Molecular Mechanisms and Kinetics between DNA and DNA Binding Ligands
Biophys. J. 2005. 88:404-411. [Abstract] [Full Text] [PDF]

Alla Shundrovsky, Thomas J. Santangelo, Jeffrey W. Roberts, and Michelle D. Wang: A Single-Molecule Technique to Study Sequence-Dependent Transcription Pausing
Biophys. J. 2004. 87:3945-3953. [Abstract] [Full Text] [PDF]

Anton S. Petrov, Gene Lamm, and George R. Pack: The Triplex-Hairpin Transition in Cytosine-Rich DNA
Biophys. J. 2004. 87:3954-3973. [Abstract] [Full Text] [PDF]

Nichola C. Garbett, Nicholas B. Hammond, and David E. Graves: Influence of the Amino Substituents in the Interaction of Ethidium Bromide with DNA
Biophys. J. 2004. 87:3974-3981. [Abstract] [Full Text] [PDF]

F. J. Solis, R. Bash, J. Yodh, S. M. Lindsay, and D. Lohr: A Statistical Thermodynamic Model Applied to Experimental AFM Population and Location Data Is Able to Quantify DNA-Histone Binding Strength and Internucleosomal Interaction Differences between Acetylated and Unacetylated Nucleosomal Arrays
Biophys. J. 2004. 87:3372-3387. [Abstract] [Full Text] [PDF]

U. Bockelmann, P. Thomen, and F. Heslot: Dynamics of the DNA Duplex Formation Studied by Single Molecule Force Measurements
Biophys. J. 2004. 87:3388-3396. [Abstract] [Full Text] [PDF]

Kamila Reblova, Nad'a Spackova, Jaroslav Koca, Neocles B. Leontis, and Jiri Sponer: Long-Residency Hydration, Cation Binding, and Dynamics of Loop E/Helix IV rRNA-L25 Protein Complex
Biophys. J. 2004. 87:3397-3412. [Abstract] [Full Text] [PDF]

Congju Chen and Irina M. Russu: Sequence-Dependence of the Energetics of Opening of AT Basepairs in DNA
Biophys. J. 2004. 87:2545-2551. [Abstract] [Full Text] [PDF]

Renaud Fulconis, Aurelien Bancaud, Jean-Francois Allemand, Vincent Croquette, Marie Dutreix, and Jean-Louis Viovy: Twisting and Untwisting a Single DNA Molecule Covered by RecA Protein
Biophys. J. 2004. 87:2552-2563. [Abstract] [Full Text] [PDF]

Nina Y. Sidorova and Donald C. Rau: Differences between EcoRI Nonspecific and "Star" Sequence Complexes Revealed by Osmotic Stress
Biophys. J. 2004. 87:2564-2576. [Abstract] [Full Text] [PDF]

Goran Pljevaljcic, David P. Millar, and Ashok A. Deniz: Freely Diffusing Single Hairpin Ribozymes Provide Insights into the Role of Secondary Structure and Partially Folded States in RNA Folding
Biophys. J. 2004. 87:457-467. [Abstract] [Full Text] [PDF]

Sean Ferree and Harvey W. Blanch: The Hydrodynamics of DNA Electrophoretic Stretch and Relaxation in a Polymer Solution
Biophys. J. 2004. 87:468-475. [Abstract] [Full Text] [PDF]

Nicola H. Green, Philip M. Williams, Omar Wahab, Martyn C. Davies, Clive J. Roberts, Saul J. B. Tendler, and Stephanie Allen: Single-Molecule Investigations of RNA Dissociation
Biophys. J. 2004. 86:3811-3821. [Abstract] [Full Text] [PDF]

M. Bastos, V. Castro, G. Mrevlishvili, and J. Teixeira: Hydration of ds-DNA and ss-DNA by Neutron Quasielastic Scattering
Biophys. J. 2004. 86:3822-3827. [Abstract] [Full Text] [PDF]

B. Banerjee, S. Balasubramanian, G. Ananthakrishna, T. V. Ramakrishnan, and G. V. Shivashankar: Tracking Operator State Fluctuations in Gene Expression in Single Cells
Biophys. J. 2004. 86:3052-3059. [Abstract] [Full Text] [PDF]

Marcelo Nollmann, W. Marshall Stark, and Olwyn Byron: Low-Resolution Reconstruction of a Synthetic DNA Holliday Junction
Biophys. J. 2004. 86:3060-3069. [Abstract] [Full Text] [PDF]

Ayome Abibi, Ekaterina Protozanova, Vadim V. Demidov, and Maxim D. Frank-Kamenetskii: Specific versus Nonspecific Binding of Cationic PNAs to Duplex DNA
Biophys. J. 2004. 86:3070-3078. [Abstract] [Full Text] [PDF]

Christopher A. Sucato, David P. Rangel, Dan Aspleaf, Bryant S. Fujimoto, and J. Michael Schurr: Monte Carlo Simulations of Locally Melted Supercoiled DNAs in 20 mM Ionic Strength
Biophys. J. 2004. 86:3079-3096. [Abstract] [Full Text] [PDF]

Haribabu Arthanari, Kristi Wojtuszewski, Ishita Mukerji, and Philip H. Bolton: Effects of HU Binding on the Equilibrium Cyclization of Mismatched, Curved, and Normal DNA
Biophys. J. 2004. 86:1625-1631. [Abstract] [Full Text] [PDF]

Raymond W. Friddle, Jennifer E. Klare, Shelley S. Martin, Michelle Corzett, Rod Balhorn, Enoch P. Baldwin, Ronald J. Baskin, and Aleksandr Noy: Mechanism of DNA Compaction by Yeast Mitochondrial Protein Abf2p
Biophys. J. 2004. 86:1632-1639. [Abstract] [Full Text] [PDF]

Thomas T. Perkins, Hung-Wen Li, Ravindra V. Dalal, Jeff Gelles, and Steven M. Block: Forward and Reverse Motion of Single RecBCD Molecules on DNA
Biophys. J. 2004. 86:1640-1648. [Abstract] [Full Text] [PDF]

