Table of Contents: Abstracts

As of May 20, 1999

Stabilization of Double Stranded Homologous poly(dA)·poly(dT) Strands by Taxol®
Gerlinde Bischoff, Ulrich Gromann, Sabine Lindau, Robert Bischoff, Christian Bohley, Walter-Vesély Meister, Siegfried Hoffmann

DNA At-Rich Regions: Some Structure-Function Relations
Anna Gabrielian

Effect of the Concentration of the Multimodal Ligands on the Stabilization of the Double Helix of DNA
Armen T. Karapetian, Grigor A. Manukin and Pogos O. Vardevanian

Experimental Study of Triple Helices with Antiparallel and Parallel Third Strands Containing G and T Bases
E. Khomyakova, H. Gousset, J. Liquier, V. Florentiev, A. Mirzabekov and E. Taillandier

Crystal Structures of Highly Bent RNA Duplexes Forming Tertiary Interactions and Superhelical Coils
Shome Nath Mitra, Ke Shi, Roopa Biswas and Muttaiya Sundaralingam

Modulation of Sequence-Specific Protein p53 DNA Binding and of p53 Binding to Supercoiled DNA by the Protein Redox State and by Metal Ions
Miroslav Fojta Marie Brazdova, Vaclav Bradza, Hana Cernocka and Emil Palecek

Solution Structure of an Antibody-bound HIV-1IIIB V3 Peptide: a Cis Proline Turn Linking Two Beta-Hairpin Strands
Vitali Tugarinov, Anat Zvi, Rina Levy and Jacob Anglister

A Method for Determining the Energy Hierarchy in Macromolecules of Globular Proteins. The Problem of Domain Structure Definition.
Igor N. Berezovsky, Vladimir A. Namiot, Vladimir G. Tumanyan and Natalia G. Esipova

Fold-Back DNA Tetraplex Specieses in DNAse I-Resistant DNA Isolated From Hela Cells
En-hua Cao Xue-guang Sun Xiao-yan Zhang Chun-li Bai

Novel Sheared A:C Pairing in DNA
Shan-Ho Chou

Structure of Photoreactive Binary System of Oligonucleotide Conjugates Assembled on the Target Nucleotide Sequence
Michail I. Dobrikov, Elena V. Bichenkova, Kenneth T. Douglas, Timur I. Gainutdinov and Valentin V. Vlassov

Solution Structure and Base-pair Opening Rates of GGCC Containing Oligonucleotides
Utz Dornberger, Mikael Leijon and Hartmut Fritzsche

Specific Binding of Lexitropsins to Okazaki Fragments Studies by PFG NMR
William H. Gmeiner, Christopher Hudalla and J. William Lown

Electrophoretic Mobility of DNA and Protein-DNA Complexes
U. Mohanty

Optical Probes of DNA Sequence-Directed Bending and Dynamics
Catherine J. Murphy

Designed Two-Dimensional DNA Holliday Junction Arrays
Chengde Mao, Weiqiong Sun and Nadrian C. Seeman

Modifying the Surface Features of Two-Dimensional DNA Crystals
Furong Liu, Ruojie Sha and Nadrian C. Seeman

Parallel Helical Domains in DNA Branched Junctions Containing 5', 5' and 3', 3' Linkages
Ruojie Sha, Furong Liu, Michael F. Bruist and Nadrian C. Seeman

Two Dimensions and Two States in DNA Nanotechnology
Nadrian C. Seeman, Furong Liu, Chengde Mao, Xiaoping Yang, Lisa A. Wenzler, Roujie Sha, Weiqiong Sun and Erik Winfree

Conformational Dynamics of a Nucleic Acid Molecule over Hydration-Dehydration Cycle: A Theoretical Study
M.Ye. Tolstorukov, S.V. Gatash and V.Ya. Maleev

M-DNA: A Physiologically Stable New Form of DNA Which is an Effective Molecular Wire
Palok Aich, Shaunivan L. Labiuk, Krista Wooller, Les W. Tari, Kenneth J. Falk, Louis J. T. Delbaere, William J. Roesler, Ronald P. Steer and Jeremy S. Lee

Triplex DNA and Terminal Differentiation
Claude E. Gagna, Hon-Reen Kuo and W. Clark Lambert

Protein-Modulated DNA Electron Transfer
Scott R. Rajski, Sanjay Kumar, Richard J. Roberts and Jacqueline K. Barton

Molecular Modelling of the HIV-1 Tat Protein - TAR RNA Complex and the Design of an Inhibitor of the Tat/TAR RNA Interaction
Gita Subba Rao, Mohd. Imran Siddiqui and Sneh Arora

Assembly of Topologically Linked Structures between Duplex DNA and a Circular Oligonucleotide
Heiko Kuhn, Vadim V. Demidov and Maxim D. Frank-Kamenetskii

Structure and Motion of an Intramolecular i-motif of Human Telomeric DNA
Anh Tuân Phan, Jean-Louis Leroy and Maurice Guéron

