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Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)
Showing 1 to 100 of 219 items.  Page: 1 3

New Biology from Ancient Enzymes

Paul Schimmel

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A prebiotic RNA apparatus functions within the contemporary ribosome

Miri Krupkin, Ella Zimmerman, Anat Bashan , Ada Yonath

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Origins and Evolution of the Translation Machinery

George E. Fox, Quyen Tran, Mario Rivas, Victor Stepanov,

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Towards Non-enzymatic RNA Replication

Jack W. Szostak

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Prebiotic RNA Synthesis: Significance of Mineral Salts in Montmorillonite-catalyzed Reactions

Prakash C. Joshi, Michael F. Aldersley, James P. Ferris

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Efficient and High-Fidelity Copying of an RNA-like Model Prebiotic System

Shenglong Zhang, Sergei M. Gryaznov, Jack W. Szostak

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Findings and hurdles on the path leading from formamide to the spontaneous generation of RNA

Samanta Pino, Raffaele Saladino, Giorgia Botta, Giovanna Costanzo, Ernesto Di Mauro

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Reconstructing the RNA world

James Attwater , Aniela Wochner , Philipp Holliger

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RNA Fitness Landscapes

Irene A. Chen

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The Montmorillonite Catalyzed Synthesis of RNA Dimer

Michael F. Aldersley, Prakash C. Joshi, and James P. Ferris

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What RNA World ?? Ancestral polypeptides likely participated in the origins of translation

Charles W. Carter, Jr , Li Li , S. Niranj Chandrasekaran, Katiria Gonzales Rivera, Martha L. Collier,

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Combinatorial chemistry in the prebiotic environment

David Deamer

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Mechanical Energy, Protein Motion, and the Possible Origin of Life between Mica Sheets

Helen Greenwood Hansma

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Origin of Life by Metabolic Avalanche Breakthrough in an Iron-Sulfur World

Günter Wächtershäuser

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Possible extraterrestrial life: A quantum-chemical look on the silicon analogs of carbon biomolecules

Maxim S. Kondratyev, Artem V. Kabanov, Alexander A. Samchenko, Vladislav M. Komarov , Nikolay N. Khechinashvili

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Quantum Chemical Studies on the Formamide-Based Origin of Life

Judit E. Šponer , Arnošt Mládek, Martin Ferus, Svatopluk Civiš, Jiří Šponer

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Ribosomal Evidence Suggests That Archaea Evolved After Fungi

William L. Duax , David Dziak, Jordan Tick

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Supramolecular Polymerization of Nucleobase-like Monomers in Water

Isaac Gállego, Brian J. Cafferty, Michael C. Chen, Katherine I. Farley, Ramon Eritja, Nicholas V. Hud

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Text segmentation approach reveals simple repeat "fossils" in genomic sequences

Zakharia M. Frenkel , Edward N. Trifonov

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The phylogenomic roots of modern biochemistry, translation and the genetic code

Gustavo Caetano-Anollés

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Evolutionary dynamics of inteins in bacteria

Olga Novikova, Samantha Merwin, Natalya Topilina, Marlene Belfort

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Inversion Approach to the Origin of Life: Theoretical Notions and Experimental Data

Vladimir N. Kompanichenko

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Synthesis of informational polymers by guided polymerization reactions in liquid crystalline matrices of lipids

Chaitanya Mungi , Sudha Rajamani

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Why No Group II Introns in Nuclear Genomes? Translational Repression, RNA-RNA Interactions and Mis-compartmentalization of mRNAs

Guosheng Qu , Xiaolong Dong, Venkata R. Chalamcharla, Sheila Lutz, M. Joan Curcio, Marlene Belfort

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Structural analyses by NMR reveal insights into the enzymatic mechanism of tRNA t6A modification biosynthesis

Kimberly A. Harris, Benjamin G. Bobay, Yann Bilbille , Paul F. Agris

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The Study of tRNA Modifications by Molecular Dynamics

Xiaoju Zhang , Ross Walker, David H. Mathews

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Accelerating Nucleic Acid Design Using Pre-Selected Sequences

Stanislav Bellaousov, David H. Mathews

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Crystal Structure Studies of RNA Molecules Containing 2ʹ-5ʹ-linkages

Jia Sheng , Li Li, Aaron E. Engelhart, Jack W. Szostak

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Imperfect RNA synthesis via model prebiotic reactions and consequences for functional RNAs

Aaron E. Engelhart, Matthew W. Powner, Jack W. Szostak,

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Simulation of RNA Tandem GA base pairs provides insights about the forces behind conformational preference

David H. Mathews, and Asaminew H Aytenfisu

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Using Pseudorotation as a Reaction Coordinate in Free Energy Simulations of Nucleic Acids

Li Li , Jack W. Szostak

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High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome

Yaser Hashem , Amedee des Georges, Jie Fu, Sarah N. Buss, Fabrice Jossinet, Amy Jobe , Qin Zhang, Hstau Y. Liao, Robert A. Grassucci, Chandrajit Bajaj, Eric Westhof, Susan Madison-Antenucci, Joachim Frank

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High-resolution cryo-EM structure of the Trypanosoma brucei 80S: A unique eukaryotic ribosome