Jin-Ok Kim, Young-Ae Lee, Byeong Hwa Yun, Sung Wook Han, Sam Tag Kwag, and Seog K. Kim: Binding of meso-Tetrakis(N-methylpyridinium-4-yl)porphyrin to AT Oligomers: Effect of Chain Length and the Location of the Porphyrin Stacking
Biophys. J. 2004. 86:1012-1017. [Abstract] [Full Text] [PDF]

Liming Ying, Samuel S. White, Andreas Bruckbauer, Lisa Meadows, Yuri E. Korchev, and David Klenerman: Frequency and Voltage Dependence of the Dielectrophoretic Trapping of Short Lengths of DNA and dCTP in a Nanopipette
Biophys. J. 2004. 86:1018-1027. [Abstract] [Full Text] [PDF]

Binh Nguyen, Donald Hamelberg, Christian Bailly, Pierre Colson, Jaroslav Stanek, Reto Brun, Stephen Neidle, and W. David Wilson: Characterization of a Novel DNA Minor-Groove Complex
Biophys. J. 2004. 86:1028-1041. [Abstract] [Full Text] [PDF]

Sergei Khrapunov and Michael Brenowitz: Comparison of the Effect of Water Release on the Interaction of the Saccharomyces cerevisiae TATA Binding Protein (TBP) with "TATA Box" Sequences Composed of Adenosine or Inosine
Biophys. J. 2004. 86:371-383. [Abstract] [Full Text] [PDF]

Ulrich Rant, Kenji Arinaga, Tsuyoshi Fujiwara, Shozo Fujita, Marc Tornow, Naoki Yokoyama, and Gerhard Abstreiter: Excessive Counterion Condensation on Immobilized ssDNA in Solutions of High Ionic Strength
Biophys. J. 2003. 85:3858-3864. [Abstract] [Full Text] [PDF]

Bae Wook Lee, Seok Joon Moon, Mi Ryung Youn, Jae Hyung Kim, Ho G. Jang, and Seog K. Kim: DNA Mediated Resonance Energy Transfer from 4',6-Diamidino-2-Phenylindole to [Ru(1,10-Phenanthroline)₂L]²⁺
Biophys. J. 2003. 85:3865-3871. [Abstract] [Full Text] [PDF]

David Pastre, Olivier Pietrement, Stephane Fusil, Fabrice Landousy, Josette Jeusset, Marie-Odile David, Loic Hamon, Eric Le Cam, and Alain Zozime: Adsorption of DNA to Mica Mediated by Divalent Counterions: A Theoretical and Experimental Study
Biophys. J. 2003. 85:2507-2518. [Abstract] [Full Text] [PDF]

Laurence R. Brewer, Raymond Friddle, Aleksandr Noy, Enoch Baldwin, Shelley S. Martin, Michele Corzett, Rod Balhorn, and Ronald J. Baskin: Packaging of Single DNA Molecules by the Yeast Mitochondrial Protein Abf2p
Biophys. J. 2003. 85:2519-2524. [Abstract] [Full Text] [PDF]

Marco Tonelli, Nikolai B. Ulyanov, Todd M. Billeci, Boleslaw Karwowski, Piotr Guga, Wojciech J. Stec, and Thomas L. James: Dynamic NMR Structures of [Rp]- and [Sp]-Phosphorothioated DNA-RNA Hybrids: Is Flexibility Required for RNase H Recognition?
Biophys. J. 2003. 85:2525-2538. [Abstract] [Full Text] [PDF]

Sean Ferree and Harvey W. Blanch: Electrokinetic Stretching of Tethered DNA
Biophys. J. 2003. 85:2539-2546. [Abstract] [Full Text] [PDF]

Richard Stefl, Thomas E. Cheatham III, Nad'a Spackova, Eva Fadrna, Imre Berger, Jaroslav Koca, and Jiri Sponer: Formation Pathways of a Guanine-Quadruplex DNA Revealed by Molecular Dynamics and Thermodynamic Analysis of the Substates
Biophys. J. 2003. 85:1787-1804. [Abstract] [Full Text] [PDF]

A. Madhumalar and Manju Bansal: Structural Insights into the Effect of Hydration and Ions on A-Tract DNA: A Molecular Dynamics Study
Biophys. J. 2003. 85:1805-1816. [Abstract] [Full Text] [PDF]

Stephanie Mangenot, Simon Keller, and Joachim Radler: Transport of Nucleosome Core Particles in Semidilute DNA Solutions
Biophys. J. 2003. 85:1817-1825. [Abstract] [Full Text] [PDF]

Anas M. Ababneh, C. C. Large, and S. Georghiou: Solvation of Nucleosides in Aqueous Mixtures of Organic Solvents: Relevance to DNA Open Basepairs
Biophys. J. 2003. 85:1111-1127. [Abstract] [Full Text] [PDF]

Mikio Kato, Shingo Hokabe, Shuji Itakura, Shinsei Minoshima, Yuri L. Lyubchenko, Theodor D. Gurkov, Hiroshi Okawara, Kuniaki Nagayama, and Nobuyoshi Shimizu: Interarm Interaction of DNA Cruciform Forming at a Short Inverted Repeat Sequence
Biophys. J. 2003. 85:402-408. [Abstract] [Full Text] [PDF]

Yongjun Lu, Brock D. Weers, and Nancy C. Stellwagen: Analysis of the Intrinsic Bend in the M13 Origin of Replication by Atomic Force Microscopy
Biophys. J. 2003. 85:409-415. [Abstract] [Full Text] [PDF]

Gilberto Villescas-Diaz and Martin Zacharias: Sequence Context Dependence of Tandem Guanine:Adenine Mismatch Conformations in RNA: A Continuum Solvent Analysis
Biophys. J. 2003. 85:416-425. [Abstract] [Full Text] [PDF]

Phiset Sa-Ardyen, Alexander V. Vologodskii, and Nadrian C. Seeman: The Flexibility of DNA Double Crossover Molecules
Biophys. J. 2003. 84:3829-3837. [Abstract] [Full Text] [PDF]