Parallel-Stranded DNA with Mixed AT/GC Content: Role of Trans G·C Pairs in Specific Sequence Dependence of the Double Helix Stability
Anna K. Shchyolkina, Olga F. Borisova, Michael A. Livshits, Galina E. Pozmogova, Reinhardt Klement and Thomas M. Jovin

Conformational Polymorphism Observed in Myoclonus Epilepsy Repeat Sequence in Solution
Shashank S Pataskar and Samir K Brahmachari

Development of Techniques for Structure Determination of Larger Systems by Means of NMR. Application to the Primer Binding Site for Reverse Transcriptase in the Pregenomic RNA from Hepatitis B Virus.
J. Cromsigt, J. Schleucher, J. Zdunek, C. Hilbers and S. Wijmenga

Binding of P53 to Supercoiled DNA and its Modulation by the Protein Redox State and by Metal Ions
M. Fojta, M. Brazdova, H. Cernocka, P. Pecinka, V. Brazda, J. Palecek, J. Buzek, B. Vojtesek, V. Subbaramanian, T. M. Jovin and E. Palecek

Protein-Nucleic Acid Interactions in Thermophiles: Crystal Structures of Specific and Non-Specific DNA-Binding Proteins
Mark J. van der Woerd, Matthew M. Skinner, Ying Luo, Zvonimir Siljkovic, Alan M. Friedman, Shuang-yong Xu, John J. Pelletier, Diaqing Liao, Patrick P. Dennis

The B-Z Transition of DNA. A Unified Electrostatic Interpretation of the Effect of Multivalent Ions at Very Low and Very High Concentrations: the Irrelevance of Specific Binding.
J.-Ph. Demaret and M. Gueron

Sites for Water and Ions in DNA Grooves: Location, Occupancy and Residence Times
Anh Tuân Phan, Jean-Louis Leroy and Maurice Guéron

Energetics of Hydrogen Bond Formation in Base Pairs in Aqueous and Non-Aqueous Media: Implications to Protein-DNA Recognition
Surjit B. Dixit and B. Jayaram

A Geometrically Organized, 3D Library of Recurrent, Isosteric Base-Base Interactions Useful for RNA Modeling
Neocles B. Leontis

Circularization of the Oligonucleotides to Form One Unic Slipped-Loop Structure
E.E. Minyat, A.D. Beniaminov, N.G. Dolinnaya and V.I. Ivanov

p53-Induced DNA Bending and Twisting: Implications for p53 Interactions With Chromatin
A.K. Nagaich1, V.B. Zhurkin, E. Appella and R.E. Harrington

Is Carboplatin Chemically Activated Before Reaching its Target Sequences?
G.Natarajan, R.Malathi and Eggehard Holler

Structural Model of DNA for Homology Search and Strand Exchange
Taro Nishinaka, Shigeyuki Yokoyama and Takehiko Shibata

Agrangian and Quaternion Dynamics of Nucleic Acids
Witold R. Rudnicki, Grzegorz Bakalarski and Bogdan Lesyng

Structural Studies on DNA Three- and Four-Way Junctions
Bernd N.M. van Buuren, Franc J.J. Overmars, Johannes H. Ippel, Cornelis Altona, Harald Schwalbe, Christian Griesinger, Juergen Schleucher and Sybren S. Wijmeng

Probing the Structure of (CGG)n Triplet Repeats in the Human FMR1 Gene via Interstrand Crosslinking
Kissinger Goldman, Meghan Lembeck, and James S. Godde

tRNA Molecules Assemble in Thin Flexible Rods up to Several Micrometers Long in the Presence of a Trivaline Derivative
Sergei A. Streltsov, Larissa P. Martinkina and Yuri Yu. Vengerov

DNA Rare Cleavage Using PNA Invaders
Vadim V. Demidov, Konstantin I. Izvolsky, Peter E. Nielsen and Maxim D. Frank-Kamenetskii

The Role of Ligand Hydrophobicity in Interaction of Minor Groove Binders with DNA
A.L. Mikheikin, A.L. Zhuze and A.S. Zasedatelev

Bridging the Prebiotic and RNA Worlds: Prebiotic RNA Synthesis on Clay
G. Ertem, K. J. Prabahar, P. C. Joshi and J. P. Ferris

ES/IS Method for Free Energy Calculation: Structure and Stability of a Four Helix Bundle ROP Mutant Proteins
Yury N. Vorobjev and Jan Hermans

Premelting Regions of DNA as Revealed by the Comparision of the Differential Melting Curves of DNA and DNA-Hoechst Complex
Genady A. Terzikian, Ara P. Antonian, Pogos O. Vardevanian, Grigir A. Manukian and Armen T. Karapetian

Structural Studies of an Alkylimidazolic Binary-Addressed Oligonucleotide System Mimicking Ribonuclease A
Elena V. Bichenkova, Susan E. Austin, Kenneth T. Douglas, Vladimir N. Sil'nikov and Valentin V. Vlassov

Universal RNA Pseudoknot is Present in the Ribosomal Peptidyl Transferase Center
Valery I. Ivanov, Sergei A. Bondarenko, Evgenyi M. Zdobnov, Artyom D. Beniaminov, Elvira E. Minyat and Nick B.Ulyanov

