Table of Contents: Abstracts
As of March 15, 1997
Combination of Metal
Ions Makes an Improved Ribozyme System
Naoki Sugimoto and Tatsuo Ohmichi
Influence of Electrostatic
Mutations on Conformation and Thermal Denaturation Parameters of Apo Calmodulin
I. Protasevich, B. Ranjbar, V.Lobachov, A. Makarov R. Gilli, C. Briand
D. Lafitte and J. Haiech
Analysis of Structural
Environment of Amino Acids That Alter in vitro Protein Stability
Boojala V B Reddy and Sunando Datta
The Regioselective
Effect of Zwitterionic DNA Substitutions on DNA Alkylation
F.-X. Chen, P. Dange, G. Liang and B. Gold
Breather Mechanism
of DNA TATA-Box Recognition
Sergey N. Volkov
The Study of the
Stability of Watson-Crick Nucleic Acids Base Pairs in Water and Dimethyl
Sulfoxide: Computer Simulation by Monte Carlo Method
V. I. Danilov, N. V. Zheltovsky, O. N. Slyusarchuk and J. L. Alderfer
Simulation of Base
and "Model" Amino Acids Complexes in DMSO by Monte Carlo Method
V. I. Danilov, O. V. Mikhaleva, O. N. Slyusarchuk, J. L. Alderfer and
V. I. Poltev
DNA Kinking as Imaged
with a New High-Resolution AFM
Mensur Dlakic, Rodney E. Harrington, Wenhai Han and Stuart M. Lindsay
NMR Studies of the
Anticancer Drug Pepleomycin and its Complexes with DNA
Janet Caceres-Cortes, Andrew H.-J. Wang, Hiroshi Sugiyama, Kenji Ikudome
and Isao Saito
Probing G·U
Mismatches in RNA Fragments Using 15N NMR
Xiaohu Zhang, Barbara L. Gaffney and Roger A. Jones
A New High-Resolution
Atomic Force Microscope for Imaging Biomolecules in Fluids
S.M. Lindsay, Wenhai Han and Tianwei Jing
Studies on the Interaction
of Nonintercalating Drugs with Parallel-Stranded DNA: Differential Effects
of Netropsin and Related Lexitropsins
Ingo Förtsch, Christoph Zimmer, Thomas M. Jovin and J. William Lown
Modulation of the
Stability of a DNA Triple Helix by Interaction with Minor Groove-Binding
Ligands
Ingo Förtsch, Christoph Zimmer and Holger Schütz
DNA-Intercalator
Interaction Measurements Using Surface Plasmon Resonance
G. Bischoff, W.-V. Meister, C. Bohley, S. Hoffman, E. Birch-Hirschfeld
and R. Bischoff
Mobility and Diffusion
of a Polymer Chain in a Dynamic Matrix
Udayan Mohanty
DNA Bending is an
Essential Component for the Site Specific Recognition by DNA Binding Domain
of Tumor Suppressor Protein p53
Akhilesh K. Nagaich, Rodney E. Harrington and Ettore Appella
Inherent DNA Duplex
Curvature Determined from 1.5 ps Molecular Dynamics Simulations for a Series
of TATA-promoter Mutants and Comparison with Experimental Physical and Biological
Observations
Osmar Norberto de Souza and Rick L. Ornstein
DNA Stress Induced
by the TATA-box Binding Protein
Anne LeBrun, Richard Lavery and Zippora Shakked
Structural Studies
on Minor Groove Binder: DNA Interactions
J. William Lown
Conformational Flexibility
of Voltage Gated Dihydropyridine Sensitive Calcium Channel: Molecular Dynamics
Simulation
V. Kothekar and D. Gupta
Intercalation of Ethidium Bromide into Short DNA Hairpins: Effect
of Hairpin-Hairpin Dimerization
Olga F. Borisova and Anna K. Shchyolkina
A Double Stranded
RNA Binding Protein
A.G. Gabrielian, K.A. Bakuntz and R.A. Zakharian
Prediction of Bendability
and Curvature in Genomic DNA
Andrei Gabrielian, Kristian Vlahovicek and Sandor Pongor
Conformational NMR-Analysis
of the Principal Neutralizing Determinant of the HIV-1 Envelope Protein
gp120
Alexander M. Andrianov and Afanasii A. Akhrem
Spatial Structure
Model of the Fragment Ala-Ser-Thr-Thr-Thr-Asn-Tyr-Thr Responsible for Binding
the HIV Envelop Prrotein gp120 to T4 Receptor of T4 Cells
Alexander M. Andrianov and Afanasii A. Akhrem
NMR Structure of
a Tetrad Forming Oligonucleotide HIV Inhibitor
Naijie Jing, Xiaolian Gao and Michael E. Hogan
Ab Initio Quantum
Mechanics Analysis of C-H...O/N Hydrogen Bonding and Implications for Modeling
Enzymes and Nucleic Acids
Rick L. Ornstein
DNA Separation by
Polymer Micelle Capillary Electrophoresis
Chunhung Wu and Benjamin Chu
Periodical Recurrence
of Translation Pause Sites in mRNA and Standard Sizes of Protein Sequence
Segments and Independently Folding Domains
C. Makhoul and E. N. Trifonov
Structural Variability
of the A-DNA in Crystals of CCCGCGGG
Lucy Malinina, Luzimar Gonzaga-Fernandes, Nuria Verdaguer, Lourdes Campos,
Juan A.Subirana and Dmitry Pyshnyi
Conformational Behavior
Of CGG Triplet Repeats That Are Associated With Fragile X Syndrome
Xuening Huang and Xiaolian Gao
Insight Into the
Stabilization of A-DNA From Molecular Dynamics Simulations Performed in
Aqueous Solvent in the Presence of Cobalt Hexaamine or Ethanol
Thomas E. Cheatham III and Peter A. Kollman
How Does Metalloprotein
Oxidation State Affect Structure, Dynamics and Function?