Therese E. Malliavin, Jocelyne Gau, Karim Snoussi, and Jean-Louis Leroy: Stability of the I-motif Structure Is Related to the Interactions between Phosphodiester Backbones
Biophys. J. 2003. 84:3838-3847. [Abstract] [Full Text] [PDF]

I. M. Kulic and H. Schiessel: Nucleosome Repositioning via Loop Formation
Biophys. J. 2003. 84:3197-3211. [Abstract] [Full Text] [PDF]

Daniel P. Aalberts, John M. Parman, and Noel L. Goddard: Single-Strand Stacking Free Energy from DNA Beacon Kinetics
Biophys. J. 2003. 84:3212-3217. [Abstract] [Full Text] [PDF]

Yi-Tao Long, Chen-Zhong Li, Heinz-Bernhard Kraatz, and Jeremy S. Lee: AC Impedance Spectroscopy of Native DNA and M-DNA
Biophys. J. 2003. 84:3218-3225. [Abstract] [Full Text] [PDF]

R. Ahmad, H. Arakawa, and H. A. Tajmir-Riahi: A Comparative Study of DNA Complexation with Mg(II) and Ca(II) in Aqueous Solution: Major and Minor Grooves Bindings
Biophys. J. 2003. 84:2460-2466. [Abstract] [Full Text] [PDF]

Roee Amit, Amos B. Oppenheim, and Joel Stavans: Increased Bending Rigidity of Single DNA Molecules by H-NS, a Temperature and Osmolarity Sensor
Biophys. J. 2003. 84:2467-2473. [Abstract] [Full Text] [PDF]

Earle Stellwagen and Nancy C. Stellwagen: Probing the Electrostatic Shielding of DNA with Capillary Electrophoresis
Biophys. J. 2003. 84:1855-1866. [Abstract] [Full Text] [PDF]

Xu Wang, Wei Cao, Aoneng Cao, and Luhua Lai: Thermodynamic Characterization of the Folding Coupled DNA Binding by the Monomeric Transcription Activator GCN4 Peptide
Biophys. J. 2003. 84:1867-1875. [Abstract] [Full Text] [PDF]

Chad S. Braun, Gouri S. Jas, Sirirat Choosakoonkriang, Gary S. Koe, Janet G. Smith, and C. Russell Middaugh: The Structure of DNA within Cationic Lipid/DNA Complexes
Biophys. J. 2003. 84:1114-1123. [Abstract] [Full Text] [PDF]

Vladimir S. Trubetskoy, Jon A. Wolff, and Vladimir G. Budker: The Role of a Microscopic Colloidally Stabilized Phase in Solubilizing Oligoamine-Condensed DNA Complexes
Biophys. J. 2003. 84:1124-1130. [Abstract] [Full Text] [PDF]

Laurence M. Edelman, Raymond Cheong, and Jason D. Kahn: Fluorescence Resonance Energy Transfer over $~$ 130 Basepairs in Hyperstable Lac Repressor-DNA Loops
Biophys. J. 2003. 84:1131-1145. [Abstract] [Full Text] [PDF]

J. C. Sitko, E. M. Mateescu, and H. G. Hansma: Sequence-Dependent DNA Condensation and the Electrostatic Zipper
Biophys. J. 2003. 84:419-431. [Abstract] [Full Text] [PDF]

Fu-Ming Chen, Feng Sha, Ko-Hsin Chin, and Shan-Ho Chou: Binding of Actinomycin D to Single-Stranded DNA of Sequence Motifs d(TGTCT_nG) and d(TGT_nGTCT)
Biophys. J. 2003. 84:432-439. [Abstract] [Full Text] [PDF]

T. M. Okonogi, S. C. Alley, A. W. Reese, P. B. Hopkins, and B. H. Robinson: Sequence-Dependent Dynamics of Duplex DNA: The Applicability of a Dinucleotide Model
Biophys. J. 2002. 83:3446-3459. [Abstract] [Full Text] [PDF]

Chia-Fu Chou, Jonas O. Tegenfeldt, Olgica Bakajin, Shirley S. Chan, Edward C. Cox, Nicholas Darnton, Thomas Duke, and Robert H. Austin: Electrodeless Dielectrophoresis of Single- and Double-Stranded DNA
Biophys. J. 2002. 83:2170-2179. [Abstract] [Full Text] [PDF]

Steven J. Koch, Alla Shundrovsky, Benjamin C. Jantzen, and Michelle D. Wang: Probing Protein-DNA Interactions by Unzipping a Single DNA Double Helix
Biophys. J. 2002. 83:1098-1105. [Abstract] [Full Text] [PDF]

Svetlana S. Zakharova, Wim Jesse, Claude Backendorf, Stefan U. Egelhaaf, Alain Lapp, and Johan R. C. van der Maarel: Dimensions of Plectonemically Supercoiled DNA
Biophys. J. 2002. 83:1106-1118. [Abstract] [Full Text] [PDF]

Svetlana S. Zakharova, Wim Jesse, Claude Backendorf, and Johan R. C. van der Maarel: Liquid Crystal Formation in Supercoiled DNA Solutions
Biophys. J. 2002. 83:1119-1129. [Abstract] [Full Text] [PDF]

Soomin Lee, Young-Ae Lee, Hyun Mee Lee, Jae Yang Lee, Dong Ho Kim, and Seog K. Kim: Rotation of Periphery Methylpyridine of meso-Tetrakis(n-N-methylpyridiniumyl)porphyrin (n = 2, 3, 4) and Its Selective Binding to Native and Synthetic DNAs
Biophys. J. 2002. 83:371-381. [Abstract] [Full Text] [PDF]

Lihua Wang, Brian E. Hingerty, A. R. Srinivasan, Wilma K. Olson, and Suse Broyde: Accurate Representation of B-DNA Double Helical Structure with Implicit Solvent and Counterions
Biophys. J. 2002. 83:382-406. [Abstract] [Full Text] [PDF]

Jay R. Wenner, Mark C. Williams, Ioulia Rouzina, and Victor A. Bloomfield: Salt Dependence of the Elasticity and Overstretching Transition of Single DNA Molecules
Biophys. J. 2002. 82:3160-3169. [Abstract] [Full Text] [PDF]