Sequence Determinants of DNA Structure and the Mechanism of DNA Structure Recognition by 434 Repressor
David R. Pawlowski, Mihai Ciubotaru and Gerald B. Koudelka

Structure of The Nucleosome Core Particle
Karolin Luger, Armin W. Muder, David F. Sargent and Timothy J. Richmond

Comparison Between Different Structures of the Oligonucleotide d(CGTATATACG) as a Site Specific Complex with Nickel Ions
Nicola G. A. Abrescia, Lucy Malinina and Juan A. Subirana

Interactions of Nucleic Acid Bases and the Structure of DNA
J. Sponer

Interactions of Metal Cations (Ia, Ib, IIa, and IIb Groups, and PtII) with Nucleobases and Nucleotides. Binding Energies, Polarization Effects, and Formation of Metal Assisted Rare Tautomers. Quantum Chemical View vs. Experiments.
J. Sponer, J.V. Burda, J.E. Sponer, M. Sabat, B. Lippert, P. Hobza and J. Leszczynski

Molecular Dynamics Simulations of Four-stranded Nucleic Acid Structures: i-DNA and G-DNA
N. Spaèková, I. Berger and J. Sponer

Conformational Flexibility of DNA G-Quadruplexes Formed From D(Gt)N And D(Ttaggg)N Repeating Telomeric Sequences
Olga F. Borisova, Anna K. Shchyolkina, Irina A. Il'icheva and Michael A. Livshits

Enzymatic Deglycosylation and Dephosphorylation of Paired Helical Filaments (PHF) Studied by Transmission Electron Microscopy (TEM)
George C. Ruben, Jian-Zhi Wang, Inge Grundke-Iqbal and Khalid Iqbal

Recognition of DNA by Fpg Protein from Escherichia coli
A. Ishchenko, V. Koval, O. Fedorova, K. Douglas and G. Nevinsky

Cooperative Interactions of Oligonucleotides Bound to Adjacent Sites of DNA: Effect of Mismatched Base Pairs at the Junction on the Parameters of Cooperativity
O. Fedorova, V. Koval, A. Adeenah-Zadah, N. Karnaukhova and S. Lokteva

Photosensitized Modification of DNA Within Tandem Complexes of Oligonucleotide Derivatives Covalently Attached to Photochemical and Sensitizing Groups: Influence of Nucleotide Composition at the Junction
Vladimir V. Koval, Elena V. Bichenkova, Kenneth T. Douglas, Michail I. Dobrikov and Olga S. Fedorova

Origins of Opposite Orientations in Adducts of Enantiomeric Anti-benzo[a]pyrene diol Epoxides and cis/trans Conformational Differences
Xie, X., Geacintov, N. E. and Broyde, S.

Nucleic Acid Structure-Based Drug Development
Thomas L. James, Zhihua Du, Anton V. Filikov, Kenneth E. Lind and Anwer Mujeeb

Aminoacylation at the Atomic Level in Class Iia Aminoacyl-Trna Synthetases
John G. Arnez, Rajan Sankaranarayanan, Anne-Catherine Dock-Bregeon, Christopher S. Francklyn and Dino Moras]

Structure and Thermostability of DNA Containing A·T Pairs in Alternating and Non-Alternating Sequences: Investigation of Premelting, Melting and Postmelting Phenomena by Raman Spectroscopy
James M. Benevides, Liviu Movileanu and George J. Thomas, Jr.

Visualizing RNA Folding at Millisecond Intervals by X-Ray Footprinting
Corie Ralston, Bianca Sclavi, Mike Sullivan, Michael Brenowitz and Mark Chance

Species Specific Identification and Characterization of Mycobacterium Habana by PCR-based Sequence Determination of a Region of the HSP65 Gene
Anjna Dixit and Uma Roy

The Effects of Ligand Binding to RNase A on the Transition Volume of Denaturation
D. Dubins, T. Chalikian and R.B. Macgregor, Jr.

Hydroxyl Radical Footprinting of the Tetracopper Domains of CUP2 and AMT1
Marie L. Estock, Kenneth R. Brown, Dennis R. Winge and Thomas D. Tullius

On the Mechanism of Long Range Electron Transfer Through DNA
Bernd Giese, Eric Meggers, Stephan Wessely and Martin Spormann

Rational vs. "Irrational" Drug Design: Combinatorial Selection and NMR Structure of Thioated DNA Aptamers
Daniel Ventura, David King, Xian Bin Yang, Sheela Venkitachalam, David E. Volk, Susan Fennewald, Allan Brasier, Norbert Herzog, Judy Aronson, Bruce Luxon and David Gorenstein

Structures of the DNA Intermediates in Cre-loxP Site-specific Recombination
Feng Guo, Deshmukh N. Gopaul and Greg D. Van Duyne

Signals for TBP/TATA-box Recognition
Avital Bareket-Samish, Ilana Cohen and Tali E. Haran

A Kinetic Study of the Effect of Polyamine on the Formation of DNA Duplexes by Surface Plasmon Resonance
Lou-sing Kan, Ming-hong Hou, Wei-chen Lin and Shwu-Bin Lin