Thomas C. Pochapsky
Satellite Tobacco
Ringspot Virus RNA in Sympton Reduction in Tobacco Ringspot Virus-Infected
Plants
N. I. Imthurn, K. L. Tessitore and G. A. Prody
Environmental Influences
on DNA Curvature
David W. Ussery and Alex Bolshoy
Extraction of Nucleosome
DNA Sequence Pattern by Match Resonance Analysis
Ilya Ioshikhes, Lev Lvovsky and Edward N. Trifonov
At Physiological
pH, d(CCG)15 Forms a Hairpin Containing Protonated Cytosines and a Distorted
Helix
Adong Yu, Maria D. Barron, Rebecca M. Romero, Mellisa
Christy, Barry Gold,
Jianli Dai, Donald M. Gray, Ian S. Haworth and Michael Mitas
The Adenylates of
Friedreich's Ataxia d(GAA) Repeats Are Nuclease-Resistant and Predominantly
Unstacked: Evidence For a New Helical Single-Stranded DNA Structure
Iang-Shan Suen, Mellisa Christy, Brian McEwen, and Michael Mitas
S-DNA and SI-DNA:
Genetic and Biophysical Evidence for Slipped DNA Structures in Disease-Associated
Triplet Repeat Instability
Pearson, C. E., Eichler, E. E., Lorenzetti, D., Acharya, S., Kramer,
P. R., Kramer, S. F., Nelson, D. L., Zoghbi, H. Y., Fishel, R. A. and Sinden,
R. R.
Design And Structural
Analysis Of Novel Nucleic Acids Duplexes With Mixed Strand Disposition
Markus W. Germann, James M. Aramini, Bernd W. Kalisch and Johan H. van
de Sande
The Helical Structure
of d(CCG)n Trinucleotide Repeat DNA Probed by Mechlorethamine Crosslinking
and Molecular Dynamics Simulations
Rebecca M. Romero, Huai Yong Cheng, Michael Mitas and Ian S. Haworth
Metals, Motifs and
Recognition: 5S rRNA Domain Crystal Structure
C.C. Correll, B. Freeborn, P.B. Moore, and T.A. Steitz
Conformation Changes
in DNA-peptide Complexes
Hana Votavová and Jaroslav Sponar
Hydration and the
Stability of Protein-Protein Complexes
M. C. Strahm and D. M. Soumpasis
Packaging and Dimer
Linkage in Retroviral RNA: NMR of a GGAG-tetraloop Substructure of the HIV-1
Packaging Signal
Lucia Pappalardo, Cui Liu, István Pelczer and Philip N. Borer
Comparision of the
Dynamics Of Angiogenin and RNase A
Madhusudhan, M.S. and Saraswathi Vishveshwara
Environmentally Dependent
Molecular Dynamic Simulations of DNA Using the BMS Nucleic Acid Force Field
David R. Langley
DNA Triplex Stabilization
by Cationic Polypeptides
Vladimir N. Potaman, David R. Corey and Richard R. Sinden
Molecular Modelling
of Interactions of Acridine Analogs With Double Helical DNA
V. K. Ganesh and D. Velmurugan
1H NMR Investigations
of Ion Binding by DNA G-quartets and A-tracts
Nicholas V. Hud and Juli Feigon
E. coli DNA Topoisomerase III is an RNA Topoisomerase
Hui Wang, Russell J. Di Gate and Nadrian C. Seeman
Switching and Looping
in i-Motif Structures
J-L Leroy, S. Nonin, X. Han, A. T. Phan, and M. Guéron
DNA Bending by Small
Molecules: Studies With Calicheamicin
Aaron A. Salzberg and Peter C. Dedon
Helix -Coil Transitions
in DNA Modified by Novel Pt(II) Complexes: A pH Mmelting Study
R. Malathi, G. Natarajan, E. Holler
Molecular Recognition
Between DNA And Chiral Intercalative Metalloprobes
K. A.Vickery, A. M. Bonin, P. A. Williams and R. S. Vagg
Effect of Vicinal
2',5' and 3',5'-Phosphodiester Linkages on the Formation of Hairpin DNA
Ravinderjit S. Braich and Masad J. Damha
Association of Branched
Oligonucleotides into C-Tetraplexes: 2-Deoxyribose and Arabinose, but not
Ribose, Stabilize the C-Tetrad Structure
S. Robidoux, M.J. Damha, K. Gehring and R. Klinck
Selective Association
and Antisense Properties of 2',5'-Linked Oligoribonucleotides
M. Wasner, A. Uddin, G. Borkow, D. Arion, M. Parniak and M.J. Damha
Hybridization Properties
of Arabinonucleic Acids (ANA) Influence of Stereochemistry at 2' on the
Stability of Double and Triple Helices
Anne Noronha and Masad J. Damha
Biophysical Studies
and Synthesis of Oligonucleotides Containing a Peptide / Aromatic Backbone
C. J. Wilds, J. F. Lunetta, Y. S. Tsantrizos and M. J. Damha
The Tunable Transmission
of the Aromatic Character of the Aglycone Through the Anomeric Effect in
C-nucleosides Drives its Own Sugar Conformation: A Thermodynamic Study
I. Luyten, C. Thibaudeau, A. Sandström and J. Chattopadhyaya
What is the Nature
of Hydration in the Minor Groove of DNA Duplex? An Investigation by Base-pair
Exchange Kinetics and NMR Study
T. V. Maltseva, P. Roselt and J. Chattopadhyaya
Solution Structure
of Tandem Oligonucleotide Duplex with two Spatially Adjacent Steroid Residues
A. Yu. Denisov, T. V. Maltseva, A. Sandstrom, D. V. Pyshnyi, E. M. Ivanova,
V. F. Zarytova and J. Chattopadhyaya
The Discovery of
Intramolecular Stereoelectronic Forces That Drive the Sugar Conformation
in Nucleosides and Nucleotides
C. Thibaudeau & J. Chattopadhyaya
Strategies in DNA
Sequence Recognition
Richard E. Dickerson, Gye-Won Han, Mary L. Kopka and David S. Goodsell
A Molecular Dynamics
Study of a DNA Oligomer Containing the TATA-box Binding Protein Target Sequence
Delphine Flatters, Matthew Young, David L. Beveridge and Richard Lavery
Effects of 5-FU
on the Structure, Stability and Dynamics of the U4-U6 snRNA Complex
William H. Gmeiner, Parag V. Sahasrabudhe, Junqu Sun and Jinqian Liu
Sequence-Specific
Ligands That use Parallel and Antiparallel Side-by-Side Peptide Motifs in
Binding to DNA
Anna N. Surovaya, Gunther Burckhardt, Sergei L. Grokhovsky,
Eckhard Birch-Hirschfeld, Georgii V. Gursky and Christoph Zimmer
p53-DNA Interactions:
DNA Bending and Flexibility
P. Balagurumoorthy, Ettore Appella and Rodney E. Harrington
High Resolution
Information on Specific Interactions Between the p53 DNA Binding Domain
and DNA Response Elements
A. K. Nagaich, P. Balagurumoorthy, H. Sakamoto, V. B. Zhurkin, G. M.
Clore, A. M. Gronenborn, E. Appella and R. E. Harrington
High Sensitivity
Pure Nuclear Quadruple Resonance (PQR) in Biopolymers
Dmitri Ivanov and Alfred G. Redfield
NMR Studies on the
Slipped-Loop Structure of DNA in Solution
Nikolai B. Ulyanov, Valery I. Ivanov & Thomas L. James
Sequence Specific
Recognition in the DNA Minor Groove: X-Ray Structure of the Di-imidazole
Lexitropsin Bound to C-A-T-G-G-C-C-A-T-G
Mary L. Kopka, Gye Won Han, Thang Chiu, David S. Goodsell, J.W. Lown
& Richard E. Dickerson
The Folding Pathway
of a Group II Intron Ribozyme Revealed by Stopped-Flow Fluorescence Spectroscopy
and Chemical Modification Footprinting
Peter Zhifeng Qin and Anna Marie Pyle
RNA Pseudoknot From
Beet Western Yellow Virus at 1.9 Å Resolution
Li Su, Liqing Chen & Alexander Rich
The Sequence Dependence
of Branch Migratory Minima
Weiqiong Sun, Chengde Mao and Nadrian C. Seeman
The Construction
of Borromean Rings from DNA
Chengde Mao, Weiqiong Sun and Nadrian C. Seeman
Direct Evidence
for Holliday Junction Crossover Isomerization
Xiaojun Li, Hui Wang and Nadrian C. Seeman
The Incorporation
of DNA Double Crossovers into DNA Triangles
Xiaoping Yang, Jing Qi, Xiaojun Li and Nadrian C. Seeman
Lengthening Sticky
Ends: Not as Easy as it Looks
Furong Liu, Hui Wang and Nadrian C. Seeman
Detection of a B-Form/A-Form
Junction in DNA
V.I. Ivanov, L.E. Minchenkova, Gunther Burckhardt,
Eckhardt Birch-Hirschfeld, Hartmut Fritzsche and Christoph Zimmer
The Structure and
Properties of a Small, Porphyrin-Metallating, DNAzyme
Dipankar Sen and Yingfu Li
DNA Sequence and
Three-dimensional Structure
Wilma K. Olson
A Cofactor-Independent
DNAzyme for RNA Hydrolysis
Dipankar Sen and C. Ronald Geyer
Manipulation of
Curvature in Plasmid DNA Molecules
Nancy C. Stellwagen and Kurt Strutz
Selforganization
of Nucleic Acids Visualized by Scanning Force Microscopy
C. Bohley, W.-V. Meister, G. Bischof, R. Bischoff, S. de Bambirra, S.
Lindau, S.Kargov, J. Barthel, S. Hoffmann
Possibilities of
Triplex-Formation by Short Oligo(deoxy)nucleotide Analogs of Tetrahymena
pre-rRNA Fragments
W.-V. Meister,
G. Bischoff, R. Bischoff, C. Bohley, S. de Bambirra, E. Birch-Hirschfeld,
S. Kargov, S. Hoffmann
Mesogenic 2-Pyridones
and 1,2-Diacylhydrazines Modelling Aspects of Recognition and Modulation
in Nucleoprotein Replication Systems
C. Bohley, S. Naumann, S. Lindau, S. de Bambirra, W.-V. Meister, S. Hoffmann
Phase-Behavior of
Long Alkyl-Chain Nucleobase Derivatives
S. de Bambirra, S. Lindau, G. Bischoff, R. Bischoff, C. Bohley, L. Kovalenko,
M. Madre, R. Zhuk, W.-V. Meister, S. Hoffmann
Message-Design Around
the ss-Casomorphin Motif within ss-Casein Informational Tracts
W.-V. Meister, F. Adler, E. Birch-Hirschfeld, S. Hoffmann
NMR Studies of the
Conserved 43 Nucleotide RNA Domain Found in the Signal Recogniton Particle
Peter Lukavsky, Stefan Behrens, Todd Billeci, Thomas L. James & Uli
Schmitz
Energetics and Geometry
of Water Clusters and Networks
Bernd U. Ihmels and D. Mario Soumpasis
Modeling DNA Structures:
From Local to Superhelical Forms
A. R. Srinivasan and Wilma K. Olson
Computer Simulations
of Polynucleosomal DNA Circles
Vsevolod Katritch and Wilma K. Olson
Slipped Loop Structure
(SLS) in Symmetrical Deoxynucleotides
E. E.Minyat, E. B.Khomyakova, M. V.Petrova and V. I. Ivanov
Role of Electrostatic
Factors in Interaction Between Minor Groove Binders and DNA
A. L. Zhuze, S. L. Grokhovsky, R. V. Brussov, A. M. Nikitin, D. V. Salmanova,
A. L. Mikheikin, S. A. Streltsov, T. A. Leinsoo, V. O. Chekhov, G. V. Gursky,
R. H. Shafer, and A. S. Zasedatelev
Chromosome Structure
and Gene Regulation
K. J. Polach, R. U. Protacio, P. T. Lowary and J. Widom
Triple Helix Formation
by (GA)-containing Oligonucleotides: An Asymmetric Sequence Effect
Paola B. Arimondo, Francesca Basolo, Jian-Sheng Sun, Jean-Claude Maurizot,
Thérèse Garestier, Claude Hélène
Interactions of
Sanguinarine with Polymorphic Structures of Deoxyribonucleic Acid
Suman Das, Anjana Sen, Arghya Ray, Gopinatha Suresh Kumar and Motilal
Maiti
Structural and Dynamics
Studies of Bacterial Regulatory Proteins
John Cavanagh
Alzheimer Disease
Hyperphosphorylated TAU Aggregates Hydrophobically
George C. Ruben, Thomas L. Ciardelli, Inge Grundke-Iqbal, and Khalid
Iqbal
DNA-backbone Modifications
That Affect Duplex Stability
Daniel Barsky, Michael E. Colvin, Gerald Zon, Sergei M. Gryaznov
Dynamical Structure
of B-DNA Oligonucleotides Containing Phased A-tracts in Salt Water Solution
M. A. Young and D. L. Beveridge
Molecular Design
for DNA Recognition: An Approach Toward Gene-Specific Transcription Inhibition