Laura B. Pasternack, Shwu-Bin Lin, Tsung-Mei Chin, Wei-Chen Lin, Dee-Hua Huang, and Lou-Sing Kan: Proton NMR Studies of 5'-d-(TC)₃ (CT)₃ (AG)₃-3' $---$ A Paperclip Triplex: The Structural Relevance of Turns
Biophys. J. 2002. 82:3170-3180. [Abstract] [Full Text] [PDF]

Lihong Jiang and Irina M. Russu: Internal Dynamics in a DNA Triple Helix Probed by ¹H-¹⁵N-NMR Spectroscopy
Biophys. J. 2002. 82:3181-3185. [Abstract] [Full Text] [PDF]

Filip Lankas, Thomas E. Cheatham III, Nad'a Spackova, Pavel Hobza, Jorg Langowski, and Jiri Sponer: Critical Effect of the N2 Amino Group on Structure, Dynamics, and Elasticity of DNA Polypurine Tracts
Biophys. J. 2002. 82:2592-2609. [Abstract] [Full Text] [PDF]

U. Bockelmann, Ph. Thomen, B. Essevaz-Roulet, V. Viasnoff, and F. Heslot: Unzipping DNA with Optical Tweezers: High Sequence Sensitivity and Force Flips
Biophys. J. 2002. 82:1537-1553. [Abstract] [Full Text] [PDF]

Nicolas Foloppe, Brigitte Hartmann, Lennart Nilsson, and Alexander D. MacKerell Jr.: Intrinsic Conformational Energetics Associated with the Glycosyl Torsion in DNA: A Quantum Mechanical Study
Biophys. J. 2002. 82:1554-1569. [Abstract] [Full Text] [PDF]

Vladimir G. Budker, Paul M. Slattum, Sean D. Monahan, and Jon A. Wolff: Entrapment and Condensation of DNA in Neutral Reverse Micelles
Biophys. J. 2002. 82:1570-1579. [Abstract] [Full Text] [PDF]

Bryant S. Fujimoto and J. Michael Schurr: Monte Carlo Simulations of Supercoiled DNAs Confined to a Plane
Biophys. J. 2002. 82:944-962. [Abstract] [Full Text] [PDF]

Noritada Kaji, Masanori Ueda, and Yoshinobu Baba: Molecular Stretching of Long DNA in Agarose Gel Using Alternating Current Electric Fields
Biophys. J. 2002. 82:335-344. [Abstract] [Full Text] [PDF]

Stephanie Mangenot, Amelie Leforestier, Patrice Vachette, Dominique Durand, and Francoise Livolant: Salt-Induced Conformation and Interaction Changes of Nucleosome Core Particles
Biophys. J. 2002. 82:345-356. [Abstract] [Full Text] [PDF]

Xian-E. Cai and Jie Yang: Molecular Forces for the Binding and Condensation of DNA Molecules
Biophys. J. 2002. 82:357-365. [Abstract] [Full Text] [PDF]

S. Patrick Walton, Gregory N. Stephanopoulos, Martin L. Yarmush, and Charles M. Roth: Thermodynamic and Kinetic Characterization of Antisense Oligodeoxynucleotide Binding to a Structured mRNA
Biophys. J. 2002. 82:366-377. [Abstract] [Full Text] [PDF]

Philip Serwer and Shirley J. Hayes: Partially Condensed DNA Conformations Observed by Single Molecule Fluorescence Microscopy
Biophys. J. 2001. 81:3398-3408. [Abstract] [Full Text] [PDF]

M. Y. Tolstorukov, V. I. Ivanov, G. G. Malenkov, R. L. Jernigan, and V. B. Zhurkin: Sequence-Dependent B $left-right-arrow$ A Transition in DNA Evaluated with Dimeric and Trimeric Scales
Biophys. J. 2001. 81:3409-3421. [Abstract] [Full Text] [PDF]

Sylvie Nonin-Lecomte, Chin H. Lin, and Dinshaw J. Patel: Additional Hydrogen Bonds and Base-Pair Kinetics in the Symmetrical AMP-DNA Aptamer Complex
Biophys. J. 2001. 81:3422-3431. [Abstract] [Full Text] [PDF]

Serguei V. Kuznetsov, Yiqing Shen, Albert S. Benight, and Anjum Ansari: A Semiflexible Polymer Model Applied to Loop Formation in DNA Hairpins
Biophys. J. 2001. 81:2864-2875. [Abstract] [Full Text] [PDF]

Tommi Ratilainen, Per Lincoln, and Bengt Norden: A Simple Model for Gene Targeting
Biophys. J. 2001. 81:2876-2885. [Abstract] [Full Text] [PDF]

R. Gargallo, M. Vives, R. Tauler, and R. Eritja: Protonation Studies and Multivariate Curve Resolution on Oligodeoxynucleotides Carrying the Mutagenic Base 2-Aminopurine
Biophys. J. 2001. 81:2886-2896. [Abstract] [Full Text] [PDF]

H. Arakawa, J. F. Neault, and H. A. Tajmir-Riahi: Silver(I) Complexes with DNA and RNA Studied by Fourier Transform Infrared Spectroscopy and Capillary Electrophoresis
Biophys. J. 2001. 81:1580-1587. [Abstract] [Full Text] [PDF]

Bernd Wellenzohn, Wolfgang Flader, Rudolf H. Winger, Andreas Hallbrucker, Erwin Mayer, and Klaus R. Liedl: Significance of Ligand Tails for Interaction with the Minor Groove of B-DNA
Biophys. J. 2001. 81:1588-1599. [Abstract] [Full Text] [PDF]

Olaf F. A. Larsen, Ivo H. M. van Stokkum, Bas Gobets, Rienk van Grondelle, and Herbert van Amerongen: Probing the Structure and Dynamics of a DNA Hairpin by Ultrafast Quenching and Fluorescence Depolarization
Biophys. J. 2001. 81:1115-1126. [Abstract] [Full Text] [PDF]