An Effective Potential for a Mezoscopic Model of DNA
Maciej Maciejczyk, Witold R. Rudnicki and Bogdan Lesyng

UV Absorption and Resonance Raman Studies of a DNA Dodecamer Containing an A3t3 Tract
Ishita Mukerji and Alison P. Williams

Molecular Dynamics Analysis of 3:70 MicrohelixAla Variants
Maria C. Nagan, Stephanie S. Kerimo, Christopher J. Cramer and Karin Musier-Forsyth

Why Salt Bridges in Thermophilic Proteins?
Sandeep Kumar, Buyong Ma, Chung Jung Tsai and Ruth Nussinov

NMR Dipolar Couplins for Improving the Local and Long-Range Structure of Nucleic Acids
Arthur Pardi, Emilia Mollova, Paul Hanson and Mark R. Hansen

Structural and Thermal Induction of the Formation of DNA Frayed Wires
Ekaterina Protozanova and Robert B. Macgregor, Jr.

Probing the Sequence-Dependent Flexibility of Short DNA Double Helices
A. R. Srinivasan, Michael Weiss and Wilma K. Olson

Determination of Structure and Diffusion Property of Human G-alpha Interacting Protein
Eva de Alba, Luc de Vries, Marilyn G. Farquhar and Nico Tjandra

Structural Chemistry of DNA Cleavage by the Hydroxyl Radical
Tom Tullius

A Structural Framework for Cre-loxP Site-Specific Recombination
Feng Guo, Deshmukh N. Gopaul and Gregory D. Van Duyne

DNA Binding of L- and D-cis-b-[Ru(RR-picchxn)(phen)]2+ as Probed by NMR and Flow Linear Dichroism Spectroscopy
Kymberley Vickery, Robert Vagg, Per Lincoln, Bengt Nordén and Magdalena Eriksson

A Universal Motif of Sex Determination: Structure of a Novel Zn Finger in the Doublesex DNA-Binding Domain
L. Zhu, J. Wilken, G. Chan, L. Milos, S. B. Kent and M. A. Weiss

Measurements of the Preferential Interaction Parameter of Oligonucleotides: A Study of End Effects
Alison P. Williams

Stereodifferentiation of Triple Helix Formation by P-chiral Chimeric Oligo(deoxyribonucleoside Methanephosphonamidate)s and Double Stranded DNA
Malgorzata Boczkowska, Barbara Nawrot and Wojciech J. Stec

Different Ability of Stereoregular Phosphorothioate Oligonucleotides of [PS]-d(CG)4 and [PS]-d(GC)4 Series to Adopt the Z-DNA Form
Malgorzata Boczkowska, Piotr Guga and Wojciech J. Stec

The Packaging Region of HIV. Dimer Formation and Protein Binding
Michael Shubsda, Mark McPike, Jerry Goodisman and James Dabrowiak

A Study of the Hydration of Deoxydinucleoside Monophosphates Containing Thymine, Uracil and Its 5-Halogen Derivatives: Monte Carlo Simulation
V. I. Danilov, J. L. Alderfer, V. I. Poltev and O. N. Slyusarchuk

bZIP protein Maf Binds DNA Using a Unique Contact Interface
Mensur Dlakic and Tom K. Kerppola

Analysis of Degenerate Tetranucleotides From B-DNA Crystal Structures
Mensur Dlakic, Wendy M. Dlakic and Rodney E. Harrington

The Fast Boundary Element Method for Solving the Linear Poisson-Boltzmann Equation
Marcia O Fenley, Alexander H. Boschitsch and Wilma K. Olson

Excess Counterion Binding and Ionic Stability of Branched DNA
Marcia O. Fenley, Gerald S. Manning and Wilma K. Olson

The Multifaceted DNA Binding Mode of Neocarzinostatin Chromophore, an Endiyne Antitumor Drug
Xiaolian Gao, Jie Ji, Adonis Stassinopoulos and Irving H. Goldberg

Friedreich's Ataxia Related GAA and CTT DNA Triplet Repeats are Capable of Forming Parallel and Antiparallel Duplexes and pH Dependent YRY Triplex
Eric M. LeProust, Christopher E. Pearson, Richard R. Sinden and Xiaolian Gao

Towards The Understanding Of Self-Stabilization And Hybridyzation Of Antisense Oligonucleotides Containing Backbone Modifications
Xueyong Yang, Laëtitia Sonigo, Hua Zhang, and Yogesh Sanghvi and Xiaolian Gao

Structural and Dynamic Properties of a DNA Duplex Containing Localized Alpha-Anomeric Nucleotides and Polarity Reversals
James M. Aramini, Anwer Mujeeb and Markus W. Germann

DNA Sequence Recognition by Bis-linked Netropsin and Distamycin Derivatives
S. L. Grokhovsky, A.N. Surovaya, G. Burckhardt, V. F. Pismensky. S.A. Rodin, B.K. Chernov, Ch. Zimmer and G.V. Gursky

Study by NMR of the Structure of a Hairpin-Loop DNA Containing Unpaired C and G Bases
Nikolai B. Ulyanov, William R. Bauer and Thomas L. James