in vivo by Synthetic Ligands
Peter B. Dervan
Evolution of Human
and Mouse Dinucleotide Repeat DNA
Pankaj Agarwal, George I. Bell, Gavin Huttley and Michael W. Smith
B-DNA Bending by
Cationic Ligands
I.F.Rouzina and V.A. Bloomfield
Self-Assembly of
DNA Oligomers with XGG Trinucleotide Repeats
Fu-Ming Chen
Two-domain Structure
of the td Intron-encoded Endonuclease I-TevI Correlates with the
two-Domain Configuration of the Homing Site
Victoria Derbyshire, Joseph C. Kowalski, John T. Dansereau, Susan Baxter,
Charles R. Hauer and Marlene Belfort
IS903 Insertion
Specificity: A Distinct Preference for the F Transfer Operon
Wen-Yuan Hu and Keith M. Derbyshire
Mutational Analysis
of IS903 Transposase
Norma Tavakoli and Keith Derbyshire
The Investigation
of DNA-Protein Interactions by Molecular Mechanics and Protein-DNA Cross-Links
Methods. Deliniation of Universal DNA, RNA-Binding and DNA-Binding Motifs
Natalya G.Esipova, Dmitry E.Kamachev, Dmitry A.Kuznetzov, Andrey
D.Mirzabekov
Structural Basis
For Heterogeneous Kinetics: Reengineering the Hairpin Ribozyme
J. Esteban, N. Walter, G. Kotzorek, J. Heckman, J. Bond and J. Burke
Effects of Different
Chemical Groups Covalently Attached to Oligodeoxyribonucleotides as well
as the Presence of the Mismatch at these Junctions on the Co-operative Interactions
Abdussalam Adeenah-Zadah and Olga Fedorova
A Theoretical Analysis
of Specificity of Nucleic Acid Interactions with Oligonucleotides and Peptide
Nucleic Acids (PNAs)
Aleksey Lomakin and Maxim Frank-Kamenetskii
Kinetic Analysis
of Specificity of Duplex DNA Targeting by Homopyrimidine PNAs
Vadim V. Demidov, Michael V. Yavnilovich and Maxim D. Frank-Kamenetskii
Salt Effects on
DNA Structure and Dynamics Studied by H1-NMR Spectroscopy
Patrick Furrer, Nick Ulyanov and Tom James
Studies on Direct
and Indirect Hydrogen Bonds and the Operator Conformation in the Interaction
of the trp Repressor with its Binding Sites
Avital Bareket-Samish, Ilana Cohen and Tali. E. Haran
Computer Modeling
of the Ternary Complex of the Lac Repressor, CAP and DNA Loop
Steve Harvey, David Case and Robert K.-Z. Tan
The Role of Water
in Complex Formation between Peptides and the MHC Molecule HLA-A2
Wilson S. Meng, Hermann von Grafenstein and Ian S. Haworth
6-Amino-6H-4,5,7,8-Tetrahydroimidazo[4,5-e][1,4]Diazepine-5,8-Dione:
A Synthetic Analogue of Azepinomycin as a Transition State-Mimicking Inhibitor
of Guanese
Vasanthakumar Rajappan and Ramachandra S. Hosmane
Affinity Reagents
For Cross-Linking Hemoglobin: Bis(Phenoxycarbonylethyl)Phosphinic Acid (Bpcep)
and Bis(3-Nitrophenoxycarbonylethyl)Phosphinic Acid (Bncep)
S. Prasad Peri, Vishweshwar S. Bhadti, Rong Liang, Ramachandra S. Hosmane
and Victor Macdonald
Inhibitors of Glycogen
Phosphorylase B: Synthesis, Molecular Modeling, and Biochemical Screening
of Analogues of Hydantocodin
Mary W. Mumper, Yankanagouda S. Agasimundin and Ramachandra S. Hosmane
NMR Structure Studies
of the Prion Protein
He Liu, Nicolai B. Ulyanov, Shauna Farr-Jones, Hong Zhang, David Donne,
Peter Wright, Fred Cohen, Darline Groth, Stanley Prusiner and Thomas L.
James
Phosphorothioate
and Phosphorodithioate Modifications of Antisense Oligomers: A Structural
Comparison by NMR
Todd M. Billeci, Patrick Furrer, Alessandro Donati, Chojiro Kojima,
Wojcieh Stec, and Thomas L. James
Induction of Self-ligation
of Hairpin Ribozyme RNAs by Freezing and Dehydration
Brian H. Johnston, Svetlana V. Balatskaya and S. A. Kazakov
Antiparallel-Parallel
Combination (APC) in DNA: The Formation is Facilitated by Groove Binding
Ligand Distamicin A
Elena B. Khomyakova, Anna K. Shchyolkina, Lucy E. Minchenkova, Elvira
E. Minyat, Valery I. Ivanov and Tomas M. Jovin
Structural Recognition
of DNA by HMG Proteins
Hong Xin, Wenjie Cheng and Neville R. Kallenbach
The Effects of
a Mutation in the B Binding Domain of rHMG-1
Susann Taudte, Amy Tam, Wenjie Cheng, Wendy P. Patton, Neville R. Kallenbach
Thermal Unfolding
of Chytochrome
C. Leyu Wang and Neville R. Kallenbach
Quantitative Footprinting
Studies On Hiv-1 Rna
Christopher Kirk, Jerry Goodisman, Lucia Pappalardo, Philip Borer and
James Dabrowiak
Diastereoselectivity
Of Nucleolytic Enzymes Towards Phosphorothioate Analogues Of Oligonucleotides
Maria Koziolkiewicz, Marzena Wojcik, Edyta Gendaszewska, Maria Maszewska
and Wojciech J. Stec
3D Domain Swapping
in an RNA Pseudoknot
Craig E. Kundrot
The High Resolution
Crystal Structure of a Guanine Tetraplex
Kathryn Phillips, Zbyzek Dauter, Alaistair Murchie, David Lilley and
Ben Luisi
High-Resolution
Solution NMR Structure of the Anticancer Drug Cisplatin Bound to its Major
Site in Duplex DNA
Andrew Gelasco and Stephen J. Lippard
Analysis of the
Interactions of the DNA binding domain of PU.1 by Hydroxyl Radical Footprinting
Petra Groß, Cheryl H. Arrowsmith and Robert B. Macgregor, Jr.