Marta de Frutos, Eric Raspaud, Amelie Leforestier, and Francoise Livolant: Aggregation of Nucleosomes by Divalent Cations
Biophys. J. 2001. 81:1127-1132. [Abstract] [Full Text] [PDF]

Yang Zhang, Haijun Zhou, and Zhong-Can Ou-Yang: Stretching Single-Stranded DNA: Interplay of Electrostatic, Base-Pairing, and Base-Pair Stacking Interactions
Biophys. J. 2001. 81:1133-1143. [Abstract] [Full Text] [PDF]

Michael Feig, Martin Zacharias, and B. Montgomery Pettitt: Conformations of an Adenine Bulge in a DNA Octamer and Its Influence on DNA Structure from Molecular Dynamics Simulations
Biophys. J. 2001. 81:352-370. [Abstract] [Full Text] [PDF]

Danny M. Hatters, Leanne Wilson, Benjamin W. Atcliffe, Terrence D. Mulhern, Nancy Guzzo-Pernell, and Geoffrey J. Howlett: Sedimentation Analysis of Novel DNA Structures Formed by Homo-Oligonucleotides
Biophys. J. 2001. 81:371-381. [Abstract] [Full Text] [PDF]

Yuichi Yamasaki, Yo Teramoto, and Kenichi Yoshikawa: Disappearance of the Negative Charge in Giant DNA with a Folding Transition
Biophys. J. 2001. 80:2823-2832. [Abstract] [Full Text] [PDF]

Carolina M. Reyes, Riccardo Nifosi, Alan D. Frankel, and Peter A. Kollman: Molecular Dynamics and Binding Specificity Analysis of the Bovine Immunodeficiency Virus BIV Tat-TAR Complex
Biophys. J. 2001. 80:2833-2842. [Abstract] [Full Text] [PDF]

Martin Zacharias: Conformational Analysis of DNA-Trinucleotide-Hairpin-Loop Structures Using a Continuum Solvent Model
Biophys. J. 2001. 80:2350-2363. [Abstract] [Full Text] [PDF]

John Day, Yuri G. Kuznetsov, Steven B. Larson, Aaron Greenwood, and Alexander McPherson: Biophysical Studies on the RNA Cores of Satellite Tobacco Mosaic Virus
Biophys. J. 2001. 80:2364-2371. [Abstract] [Full Text] [PDF]

Mark C. Williams, Jay R. Wenner, Ioulia Rouzina, and Victor A. Bloomfield: Entropy and Heat Capacity of DNA Melting from Temperature Dependence of Single Molecule Stretching
Biophys. J. 2001. 80:1932-1939. [Abstract] [Full Text] [PDF]

Helmut Schiessel, William M. Gelbart, and Robijn Bruinsma: DNA Folding: Structural and Mechanical Properties of the Two-Angle Model for Chromatin
Biophys. J. 2001. 80:1940-1956. [Abstract] [Full Text] [PDF]

Jun-Seok Yoo, Hae-Kap Cheong, Bong Jin Lee, Yang-Bae Kim, and Chaejoon Cheong: Solution Structure of the SL1 RNA of the M1 Double-Stranded RNA Virus of Saccharomyces cerevisiae
Biophys. J. 2001. 80:1957-1966. [Abstract] [Full Text] [PDF]

Eva Lai and John H. van Zanten: Monitoring DNA/Poly-L-Lysine Polyplex Formation with Time-Resolved Multiangle Laser Light Scattering
Biophys. J. 2001. 80:864-873. [Abstract] [Full Text] [PDF]

Mark C. Williams, Jay R. Wenner, Ioulia Rouzina, and Victor A. Bloomfield: Effect of pH on the Overstretching Transition of Double-Stranded DNA: Evidence of Force-Induced DNA Melting
Biophys. J. 2001. 80:874-881. [Abstract] [Full Text] [PDF]

Ioulia Rouzina and Victor A. Bloomfield: Force-Induced Melting of the DNA Double Helix 1. Thermodynamic Analysis
Biophys. J. 2001. 80:882-893. [Abstract] [Full Text] [PDF]

Ioulia Rouzina and Victor A. Bloomfield: Force-Induced Melting of the DNA Double Helix. 2. Effect of Solution Conditions^*
Biophys. J. 2001. 80:894-900. [Abstract] [Full Text] [PDF]

J. Ruiz-Chica, M. A. Medina, F. Sanchez-Jimenez, and F. J. Ramirez: Fourier Transform Raman Study of the Structural Specificities on the Interaction between DNA and Biogenic Polyamines
Biophys. J. 2001. 80:443-454. [Abstract] [Full Text] [PDF]

Richard Stefl, Nad'a Spackova, Imre Berger, Jaroslav Koca, and Jiri Sponer: Molecular Dynamics of DNA Quadruplex Molecules Containing Inosine, 6-Thioguanine and 6-Thiopurine
Biophys. J. 2001. 80:455-468. [Abstract] [Full Text] [PDF]

Alexei A. Podtelezhnikov, Chengde Mao, Nadrian C. Seeman, and Alexander Vologodskii: Multimerization-Cyclization of DNA Fragments as a Method of Conformational Analysis
Biophys. J. 2000. 79:2692-2704. [Abstract] [Full Text] [PDF]

Feng Sha and Fu-Ming Chen: Actinomycin D Binds Strongly to d(CGACGACG) and d(CGTCGTCG)
Biophys. J. 2000. 79:2095-2104. [Abstract] [Full Text] [PDF]

Charbel Haber and Denis Wirtz: Shear-Induced Assembly of $lambda$ -Phage DNA
Biophys. J. 2000. 79:1530-1536. [Abstract] [Full Text] [PDF]

Jan Norberg and Lennart Nilsson: On the Truncation of Long-Range Electrostatic Interactions in DNA
Biophys. J. 2000. 79:1537-1553. [Abstract] [Full Text] [PDF]

A. B. Steel, R. L. Levicky, T. M. Herne, and M. J. Tarlov: Immobilization of Nucleic Acids at Solid Surfaces: Effect of Oligonucleotide Length on Layer Assembly
Biophys. J. 2000. 79:975-981. [Abstract] [Full Text] [PDF]