Multiple-Copy Refinement of Nucleic Acids via Fitting Dipolar Relaxation Rates
Adrian Goerler, Nikolai B. Ulyanov and Thomas L. James

Deducing Functional Behavior from Protein Structures
R.L. Jernigan

Dissociation of Human Rad51 Pprotein From ssDNA Upon Addition of ATP
Hye-Kyung Kim, Katsumi Morimatsu, Eimer Tuite, Bengt Norden and Masayuki Takahashi

Thermodynamic and Structural Studies of RNA Hairpins Containing Six-Nucleotide Loops
Hong Zhang and Thomas R. Krugh

A Unified Approach to the Synthesis of Labeled Purine Deoxynucleosides and Its Application to NMR Studies of DNA Oligonucleotides
Ryszard Michalczyk, Charles C. Orji and L. A. "Pete" Silks

Effect of Metals on Binding of Tumor Suppressor Protein P53 to DNA
E. Palecek, M. Brazdova, H. Cernocka, V. Brazda and B. Vojtesek

Interaction of PNA and DNA Oligomers With Charged Surfaces
M. Tomschik, F. Jelen, L. Havran, P. E. Nielsen, M. Fojta and E. Palecek

Electrodes Modified With Supercoiled DNA: Electrochemical Probes of DNA Structural Transitions, Interactions and Damage
M. Fojta, T. Kubicarova, L. Havran and E. Palecek

Different Tertiary Structures of DNA Heteroduplex Isomers from the Gel Mobility and Atomic Force Microscopy Data
Vladimir N. Potaman, Elena A. Oussatcheva, Richard R. Sinden, Luda S. Shlyakhtenko and Yuri L. Lyubchenko

Structural Effects in DNA Polymerization on a Single-Stranded Template
Vladimir N. Potaman

Modular Assembly and Characterization of Minor Groove Binders: Part I. Nylon-Like Amide Linkers in the Design of Covalently-Linked Distamycin Dimers
Manashi Chatterjee and Malvinder P. Singh

Modular Assembly and Characterization of Minor Groove Binders: Part II. Novel Pyrrolyl-Benzimidazole Combinations as Distamycin and Hoechst 33258 Mimics
Malvinder P. Singh and Wei Lu

Peptide Nucleic Acid Helices Studied by Vibrational Circular Dichroism Spectroscopy
M. Krasteva, H. Wieser and J.H. van de Sande

Metal Ion Interaction with Synthetic Oligonucleotides Studied by Vibrational Circular Dichroism Spectroscopy (VCD)
V. Andrushchenko, H.Wieser, J.H. van de Sande, S. Kornilova and Yu. Blagoi

Conformation and Polymorphism of HIV-1 Principal Neutralizing Determinant
Alexander M. Andrianov

A Structure-Function Study of Nucleic Acid-Fluorenone Complexes
G. Bischoff, U. Gromann, S. Lindau, R. Skölziger, W. Witkowski, C. Bohley, W.-V. Meister and S. Hoffmann

An 1H NMR Study of the Interactions of Formamide with 5'-GMP
S. Vaitheeswaran, R. D. Blake, C. E. Tarr and K. D. Bishop

Loop Conformations in Proteins: Buried Water Considerations
Louis Carlacci

Actinomycin D Binds Strongly to d(CGACGACG) and d(CGTCGTCG)
Feng Sha and Fu-Ming Chen

Use of the Orientational Dependence of 15N NMR Relaxation for Direct Determination of Changes of Interdomain Orientation in Abl SH(32) on Ligation
David Fushman, R.Xu and David Cowburn

NMR Studies of a Cyanocobalamin Binding RNA Aptamer
L. David Finger and Juli Feigon

Direct Determination of Protein Dynamics From 15N NMR Relaxation Data at Multiple Fields, Independent of 15N Chemical Shift Anisotropy and Chemical Exchange Line Broadening
David Fushman, Nico Tjandra and David Cowburn

A New Class Of Models For Computing Receptor-Ligand Binding Affinities
Michael K. Gilson, Laurent David, Martha S. Head, Ray Luo, Kristy Mardis, Michael J. Potter

Solution Structure of A Replicable Nonpolar Base Pair In DNA
Kevin M. Guckian, Thomas R. Krugh and Eric T. Kool

Biomesogenic Matrix Systems
W.-V. Meister, S. Lindau, A.L. Hauser, C. Bohley, U. Gromann, M. Madre, L. Kovalenko, G. Bischoff, R. Zhuk and S. Hoffmann

HU-DNA Complex Formation Studied By Fluorescence Anisotropy
K. Wojtuszewski, M. Hawkins and I. Mukerji

On Comparative Conformational Analysis of Nucleic Acid Structures
Xiang-Jun Lu and Wilma K. Olson

Stability of Quadruplex Structures Formed by Parallel d(GT)n Strands
Michael A. Livshits, Olga F. Borisova, Olga K. Mamaeva and Anna K. Shchyolkina