Infrared Spectroscopy
of (dA)·(dT) Polymers at High Pressure
M.-C. Lin, P. Eid, P. T. T. Wong and R. B. Macgregor, Jr.
Working Towards
an Optimized Library of Routines for the Analysis and Reconstruction of
Nucleic Acid Structure
Xiangjun Lu and Wilma K. Olson
Influence of Stretching
Deformations on DNA Structure
Konstantin Kosikov, Andrey Gorin, Victor Zhurkin and Wilma Olson
Gaussian-Chain
Model For Interphase Chromosomes
Joseph Y. Ostashevsky
DNA-Modified Electrodes:
New Tools in Molecular Recognition, Detection of DNA Damage and Analysis
of Environmental Pollutants
E. Palecek, M.Fojta, M. Tomschik, F. Jelen, V. Vetterl, L. Havran and
V. Stankova
Modeling of DNA-polyamine
Interactions by Cobalt Amine Complexes
Andrew Parkinson and Alison Rodger
Genome Sequence
Analysis: A Pointer Towards Triplex-mediated cis Regulation of Gene Expression
Sowmya Raghavan, Pradeep K. Burma and Samir K. Brahmachari
Crystal Structures
of DNA Targets of the E2 Protein from Bovine Papillomavirus-1
H. Rozenberg, D. Rabinovich, F. Frolow, R. H. Hegde and Z. Shakked
The Crystal Complex
of Tetrameric PheRS and Cognate tRNA: The Pattern of Recognition
Mark Safro, Yehuda Goldgur, Lidia Mosyak, Ludmila Reshetnikova, Valentina
Ankilova, Olga Lavrik, Svetlana Khodyreva
Proline Is An Artificial
Protein Folding Chaperone
D. Samuel and Chin Yu
New Single Molecule
Approaches to Genomic Analaysis: Optical Mapping
Schwartz, D.C., Anantharaman, T., Cai, W., Clarke, V., Delobette, S.,
Dimalanta, E., Edington, J., Giacalone, J., Hiort, C., Hu, X., Huff, E.,
Jing, J., Lai, Z., Lee, E., Mishra, B., Murti, J. R., Porter, B., Qi, R.,
Rabbah, R., Ramanathan, A., Reed, J., Samad, A., Shenker, A., Skiadas, Y.,
Tankhoveya, K., Wang, W. and Lin, J.
Quantitative Gel
Studies of the Dimer Linkage Site of Hiv
Michael Shubsda, Jerry Goodisman, Philip Borer and James Dabrowiak
Genetic Control
of Microsatellite Instability in Saccharomyces cerevisiae
E. A. Sia, R. J. Kokoska, M. Dominska, P. Greenwell, M. Wierdl and
T. D. Petes
Conformational
Changes in Fluoromethemoglobin S and Fluoromethemoglobin A Probed by Ultraviolet
Resonance Raman Spectroscopy
L. Sokolov, K. Sheffield and I. Mukerji
AMBER4.1/PME simulations
of the "Hagerman" sequences d[G5-{GA4T4C}2-C5] and d[G5-{GT4A4C}2-C5]
Dennis Sprous, Matthew A. Young and David L. Beveridge
The AMBER4.1 Force
Field Favors B-DNA Pucker in 75% Methanol:TIP3P Water (v/v) and in Straight
TIP3P Water
Dennis Sprous, Kevin J. McConnell and David L. Beveridge
Kinetic Study of
a (T,C)-motif Triple Helix Formation by Biomolecular Interaction Analysis
Technology: a Comparative Solution and Biosensor-Based Study
Jian-sheng Sun, Thérèse Garestier and Claude Hélène
Establishing in
vitro Assays for IS903 Transposition
Valeri J. Thomson and Keith Derbyshire
Left-handed Kind
Conformation of Polypeptide Chain in the DNA Minor Groove
Vladimir G.Tumanyan, Dmitry A.Kuznetsov and Natalya
G.Esipova
Raman Spectroscopy
as a Probe of DNA Minor-Groove Binding: The Complex of a High-Mobility-Group
Domain (hSRY) and its Target DNA
James M. Benevides, Michael A. Weiss and George J. Thomas, Jr.
Oligodeoxyribonucleotide
N3-P5' Phosphoramidate Duplexes Have A-Helix Conformations And Can Serve
As Decoys In Binding The HIV-1 Rev Protein
W. David Wilson, Daoyuan Ding, C. Ted Rig, Sergei M. Gryaznov and
David H. Lloyd
Interaction of DNA
Bases and Base Pairs with Various Metal Cations (Li+ Na+, K+, Rb+, Cs+,
Mg2+, Ca2+, Sr2+, Ba2+, Cu+, Ag+, Au+, Zn2+, Cd2+, and Hg2+): ab initio
MP2 Calculations and Nonadditivity of the Interaction
Jaroslav V. Burda, Jirí Sponer, Jerzy Leszczynski and Pavel Hobza
CD and NMR Studies
on a La3+ Binding Nucleated Synthetic EF Peptide
Youxiang Gong, Jianxin Yang, Andrew J. Bierzynski and Neville R. Kallenbach
Theoretical Study
on Structure, Dynamics and Properties of DNA Bases and Base Pairs
Pavel Hobza, Jirí Sponer and Vladimír Spirko
DNA Supercoiling
Alters Calicheamicin g1I Activation by Glutathione
William A. LaMarr and Peter C. Dedon
The Iso-Competition
Point For Multivalent: Univalent Cation Binding To DNA
Anzhi Z. Li, Haiyan Huang and Kenneth A. Marx
Comparison Of Theoretical
And Experimental Melting Curves Of The Yeast Genome And Simulation Of Individual
Yeast Chromosome Melting Using The Program Meltsim
J. W. Bizzaro, Kenneth A. Marx and R.D. Blake
MELTSIM, A Windows
Program for Simulating the Thermal Dissociation of Polymeric DNAs
R. D. Blake, J. W. Bizzaro, John Knowles, Gary Day, Jonathan Blake and
Kenneth A. Marx
Refinements of Thermodynamic
Parameters Associated With Helix-Coil Transitions of Polymeric DNAs
D. Blake and Scott G. Delcourt
Studies of the Dynamics
of Adenine Amino Protons in DNA by 15N-Labeling and Heteronuclear NMR Spectroscopy
Ryszard Michalczyk and Irina M. Russu
Modeling DNA Replication
Intermediates
Roy, D., Hingerty, B.E. and Broyde, S.