Torunn Berge, Darren J. Ellis, David T. F. Dryden, J. Michael Edwardson, and Robert M. Henderson: Translocation-Independent Dimerization of the EcoKI Endonuclease Visualized by Atomic Force Microscopy
Biophys. J. 2000. 79:479-484. [Abstract] [Full Text] [PDF]

M. Zacharias and H. Sklenar: Conformational Deformability of RNA: A Harmonic Mode Analysis
Biophys. J. 2000. 78:2528-2542. [Abstract] [Full Text] [PDF]

A. Slama-Schwok, K. Zakrzewska, G. Leger, Y. Leroux, M. Takahashi, E. Kas, and P. Debey: Structural Changes Induced by Binding of the High-Mobility Group I Protein to a Mouse Satellite DNA Sequence
Biophys. J. 2000. 78:2543-2559. [Abstract] [Full Text] [PDF]

T. M. Okonogi, S. C. Alley, A. W. Reese, P. B. Hopkins, and B. H. Robinson: Sequence-Dependent Dynamics in Duplex DNA
Biophys. J. 2000. 78:2560-2571. [Abstract] [Full Text] [PDF]

Christoph G. Baumann, Victor A. Bloomfield, Steven B. Smith, Carlos Bustamante, Michelle D. Wang, and Steven M. Block: Stretching of Single Collapsed DNA Molecules
Biophys. J. 2000. 78:1965-1978. [Abstract] [Full Text] [PDF]

Zhang Yang, Zhou Haijun, and Ou-Yang Zhong-can: Monte Carlo Implementation of Supercoiled Double-Stranded DNA
Biophys. J. 2000. 78:1979-1987. [Abstract] [Full Text] [PDF]

Leonardo Pardo, Mercedes Campillo, David Bosch, Nina Pastor, and Harel Weinstein: Binding Mechanisms of TATA Box-Binding Proteins: DNA Kinking is Stabilized by Specific Hydrogen Bonds
Biophys. J. 2000. 78:1988-1996. [Abstract] [Full Text] [PDF]

Hauke Clausen-Schaumann, Matthias Rief, Carolin Tolksdorf, and Hermann E. Gaub: Mechanical Stability of Single DNA Molecules
Biophys. J. 2000. 78:1997-2007. [Abstract] [Full Text] [PDF]

Jaroslav Malina, Ctirad Hofr, Luciana Maresca, Giovanni Natile, and Viktor Brabec: DNA Interactions of Antitumor Cisplatin Analogs Containing Enantiomeric Amine Ligands
Biophys. J. 2000. 78:2008-2021. [Abstract] [Full Text] [PDF]

Alexei N. Naimushin, Bryant S. Fujimoto, and J. Michael Schurr: Dynamic Bending Rigidity of a 200-bp DNA in 4 mM Ionic Strength: A Transient Polarization Grating Study
Biophys. J. 2000. 78:1498-1518. [Abstract] [Full Text] [PDF]

Da-Guang Xu and Thomas M. Nordlund: Sequence Dependence of Energy Transfer in DNA Oligonucleotides
Biophys. J. 2000. 78:1042-1058. [Abstract] [Full Text] [PDF]

Perrine Cahen, Michel Luhmer, Catherine Fontaine, Claude Morat, Jacques Reisse, and Kristin Bartik: Study by ²³Na-NMR, ¹H-NMR, and Ultraviolet Spectroscopy of the Thermal Stability of an 11-Basepair Oligonucleotide
Biophys. J. 2000. 78:1059-1069. [Abstract] [Full Text] [PDF]

M. Gueron, J.-Ph. Demaret, and M. Filoche: A Unified Theory of the B-Z Transition of DNA in High and Low Concentrations of Multivalent Ions
Biophys. J. 2000. 78:1070-1083. [Abstract] [Full Text] [PDF]

Leila Ayadi, Christian Coulombeau, and Richard Lavery: Abasic Sites in Duplex DNA: Molecular Modeling of Sequence-Dependent Effects on Conformation
Biophys. J. 1999. 77:3218-3226. [Abstract] [Full Text] [PDF]

Mark Akeson, Daniel Branton, John J. Kasianowicz, Eric Brandin, and David W. Deamer: Microsecond Time-Scale Discrimination Among Polycytidylic Acid, Polyadenylic Acid, and Polyuridylic Acid as Homopolymers or as Segments Within Single RNA Molecules
Biophys. J. 1999. 77:3227-3233. [Abstract] [Full Text] [PDF]

Jay R. Wenner and Victor A. Bloomfield: Crowding Effects on EcoRV Kinetics and Binding
Biophys. J. 1999. 77:3234-3241. [Abstract] [Full Text] [PDF]

Ioulia Rouzina and Victor A. Bloomfield: Heat Capacity Effects on the Melting of DNA. 1. General Aspects
Biophys. J. 1999. 77:3242-3251. [Abstract] [Full Text] [PDF]

Ioulia Rouzina and Victor A. Bloomfield: Heat Capacity Effects on the Melting of DNA. 2. Analysis of Nearest-Neighbor Base Pair Effects
Biophys. J. 1999. 77:3252-3255. [Abstract] [Full Text] [PDF]

T. M. Okonogi, A. W. Reese, S. C. Alley, P. B. Hopkins, and B. H. Robinson: Flexibility of Duplex DNA on the Submicrosecond Timescale
Biophys. J. 1999. 77:3256-3276. [Abstract] [Full Text] [PDF]

Carlo Ciatto, Maria L. D'Amico, Giovanni Natile, Fernando Secco, and Marcella Venturini: Intercalation of Proflavine and a Platinum Derivative of Proflavine into Double-Helical Poly(A)
Biophys. J. 1999. 77:2717-2724. [Abstract] [Full Text] [PDF]

Cecilia Balbi, Paola Sanna, Paola Barboro, Ingles Alberti, Marta Barbesino, and Eligio Patrone: Chromatin Condensation Is Confined to the Loop and Involves an All-or-None Structural Change
Biophys. J. 1999. 77:2725-2735. [Abstract] [Full Text] [PDF]