DNA and Buffers: The Hidden Danger of Complex Formation
Nancy Stellwagen

DNA Structure: Cations in Charge?
Loren Dean Williams, Lori McFail-Isom and Chad C. Sines

Revealing Selected Components and Architectural Elements In Ribosomal Particles at Medium Resolution
Ada Yonath

DNA Sequence Recognition of a Cross-Linked Lexitropsin: CD Studies, Footprinting and Effects on the Activity of DNA Gyrase
Günther Burckhardt, Ingo Förtsch, Hannelore Simon, Eckhard Birch-Hirschfeld, Leonhard Kittler, J.William Lown and Christoph Zimmer

New Insights from Atomic Force Microscopy of DNAHelen
G. Hansma

Structural Studies of Model RNA Helices with Relevance to HIV Reverse Transcription and Aminoacyl-tRNA Synthetase Specificity
Udo Heinemann, Uwe Mueller, Hermann Heumann and Mathias Sprinzl

Binding of [Ru(phenanthroline)2L]2+ to Double Stranded DNA: From Major Groove or Minor Groove?
Chang-Beom Cho, Sung Wook Han and Seog K. Kim

Cofactors and DNAs Dependent Melting Profile of yeast Rad51 Protein
Young Ae Lee, Sung Wook Han and Seog K. Kim

Functional Roles of DNA-Induced Conformational Changes in 434 Repressor
Mihai Ciubotaru, Frank V. Bright, Christine Ingersoll and Gerald B. Koudelka

Fractional DNA Structures
Vitaly V. Kuryavyi and Dinshaw J. Patel

Higher-Order Structure of Mammalian Chromatin Deduced From Viscoelastometry Data
J.Y. Ostashevsky, B.I. Reichman and C.S. Lange

Antisense Oligonucleotide Binding to Human Serum Albumin
Elena A. Lesnik, Nathan B. Sioufi and Susan M. Freier

Multiple Equilibria in DNA Rings Induced by Intrinsic Curvature
Patrick Furrer, Rob Manning and John Maddocks

The Loci Project
J. W. Bizzaro and Kenneth A. Marx

Endothelial Cell Adhesion and Spreading Studied with the Quartz Crystal Microbalance
Tiean Zhou, Kenneth A. Marx, Michael Warren and Susan J. Braunhut

Simple Efficient Protocol for Enzymatic Synthesis of Uniformly 13C and 15N Labeled DNA and Use in Heteronuclear NMR Studies
James E. Masse, Frederic H.-T. Allain, Yi-Meng Yen, Reid C. Johnson and Juli Feigon

A Conformational Comparison of a Pair of Cyclic Peptides with Bioadhesive Implications
Marion P. Olivieri, Robert M. Wollman and Michael F. Swartz

A Polymer Model For the Structural Organization of Chromatin Loops and Minibands in Interphase Chromosomes
J.Y. Ostashevsky

Prophyrin Self-Assembly on DNA
Matthew A. Ismail and Alison Rodger

A Paradigm for a Tight Biological Switch: X-ray Studies on Tetracycline Repressor and its Complexes with Tetracycline and Operator DNA
W. Saenger, P. Orth, C. Kisker, W. Hillen and W. Hinrichs

Parallel Side-by-Side Peptide Motif as a Probe for DNA Minor Groove Local Conformation
A.N. Surovaya, G. Burckhardt, S. L. Grokhovsky, V. F. Pismensky, Ch. Zimmer and G. Gursky

Average Local Helical Parameters of DNA: A Comparison of AMBER and X-ray Data
Dmitry Bondarev and Carol A. Venanzi

The fMet-tRNA Binding Domain of Translational Initiation Factor IF2 is Composed of Two Sub-Domains
Rolf Misselwitz, Karin Welfle, Christoph Krafft, Enrico Caserta, Letizia Brandi, Cynthia L. Pon, Claudio O. Gualerzi and Heinz Welfle

Algorithmic Self-Assembly of DNA
Erik Winfree

Iodine-125 Radioprobing: A Novel Method to Study DNA Conformation in Nucleoprotein Complexes in Solution
Igor G. Panyutin, Valeri N. Karamychev, Ronald D. Neumann, Susan Garges and Victor B. Zhurkin

EVENING LECTURE
8:00 pm, Wednesday, June 16, 1999
Structure Function Studies in the Mammalian Photoreceptor Rhodopsin
H. Gobind Khorana

Exocyclic Group Interactions in Minor Groove
Determine Groove Dimensions in DNA
Manju Bansal and Anirban Ghosh

Our Vision For The New Protein Data Bank: The Research Collaboratory for Structural Bioinformatics
Helen M. Berman, John Westbrook, Kyle Burkhardt, Zukang Feng, Shri Jain, Rachel Kramer, Bohdan Schneider, Christine Zardecki, Peter Arzberger, Phil Bourne, John Badger, Helge Weissig, Gary Gilliland, Phoebe Fagan, Hillary Gilson, Diane Hancock, Narmada Thanki and Greg Vasquez

Biochemical and Structural Studies of a DNA/Dirhodium Adduct: A Potential Chemotherapeutic Agent
Karl D. Bishop, Lee Bickerstaff, Elizabeth Lozada and Kim Dunbar