Proton Exchange
and Internal Rotation of Cytosine Amino Groups in DNA Double Helices
Irina M. Russu and Ryszard Michalczyk
(CTG)n·(CAG)n
and (CGG)n·(CCG)n Triplet Repeats: Unusual Helical Properties and
Alternative DNA Secondary Structures
Richard R. Sinden, Paul D. Chastain II, Evan E. Eichler,
Stephen D. Levene, David L. Nelson and Christopher E. Pearson
Nonadditivity of
Interactions in H-bonded and Stacked Complexes of Nucleic Acid Bases. An
Important Contribution, Not Included in the Empirical Potentials
J. Sponer, J.V. Burda, J. Leszczynski and P. Hobza
Molecular Interactions
in i-DNA and Z-DNA. A Crystallographic, Quantum-Chemical and Preliminary
Empirical Potential Study
J. Sponer, I. Berger, M. Egli, H.A. Gabb, N. Spacková, P. Hobza
and A. Rich
Crystal Structure
of r(GUAUACA)dC: 3' Double Base Overhangs With Hemiprotonated Trans (dC·dC)+
Base Pairs and Minor Groove A*(G·C) Triplets
Ke Shi, Roopa Biswas, Shome Nath Mitra and Muttaiya Sundaralingam
Side-by-Side Binding
of Distamycin A to B-DNA: Crystal Structure of d(GTATATAC)2 - Distamycin
Complex With Two Independent Molecules
Shome Nath Mitra, Markus C. Wahl and Muttaiya Sundaralingam
The A-DNA Duplex
- How it Differs From B-DNA
Muttaiya Sundaralingam
Crystal Structure
of r(CCCIUGGG) with Tandem I·U Wobble Base Pairs-Three Independent
Octamer Duplexes
Baocheng Pan, Shome Nath Mitra and Muttaiya Sundaralingam
Effect of the Substitution
of Inosine on the Structure of A-tract DNA
Ruth M. Ganunis and Thomas D. Tullius
External Nucleophiles
That Induce DNA Cleavage in Conjunction With an Organometallic Complex
Celeste P. Jamison McDaniels and Thomas D. Tullius
Chimeric Homeodomains
Reveal the Importance of the N-terminal Arm in Determining the Structural
DNA Binding Characteristics of Dfd and Ubx Homeodomains
Richard W. Frazee and Thomas D. Tullius
Base-Triple Interactions
in the Triple Helical Domain of Self-Splicing Group I Introns
Martina Lindqvist, Munna Sarkar and Astrid Gräslund
Supercoiled DNA
Polyelectrolyte
Marcia O. Fenley, A. H. Boschitsch, Todd R. Quackenbush and Wilma K.
Olson
Slow Disproportionation
of Duplexes Formed by Ssdna/RNA Targets and Mixed Purine-Pyrimidine Pnas
With Lysines in the Backbone
E. Lesnik, F. Hassman, J. Barbeau, K. Teng, K. Weiler, R. Griffey and
S. Freier
Function and Mechanism
of Type -2 Topoisomerases
Rybenkov V., Vologodskii A., Ullsperger C., Khodursky A., Hildebrandt
E., Zechiedrich E.L., Peter B. and Cozzarelli N.R.
Interdomain Interactions
and Multivalent Association in Signal Transducing Domains
David Cowburn, David Fushman, Jie Zheng, Quinghong Xu, James McDonnell,
Sean Cahill and Rong Xu
DNA Recognition
by Peptide Nucleic Acid (PNA)
Pernilla Wittung-Stafshede
Eukaryotic Recombinant
Protein Rad51; its Thermal Stability and Complex Formation with Oligo(dT*)
Jong-Moon Kim, Masayuki Takahashi and Seog K. Kim
Binding Mode and
Base Specificity of Norfloxacin with DNAs
Gwan-Su Son, Jeong-Ah Yeo, Mi-Sun Kim and Seog K. Kim
Structure-Based
Design of Nucleic Acid Binding Ligands
Qi Chen, Irwin D. Kuntz and Richard H. Shafer
Optical Imaging
Approach to Study Protein-DNA Interaction and Nuclear Organization in Cultured
Living Cells
Han Htun, Julia Brsony and Gordon L. Hager
NMR Strategies for
Structure Based Drug Design
Jonathan M. Moore
Solution Structure
of an Oligodeoxynucleotide Duplex Containing the Exocyclic Lesion 3, N4-Etheno-2'-deoxycytidine
Opposite Deoxyguanosine: Determined by NMR Spectroscopy and Restrained Molecular
Dynamics
David Cullinan, Moshe Eisenberg, Arthur P. Grollman and Carlos de los
Santos
1H - NMR and Molecular
Dynamics Studies of a Model Hexapeptide GRGDTP
R. P. Ojha and A. K. Kulkarni
Molecular Dynamics