Nikolay Korolev, Alexander P. Lyubartsev, Allan Rupprecht, and Lars Nordenskiold: Competitive Binding of Mg²⁺, Ca²⁺, Na⁺, and K⁺ Ions to DNA in Oriented DNA Fibers: Experimental and Monte Carlo Simulation Results
Biophys. J. 1999. 77:2736-2749. [Abstract] [Full Text] [PDF]

E. Raspaud, I. Chaperon, A. Leforestier, and F. Livolant: Spermine-Induced Aggregation of DNA, Nucleosome, and Chromatin
Biophys. J. 1999. 77:1547-1555. [Abstract] [Full Text] [PDF]

Hong Deng and Victor A. Bloomfield: Structural Effects of Cobalt-Amine Compounds on DNA Condensation
Biophys. J. 1999. 77:1556-1561. [Abstract] [Full Text] [PDF]

Guillaume Bertucat, Richard Lavery, and Chantal Prevost: A Molecular Model for RecA-Promoted Strand Exchange via Parallel Triple-Stranded Helices
Biophys. J. 1999. 77:1562-1576. [Abstract] [Full Text] [PDF]

Arthur Pichler, Simon Rudisser, Martin Mitterbock, Christian G. Huber, Rudolf H. Winger, Klaus R. Liedl, Andreas Hallbrucker, and Erwin Mayer: Unexpected B_II Conformer Substate Population in Unoriented Hydrated Films of the d(CGCGAATTCGCG)₂ Dodecamer and of Native B-DNA from Salmon Testes
Biophys. J. 1999. 77:398-409. [Abstract] [Full Text] [PDF]

Feng Sha, Rixiang Mu, Don Henderson, and Fu-Ming Chen: Self-Aggregation of DNA Oligomers with XGG Trinucleotide Repeats: Kinetic and Atomic Force Microscopy Measurements
Biophys. J. 1999. 77:410-423. [Abstract] [Full Text] [PDF]

D. Jeremy Williams and Kathleen B. Hall: Unrestrained Stochastic Dynamics Simulations of the UUCG Tetraloop Using an Implicit Solvation Model
Biophys. J. 1999. 76:3192-3205. [Abstract] [Full Text] [PDF]

Nicolas Foloppe and Alexander D. MacKerell Jr.: Intrinsic Conformational Properties of Deoxyribonucleosides: Implicated Role for Cytosine in the Equilibrium Among the A, B, and Z Forms of DNA
Biophys. J. 1999. 76:3206-3218. [Abstract] [Full Text] [PDF]

J. R.�C. van der Maarel: Effect of Spatial Inhomogeneity in Dielectric Permittivity on DNA Double Layer Formation
Biophys. J. 1999. 76:2673-2678. [Abstract] [Full Text] [PDF]

Ryszard Michalczyk and Irina M. Russu: Rotational Dynamics of Adenine Amino Groups in a DNA Double Helix
Biophys. J. 1999. 76:2679-2686. [Abstract] [Full Text] [PDF]

J. F. Neault and H. A. Tajmir-Riahi: Structural Analysis of DNA-Chlorophyll Complexes by Fourier Transform Infrared Difference Spectroscopy
Biophys. J. 1999. 76:2177-2182. [Abstract] [Full Text] [PDF]

Wentao Zhang, Haihong Ni, Michael W. Capp, Charles F. Anderson, Timothy M. Lohman, and M. Thomas Record Jr.: The Importance of Coulombic End Effects: Experimental Characterization of the Effects of Oligonucleotide Flanking Charges on the Strength and Salt Dependence of Oligocation (L⁸⁺) Binding to Single-Stranded DNA Oligomers
Biophys. J. 1999. 76:1008-1017. [Abstract] [Full Text] [PDF]

Pascal Auffinger, Shirley Louise-May, and Eric Westhof: Molecular Dynamics Simulations of Solvated Yeast tRNA^Asp
Biophys. J. 1999. 76:50-64. [Abstract] [Full Text] [PDF]

Jason P. Rife, Sarah C. Stallings, Carl C. Correll, Anne Dallas, Thomas A. Steitz, and Peter B. Moore: Comparison of the Crystal and Solution Structures of Two RNA Oligonucleotides
Biophys. J. 1999. 76:65-75. [Abstract] [Full Text] [PDF]

C. Bouchiat, M. D. Wang, J.-F. Allemand, T. Strick, S. M. Block, and V. Croquette: Estimating the Persistence Length of a Worm-Like Chain Molecule from Force-Extension Measurements
Biophys. J. 1999. 76:409-413. [Abstract] [Full Text] [PDF]

Nikolay Korolev, Alexander P. Lyubartsev, and Lars Nordenskiold: Application of Polyelectrolyte Theories for Analysis of DNA Melting in the Presence of Na⁺ and Mg²⁺ Ions
Biophys. J. 1998. 75:3041-3056. [Abstract] [Full Text] [PDF]

Markus Hammermann, Nathalie Brun, Konstantin V. Klenin, Roland May, Katalin Toth, and Jorg Langowski: Salt-Dependent DNA Superhelix Diameter Studied by Small Angle Neutron Scattering Measurements and Monte Carlo Simulations
Biophys. J. 1998. 75:3057-3063. [Abstract] [Full Text] [PDF]

Juliana Woda, Bohdan Schneider, Ketan Patel, Kavin Mistry, and Helen M. Berman: An Analysis of the Relationship between Hydration and Protein-DNA Interactions
Biophys. J. 1998. 75:2170-2177. [Abstract] [Full Text] [PDF]

Leonardo Pardo, Nina Pastor, and Harel Weinstein: Selective Binding of the TATA Box-Binding Protein to the TATA Box-Containing Promoter: Analysis of Structural and Energetic Factors
Biophys. J. 1998. 75:2411-2421. [Abstract] [Full Text] [PDF]