Reading Chips by Automated Mass Spectrometry
Charles R. Cantor

Affinity and Specificity Mechanisms of DNA-Binding Proteins
Jannette Carey

RNA as Molecular Wire
P. Acharaya, A. Trifonova, C. Thibaudeau and J. Chattopadhyaya

Solution Structure of the Tachykinin Neuropeptide Kassinin
C.R. Grace, Andrew Lynn and Sudha M. Cowsik

Solution Structure of the TYMV Pseudoknot and New RNA Structural Motifs
C.W. Hilbers, M.H. Kolk, P.J.A. Michiels, S.S. Wijmenga, C.W.A. Pleij and H.A. Heus

PrISM: A Protein Informatics System for Modeling
An-Suei Yang and Barry Honig

Computing with RNA
Laura Landweber

Direct Optimization of Nucleic Acid Base Sequences
Ingrid Lafontaine and Richard Lavery

Structure of a Double Stranded Oligonucleotide Containing a Cisplatin Interstrand Cross-link: NMR and Crystallographic Models
Jean-Marc Malinge, Franck Coste, Charles Zelwer and Marc Leng

Sequence Determinants of Protein Structure: Evolution of a Fold in Vitro
Robert T. Sauer, Matthew H.J. Cordes, Nathan P. Walsh and C. James McKnight

The Ligand-Binding Domain of Nuclear Hormone Receptor
Dino Moras and Jean-Marie Wurtz

Protein-Dominated Folding of the Double Helix into Chromatin: Architecture and Dynamics of the Nucleosome
E. N. Moudrianakis

Enhanced Flexibility of Charged Membranes and Polyelectrolytes Screened by Multivalent Counterions
T. Nguyen, I. Rouzina and B. I. Shklovskii

Human Centromeric Satellite III Cytosine-Rich Repeats (CCATT)n Fold Into the i-motif in vitro; Solution Structure of the d(mCCATTCCAUTCCUTTCC) Monomer
Sylvie Nonin and Jean Louis Leroy

Sequence Recognition in the Minor Groove of a Duplex DNA by a Homologous Single Strand Complexed to RecA Protein: A Multi-Step Recognition Process
Guillaume Bertucat, Richard Lavery and Chantal Prévost

Structural Basis for DNA-Response Element Recognition in the Nuclear Receptor Family
Qiang Zhao1, Trixie Wagner, Sepideh Khorasanizadeh, Paul B. Sigler, Mitchell A. Lazar and Fraydoon Rastinejad

Features of Specific Recognition of Z-DNA by a Protein: the Za Domain of ADAR1 Bound to Left-Handed Z-DNA
Thomas Schwartz, Mark A. Rould, Ky Lowenhaupt, Alan Herbert and Alexander Rich

RNA-Dependent Amino Acid Fine Structure Recognition in Translational Editing
Paul Schimmel

Kinetics of Recognition of the lacUV5 Promoter by the s70 Escherichia coli RNA Polymerase
Bianca Sclavi, Pascal Roux, Malcolm Buckle and Henri Buc

NMR Structure of HTLV-I Capsid Protein
Sepideh Khorasanizadeh, Ramon Campos-Olivas and Michael F. Summers

Interaction of Taxol with Calf-Thymus DNA and Yeast RNA
J. F. Neault, M. Hermann and H. A. Tajmir-Riahi

tRNA Synthetase Recognition in the E. coli tRNAAsp-aspartyl-tRNA Synthetase Complex; Water Molecules at the Interface Between the tRNA and the Protein
Sylvia Eiler, Luc Moulinier, Jean-Claude Thierry and D. Moras

Symmetry and Chirality in DNA Crossover and Holliday Junction Recognition
Youri Timsit

Recognition and Hydration of Methylated CpG Steps in DNA
Claudine Mayer-Jung, Dino Moras and Youri Timsit

DNA Wires: Facts and Fiction
Eimer Tuite, Per Lincoln, Hans-Christian Becker, Björn Önfelt, Donats Erts and Bengt Nordén

Strand Invasion of Duplex [poly(dA-dT)]2 by a PNA Containing Diamoinopurine and Thiouracil Bases
Eimer Tuite, Peter Nielsen and Bengt Norden

Binding of the Chromosomal Proteins Sac7d and Sso7d to DNA
Andrew H.-J. Wang Shao-Yu Su, Yi-Gui Gao, Howard Robinson, Bradford S. McCrary, Stephen P. Edmondson and John W. Shriver

Structural Studies of Designed, Sequence Specific Minor Groove Ligands
David Wemmer

Mutating Residues at the RNA-Protein Interface: The Yeast Ribosomal L30 System
Susan A. White and Valerie Shipilov

Computer Modeling on Interactions of a TIBO derivative with HIV-1 ReverseTranscriptase and its Drug-Resistant Variants
V.K. Ganesh and D. Velmurugan

Allosteric Interactions in Protein-DNA Recognition
Robert Kaptein

DNA Bending and Sequence-Dependent Backbone Conformation: NMR Coupling Constants and Computer Experiments
Rejadra P. Ojha, Madan M. Dhingra, Mukti H. Sarma, Masayuki Shibata, Margaret Farrar, Christopher J. Turner and Ramaswamy H. Sarma

Structural Biology of the HIV gp120 Envelope Glycoprotein
Wayne A. Hendrickson.