Simulations of the DNA Triplexe D(TG)5.D(CA)5.D(TG)5
R. P. Ojha and R. K. Tiwari
Ligands for DNA
and RNA
K. T. Douglas
The DNA Helical
Phasing Between Promotes and Regulatory Sites of Escherichia Coli
Vladimir Yu. Shumilov
RNA Splicing, Introns
and Biology
Phillip A. Sharp
X-Ray Diffraction
Study of Histone Proteins HMfA and HMfB from the Hyperthermophilic Archaeon
Methanothermus Fervidus
Klaas Decanniere, Kathleen Sandman, John N. Reeve and Udo Heinemann
Studies of Sequence-Dependent
Tertiary Structure in Supercoiled DNA by Site-specific Recombination
S. D. Levene and H. Tsen
Interactions of
the Antiviral Quinoxaline Derivative 9-OH-B220 {2,3-dimethyl-6-(dimethylaminoethyl)-9-hydroxy-6H-indolo-[2,3-b]quinoxaline}
with Duplex and Triplex Forms of Synthetic DNA and RNA
Ulrica Sehlstedt, Palok Aich, Jan Bergman, Hans Vallberg, Bengt Nordén
and Astrid Gräslund
Covalently Dimerized
DNA-Binding Domains of the Phage 434 Repressor: A Novel Protein Framework
to Study Protein-DNA Interactions
András Simoncsits and Sándor Pongor
DNA Structures Associated
With Class I Expansion of GAA in Friedreich's Ataxia
Cynthia T. McMurray, A. Marquis Gacy, Geoff M. Goellner, Craig Spiro,
Roy Dyer, Marci Mikesell, Janet Z. Yao, Aaron J. Johnson, Nenad Juranic,
Slobodan Macura, Andrea Richter* and Serge B. Melancon*
Structural Ensemble
of a Methylphosphonated-DNA·RNA Hybrid: Analysis of NMR Data
Anwer Mujeeb and Thomas L. James
Impact of pi - sigma*
Interactions on the Axial Preference of the Purine vs. Pyrimidine Nucleobase
in 2',3'-unsaturated Pentopyranosyl Nucleosides
Janez Plavec, Matjaz Polak and Piet Herdewijn
The Use of Suicide
Substrates to Probe the Mechanism of E. coli Topoisomerase I
Camille J. Roche, Chang-Xi Zhu and Yuk-Ching Tse-Dinh
Architectural Role
of p53 in the Spatial Organization of the DNA Response Element. Computer
Modeling and Comparison with Experiment
V. Zhurkin, A. Gorin, E. Appella, R. Harrington, R. Jernigan and S. Durell
Protein-DNA Recognition:
A Role for CH...O Interactions in the Major Groove
Y. Mandel-Gutfreund, H. Margalit, R.L. Jernigan and V.B. Zhurkin
Hydration, Electrostatics
and Dynamics of the HIV Tar-Tar* RNA Kissing Loops
Chang-Shung Tung and Angel E. García
Aggregation of
Guanine Dinucleotides: An Analytical Ultracentrifugation Study
Consuelo Walss, Borries Demeler, Jeffrey C. Hansen and Judith A. Walmsley
Are There Universal
Statistical Differences Between Coding and Noncoding DNA?
Ivo Grosse, Hanspeter Herzel, Sergey V. Buldyrev and H. Eugene
Data Mining of
Large Gene Datasets Using the Mutual Information Function
Ivo Grosse, Kenneth A. Marx, Sergey V. Buldyrev, Georges Grinstein, Hanspeter
Herzel, Pat Hoffman, Anzhi Li, Claudio Meneses and H. Eugene Stanley
Asymmetric Cleavage
of Nucleosomal DNA by Calicheamicing1I
Prasad N. Kuduvalli, Craig A. Townsend and Thomas D. Tullius
Relationships between
Crystal Packing and Conformation in Crystals of DNA Oligonucleotides
Helen M. Berman, Samuel Engel, Michael Mehnert and John Westbrook
Effects of Histone
Acetylation on Nucleosome Structure
E. M. Bradbury, F. Dong, J. Gatewood, S. Usachenko and P. Yau
Structure/Function
Relationship of the Insulin-Linked Polymorphic Region: Implications in the
Length Polymorphism and Gene Regulation
Paolo Catasti, X. Chen, E. Morton Bradbury and Goutam Gupta
Theoretical and
Experimental Investigations of the Conformational Transitions of Complexes
of DNA with Ligands Having Several Types of Binding Sites of Different Forms
of DNA
Armen T. Karapetian, Genady A. Terzikian, Ara P. Antonian, Pogos O. Vardevanian
and Maxim D. Frank-Kamentskii
The Topological
Complementarity of the Histone Octamer and DNA in the Nucleosome
Khrapunov S.N., Dragan A.I. and Sivolob A.I.