Bohdan Schneider, Ketan Patel, and Helen M. Berman: Hydration of the Phosphate Group in Double-Helical DNA
Biophys. J. 1998. 75:2422-2434. [Abstract] [Full Text] [PDF]

Xiang-Lei Yang, Hiroshi Sugiyama, Shuji Ikeda, Isao Saito, and Andrew H.-J. Wang: Structural Studies of a Stable Parallel-Stranded DNA Duplex Incorporating Isoguanine:Cytosine and Isocytosine:Guanine Basepairs by Nuclear Magnetic Resonance Spectroscopy
Biophys. J. 1998. 75:1163-1171. [Abstract] [Full Text] [PDF]

Gary D. Strahan, Max A. Keniry, and Richard H. Shafer: NMR Structure Refinement and Dynamics of the K⁺-[d(G₃T₄G₃)]₂ Quadruplex via Particle Mesh Ewald Molecular Dynamics Simulations
Biophys. J. 1998. 75:968-981. [Abstract] [Full Text] [PDF]

Ekaterina Protozanova and Robert B. Macgregor Jr.: Circular Dichroism of DNA Frayed Wires
Biophys. J. 1998. 75:982-989. [Abstract] [Full Text] [PDF]

Delphine Flatters and Richard Lavery: Sequence-Dependent Dynamics of TATA-Box Binding Sites
Biophys. J. 1998. 75:372-381. [Abstract] [Full Text] [PDF]

John G. Duguid, Cynthia Li, Mei Shi, Mark J. Logan, Hector Alila, Alain Rolland, Eric Tomlinson, James T. Sparrow, and Louis C. Smith: A Physicochemical Approach for Predicting the Effectiveness of Peptide-Based Gene Delivery Systems for Use in Plasmid-Based Gene Therapy
Biophys. J. 1998. 74:2802-2814. [Abstract] [Full Text] [PDF]

Ben Laurie, Vsevolod Katritch, Jose Sogo, Theo Koller, Jacques Dubochet, and Andrzej Stasiak: Geometry and Physics of Catenanes Applied to the Study of DNA Replication
Biophys. J. 1998. 74:2815-2822. [Abstract] [Full Text] [PDF]

Shashidhar N. Rao: Molecular Mechanics Studies on the Conformations of 2',3'-Dideoxy-2',3'-Didehydroguanine Nucleoside, D4G
Biophys. J. 1998. 74:3131-3139. [Abstract] [Full Text] [PDF]

Bjorn Akerman: Effects of Supercoiling in Electrophoretic Trapping of Circular DNA in Polyacrylamide Gels
Biophys. J. 1998. 74:3140-3151. [Abstract] [Full Text] [PDF]

Ioulia Rouzina and Victor A. Bloomfield: DNA Bending by Small, Mobile Multivalent Cations
Biophys. J. 1998. 74:3152-3164. [Abstract] [Full Text] [PDF]

Leonardo Pardo, Nina Pastor, and Harel Weinstein: Progressive DNA Bending Is Made Possible by Gradual Changes in the Torsion Angle of the Glycosyl Bond
Biophys. J. 1998. 74:2191-2198. [Abstract] [Full Text] [PDF]

Lucy Malinina, Valya Tereshko, Eugeniya Ivanova, Juan A. Subirana, Valya Zarytova, and Yurii Nekrasov: Structural Variability and New Intermolecular Interactions of Z-DNA in Crystals of d(pCpGpCpGpCpG)
Biophys. J. 1998. 74:2482-2490. [Abstract] [Full Text] [PDF]

Jennifer A. Martino and Wilma K. Olson: Modeling Chain Folding in Protein-Constrained Circular DNA
Biophys. J. 1998. 74:2491-2500. [Abstract] [Full Text] [PDF]

Philip Nelson: New Measurements of DNA Twist Elasticity
Biophys. J. 1998. 74:2501-2503. [Abstract] [Full Text] [PDF]

I. Klapper and H. Qian: Remarks on Discrete and Continuous Large-Scale Models of DNA Dynamics
Biophys. J. 1998. 74:2504-2514. [Abstract] [Full Text] [PDF]

David Swigon, Bernard D. Coleman, and Irwin Tobias: The Elastic Rod Model for DNA and Its Application to the Tertiary Structure of DNA Minicircles in Mononucleosomes
Biophys. J. 1998. 74:2515-2530. [Abstract] [Full Text] [PDF]

Ariel Prunell: A Topological Approach to Nucleosome Structure and Dynamics: The Linking Number Paradox and Other Issues
Biophys. J. 1998. 74:2531-2544. [Abstract] [Full Text] [PDF]

Irwin Tobias: A Theory of Thermal Fluctuations in DNA Miniplasmids
Biophys. J. 1998. 74:2545-2553. [Abstract] [Full Text] [PDF]

Jordanka Zlatanova, Sanford H. Leuba, and Kensal van Holde: Chromatin Fiber Structure: Morphology, Molecular Determinants, Structural Transitions
Biophys. J. 1998. 74:2554-2566. [Abstract] [Full Text] [PDF]

T. R. Strick, J.-F. Allemand, D. Bensimon, and V. Croquette: Behavior of Supercoiled DNA
Biophys. J. 1998. 74:2016-2028. [Abstract] [Full Text] [PDF]

Jason R. Schnell, Judith Berman, and Victor A. Bloomfield: Insertion of Telomere Repeat Sequence Decreases Plasmid DNA Condensation by Cobalt (III) Hexaammine
Biophys. J. 1998. 74:1484-1491. [Abstract] [Full Text] [PDF]

Anzhi Z. Li, Haiyan Huang, Xiaodan Re, Lai J. Qi, and Kenneth A. Marx: A Gel Electrophoresis Study of the Competitive Effects of Monovalent Counterion on the Extent of Divalent Counterions Binding to DNA
Biophys. J. 1998. 74:964-973. [Abstract] [Full Text] [PDF]

C Krafft, W Hinrichs, P Orth, W Saenger, and H Welfle: Interaction of Tet repressor with operator DNA and with tetracycline studied by infrared and Raman spectroscopy
Biophys. J. 1998. 74:63-71. [Abstract] [Full Text] [