Mechanisms of Transcription and Transcription Regulation in Single RNA Polymerase Molecules
J. Gelles, H. Yin, R. Landick, M.D. Wang, M.J. Schnitzer and S.M. Block

A One Nanosecond Molecular Dynamics Simulation in Solvent of the Phage 434 cl Repressor Protein DNA Binding Domain Amino Acids (R1-69) in Complex With Its Cognate Operator (OR1) DNA Sequence
Lester F. Harris, Michael R. Sullivan and Pamela D. Popken-Harris

Exploring the Minor Groove Binding Track of DNA Polymerases with Nonpolar Nucleoside Analogs
Juan C. Morales and Eric T. Kool

Multi-nanosecond Molecular Dynamic Simulations of the d(C5T5)(d(A5G5) B-Form and B-Form/A-Form Junction: Calculations Designed to Examine the Relationship Between Nucleic Acid Structure and Solvent and Ion Around the DNA
David R. Langley

Protein Crystallization:The Bottleneck for Finding Structures
D.M.Soumpasis and Y.Georgalis

Molecular Dynamics Studies on Parallel G-quadruplex -- Effect of Coordinated Ions
Manju Bansal and Shibasish Chowdhury

Free Energy Component Analysis of Ligand-DNA Binding
Anke Gelbin, Dennis Sprous and David L. Beveridge

A Novel DNA-Binding Motif Shares Structural Homology to DNA Replication and Repair Nucleases and Polymerases
Yate-Ching Yuan, Robert H. Whitson, Qin Liu, Keiichi Itakura and Yuan Chen

Magnesium and Calcium Binding to B-DNA: 1A Crystal Structures of the B-DNA Decamers CCAACGTTGG and CCAGCGCTGG, and 1.43A Crystal Structure of the Sodium-free and Potassium-free A6/A18 Dithiobispropane-Crosslinked Dickerson-Drew Dodecamer
Thang Kien Chiu and Richard E. Dickerson

The Deformability of G-Tracts: The Crystal Structure of a Complete Turn of an A/B-DNA Intermediate
Ho Leung Ng, Mary L. Kopka and Richard E. Dickerson

Structure Determination of the N-terminal 15-Peptide of Human Protamine HP2 by Nuclear Magnetic Resonance, Distance Geometry and Simulated Annealing
Wojciech Bal, Jacek Wojcik, Maciej Maciejczyk and Kazimierz S. Kasprzak

Solution Structure of DNA Oligonucleotides: Comparing Molecular Dynamics and Crystal Structure with NMR Refined Structure and NOE Data
K. J. McConnel, H. Arthanari, M. A. Young, R. Beger, P. H. Bolton and D. L. Beveridge

Determination of the Bridging Ligand in the Active Site of Zinc-Containing Phosphotriesterase by Molecular Dynamics Simulation and Quantum Chemical Calculation
R. L. Ornstein, C.-G. Zhan, O. Norberto de Souza and R. Rittenhouse

Binding Measurements on Protein-Protein and Protein-DNA Complexes
Paolo Catasti

Protein-Induced Structural Distortion of Target DNA Directs Transposition by Tn7
Prasad Kuduvalli and Nancy L. Craig

Transposon Tn7 Selectivley Recognizes Triplex DNA
Jason E. Rao, Paul S. Miller and Nancy L. Craig

Glass-like Dynamics in DNA: Role of Water of Hydration
A.P.Sokolov and H.Grimm

Binding of the Metal Ion Cofactor and an Inhibitor at the Active Site of HIV-1 Integrase
Yehuda Goldgur, Alison B. Hickman, Tamio Fujiwara, Tomokazu Yoshinaga, Toshio Fujishita, Hirohiko Sugimoto, Takeshi Endo, Hitoshi Murai, Robert Craigie and David R. Davies

Computational Studies of U1A-RNA Recognition
Carolina M. Reyes and Peter A. Kollman

An Ancient tRNA Binding Element
Manal A. Swairjo, Arturo J. Morales and Paul Schimmel

DNA Sequence Periodicity in Pro- and Eukaryotic Protein Binding Sites
Yael Mandel-Gutreund and Victor B. Zhurkin

Rational Design of a Triple Helix Specific Cleaving Agent
Christophe Escudé, Rula Zain, Christophe Marchand, Jian-Sheng Sun, Chi-Hung Nguyen, Thérèse Garestier and Claude Hélène

Structural Modeling and Molecular Dynamics Simulation of the Nucleosome Core Particle
Angel E. Garcia, Chang-Shung Tung, Gina Arents and Evangelos N. Moudrianakis

A High Resolution Model of the Troponin C/Troponin I Interaction Using Computational Methods with Constraints from Crystallogaphy, NMR, Neutron Scattering and Cross-linking
Chang-Shung Tung, Stephen Gallagher and Jill Trewhella

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