Structural Characterization
of Modified Nucleic Acids
Samuel S. Woodley, Linda Eckel, Charles W. Bailey, Christopher Lawrence
and Thomas R. Krugh
Experimental and
Computational Strategies for NMR Structure Determination of Troublesome
Proteins
F. Y. Luh, S. J. Archer, B. O. Smith, A. R. C. Raine, W. Boucher, S.
L. Brenner, P. J. Domaille and E. D. Laue
tRNAAsp-Aspartyl-Trna
Synthetase: Two Base-Pairs Make the Difference
D. Moras
Modes of Motions
and Mechanisms of Regulation in the Regulatory Domains of pp60 c-Src
Linda Nicholson
Conformational
Analysis of a Fourteen Amino Acid Mussel Adhesive Protein Peptide
Marion P. Olivieri, Robert M. Wollman, Emily A. Mysliwiec-Levandusky
and James L. Alderfer
Structure of the
A-Site of E. Coli 16s rRNA Complexed with an Aminoglycoside Antibiotic
Dominique Fourmy and Joseph D. Puglisi
A Link Between
Conformational Change and Ribozyme Specificity in Group II Introns
Anna Marie Pyle
Crystal Structure
of an IHF-DNA Complex: A Protein-Induced DNA U-Turn
Phoebe A. Rice, Shu-wei Yang, Kiyoshi Mizuuchi, and Howard Nash
DNA Methylation,
X Chromosome Inactivation, and Epigenetic Mechanisms
Arthur D. Riggs, Zhenggang Xiong, Lijun Wang and Jeanne M. LeBon
Interaction of
an Anti-HIV-1 Hammerhead Ribozyme With a 17-mer DNA Analog Substrate of
HIV-1 gag RNA: A 750 MHz NMR and Computer Experiments
Sarma, Ramaswamy H., Dhingra, M. M., Sarma, Mukti H.,Turner, Christopher
J.Setlik, R. F., Shibata, M., Rein, R., Kazim, A. L., Cairo, A. and Ornstein,
R. L.
Common Structural
Elements in Eukaryotic Promoters
Tanja Schätz and Jörg Langowski
A Global Overview
of Protein Folds
Dikeos Mario Soumpasis & Martin Christian Strahm
An RNA Bridge in
the l N Antitermination Complex Requires Tryptophan-Purine Stacking and
Base Flipping
Leila Su, James T. Radek, Patrick Hermanto, Klaas Hallenga, Huifen Chen,
Ging Chan, Laua A. Labeots and Michael A. Weiss
Evidence That the
DNA A-Tract is Bent and Rigid in Solution Obtained by Time-Resolved Fluorescence
Resonance Energy Transfer
Lukasz Milos, Sherri Oslick and Michael A. Weiss
Exploring the Energy
Landscape of Proteins: The Temperature Dependence of Dynamics of Ribonuclease
H
Arthur G. Palmer, III
Marked Discreteness
in Coil-globule Transition of Large DNA Molecules Induced by PEG (Polyethylene
Glycol)
Yukiko Matsuzawa and Kenichi Yoshikawa
Stereochemistry
of Protein/DNA Interactions
Paul B. Sigler
Structural Investigation
of a Binary-Addressed Oligonucleotide System Juxtaposing Pyrene and Perfluoroazide
Units by Means of High-Field NMR Spectroscopy and Molecular Modeling
Elena V. Bichenkova, Debora S. Marks, Sergei G. Lokhov, Michail I. Dobrikov,
Valentin Vlassov and Kenneth T. Douglas
How the TATA Box
Selects its Protein Partner
Nina Pastor and Harel Weinstein
A Backward Glance
at the Nucleic Acids
Alexander Rich
Structural Studies
on the Unstable Triplet Repeats
S.V. Santhana Mariappan, Paolo Catasti, Xian Chen, Louis A. Silks III,
Robert K. Moyzis, Larry L. Deavan, E. Morton Bradbury and Goutam Gupta
Simulations of DNA
Cyclization by Brownian Dynamics
Alexi Podtelzhnikov and Alexander Vologodskii
DNA Replication
in a Crystal: a High Resolution Snapshot of a Polymerase in Action
James Kiefer, Chen Mao and Lorena S. Beese
RNA-Protein Recognition
in the HIV Rev-RRE Complex
J.L. Battiste, H. Mao, Thomas J. Tolbert, Kwaku T. Dayie, R.Tan,
R. Sambasiva, L. E. Kay, A.D.Frankel and J.R.Williamson
Molecular-Dynamics
Simulation of (dA·dT:dT)6 on Nanosecond Trajectories
S. Yu. Tsybenko, I. A. Il'icheva and V. L. Florentiev
Heterogen Complexes
of Ethidium Bromide and Their Role in Stabilization of Helix DNA
Ara P. Antonian, Pogos O.Vardevanian, Genady A. Terzikian,Armen T. Karapetian
and Olga F. Borisova
New Methods for
the Free Energy Calculation with Implicit Solvent Model
Yury N. Vorobjev and Jan Hermans
Beta-Sheet Assembles
DNA's Homo- and Heterologous Quadruplexes
Sergei A. Streltsov, Marina V.Borodina and Tymur E.Semenov
Spectroscopic Studies
of the Stability Enhancement of Selective
5-Substituted Cytidine and Hydration on the Conformations of DNA Triple
Helices Containing a TTTT Loop
Lou-sing Kan, Ye Fang, Chunli Bai and S. B. Lin
Identification and
Characterization of Genomic Nucleosome-Positioning Sequences
Hans R. Widlund, Hui Cao, Stina Simonsson, Elisabet Magnusson, Tomas
Simonsson, Peter E. Nielsen, Jason D. Kahn, Donald M. Crothers and Mikael
Kubista
GAT(G)-Repeats Form
Unstable Nucleosomes
Hui Cao, Hans R. Widlund and Mikael Kubista
Mouse Major Satellite
DNA in a Positioned Nucleosome
Hans R. Widlund, Prasad N. Kuduvalli, Thomas D. Tullius and Mikael Kubista
Genome Instability:
Structural Basis of Triplet Repeat Expansion and Genetic Disorders
Samir K. Brahmachari, P.S. Sarkar, U. Shaligram, M. Mutsuddi, S. Raghavan,
R. Bhandari, S.S.Pataskar, M. Narayan and Quasar, S.P
Analogues of Hoechst
33258 Bind to Transfer RNA with 1:1 Stoichiometry
S.E. Sadat Ebrahimi, Amanda N. Wilton and Kenneth T. Douglas
The Bi-loop, a New
General Four-Stranded DNA Motif
Stephen A. Salisbury, Sarah E. Wilson, Harold R. Powell, Olga Kennard,
Paolo Lubini, George M. Sheldrick, Nuria Escaja, ElMostafa Alazzouzi, Anna
Grandas and Enrique Pedroso
Role of the C-terminal
Zinc Finger in the Recognition of Damaged DNA by Fpg, a DNA Repair Enzyme
Serge Smirnov, Carlos de los Santos, Teri Klein, Arthur Grollman and
Moises Eisenberg
Structure of Mispairs
Formed by 2'-Deoxy-6-Thioguanosine in DNA
Rahul Mitra and B. Montgomery Pettitt
Inhibition of the
HIV-1 Integrase by DNA Quadruplexes is Dependent on Their Structure
Rahul Mitra, Sandy Lee, Michael E. Hogan and B. M. Pettitt
Protein Displacement
By Sequence-Directed DNA-Binding Molecules: The MERLINTM Assay System for
Drug Discovery
Lisa M. Turin, Alka Chawla, Gary P. Schroth and Cynthia A. Edwards
Tet Repressor Binding
to Operator DNA and Tetracycline Studied by Infrared and Raman Spectroscopy
C. Krafft, W. Hinrichs, P. Orth, W. Saenger and H. Wefle
Mutational Analysis
of Active Site of RNase Bacillus Intermedius (Binase)
N. Struminskaya, G. Yakovlev, G. Moiseev, L. Kipenskaya, L. Znamenskaya,
I. Leschinskaya and R. Hartley
Computer Simulation
of Codon - Codon Replacements
B. Borstnik
Triple Helical Structures
Involving Deoxyinosine: There is a Penalty for Promiscuity
Martin Mills, Jens Völker and Horst H. Klump
Influence of DNA
Topology on the Homologous Sequence Search Mediated by RecA Protein of E.
Coli
U. Marquardt and J. Chen
The Sep1 Strand
Exchange Protein From Saccaromyces Cerevisiae Does Not Promote Strand
Exchange Reaction
Z. Zhang and J. Chen
The Topological
Linkage of the Kinetoplast Minicricle DNA From Leshimania Tarentolae
W. A. McLaughlin, R. Hanson and J. Chen
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