Amy Jobe , Yaser Hashem, Amedee des Georges, Jie Fu, Sarah N. Buss, Fabrice Jossinet, Qin Zhang, Hstau Y. Liao, Bob Grassucci, Chandrajit Bajaj, Susan Madison-Antenucci, Eric Westhof, Joachim Frank

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The Energy Landscapes of Ribosome Function

Jeffrey K. Noel, Karissa Y. Sanbonmatsu, Paul C. Whitford,

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Identification and characterization of small subunit ribosomal intermediates

Neha Gupta, Keith Connolly, and Gloria M. Culver

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A Comparative Study of Ribosomal Proteins: Linkage between Amino Acid Distribution and Ribosomal Assembly

Brittany Burton Lott , Takuya Nakazato, Yongmei Wang

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Cryo-EM Visualization of Mycobacterium 70S Ribosome Reveals Unique Structural Components at the Functional Sites

Jayati Sengupta, Manidip Shasmal

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Discovery of Novel ncRNA by Scanning Multiple Genome Alignments

Yinghan Fu, Zhenjiang Xu, Zhi J. Lu, Shan Zhao, and David H. Mathews

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Probing Single Molecule RNA Folding Using Temperature and Force

William Stephenson, Rachel Santiago, Sean Keller, Scott Tenenbaum, Michael Zuker, and Pan T.X. Li

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Secondary Structure and Domain Architecture of the 23S and 5S rRNAs

Anton S. Petrov , Chad R. Bernier, Eli Hershkovits, Yuzhen Xue, Chris C. Waterbury, Chiaolong Hsiao, Victor G. Stepanov, Eric A. Gaucher, Martha A. Grover, Stephen C. Harvey, Nicholas V. Hud, Roger M. Wartell, George E. Fox, Loren Dean Williams

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The Essential Adenosine Stacking in a Two-Base-Pair Minimal Kissing Complex

William Stephenson ╪ , Papa Nii Asare-Okai ╪ , Alan A. Chen , Scott Tenenbaum , Angel E. Garcia , Daniele Fabris , and Pan T.X. Li

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A network of interactions within the supraspliceosome

Joseph Sperling , Ruth Sperling

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In-Silico Study of the Arrangement of the snRNPs within the Native Spliceosome

Ziv Frankenstein , Joseph Sperling , Ruth Sperling , Miriam Eisenstein

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Computer folding of RNA tetraloops? Are we there yet?

Petra Kührová , Pavel Banáš , Robert B. Best , Jiří Šponer , Michal Otyepka

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NMR based structure of berberine bound to parallel stranded DNA quadruplex d-(TTAGGGT)4 containing human telomeric repeat

Ritu Barthwal , Rahul Yadav, Sweta Tripathi , Tarikere Palakshan Pradeep

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Why G? Aggregation and Gelation of GMP with XMP: The Plot Thickens

Linda B. McGown, Lauren Cassidy, Akshar Gupta

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Circular dichroism (CD) studies of the interaction between G-quadruplexes/ I-motif with saffron secondary active metabolites

S.Zahra Bathaie , Reyhane Hoshyar , Nasim Shahhamzeie

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Effect of Guanine Substitutions in Human Telomeric G3 (T2 AG3)3 DNA Sequence

Martin Tomaško , Michaela Vorlíčková, Miroslav Fojta, Janos Sagi

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Electrochemical investigation of the interaction between G-quadruplex and some ligands using MWCNT modified carbon paste electrode

S. Malelahi, S. Zahra Bathaie, M.F. Mousavi, H. Ilkhani

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Incorporation of alternative nucleic acid chemistries into G-quadruplex structure

Christopher J. Lech, Anh Tuan Phan

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NMR study of the interaction between G-quadruplexes and small molecules

Wan Jun Chung, Brahim Heddi, Anh Tuân Phan

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Nucleic Acids in Anhydrous Media: G-quadruplex Folding Governed by Kramers Rate Theory

Irena Mamajanov, Ford M. Lannan,, Nicholas V. Hud

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Single-molecule studies of human telomeric G-quadruplexes and the effect of oxidative damage

Aaron M. Fleming, Na An, Cynthia J. Burrows

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Platinum(II) Phenanthroimidazoles with “Clicked” Sidechains as Selective G-Quadruplex DNA Binders

Katherine J Castor, Johans akhoury, Zhaomin Liu, Mark Hancock, Anthony Mittermaier, Nicolas Moitessier, Hanadi F Sleiman

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Examining the Effects of 2’-OH Substitutions on the Structure and Stability of the S. cerevisiae Telomerase RNA Pseudoknot and Tertiary Structure

Carla A. Theimer, Fei Liu , Katelyn M. Jasper

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2D to 3D: Interaction Frequency Maps to Chromatin Higher-Order Folded Conformations

Dario Meluzzi, Gaurav Arya

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DNA Conformation and Energy in Nucleosome Core: A Theoretical Approach

Davood Norouzi

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Dynamics of the nucleosome core particle revealed from a new database of high resolution x-ray crystallographic and simulated structures

Gautam Singh, Andrew V. Colasanti, Nicolas Clauvelin, Wilma K. Olson

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Large scale alternation of Nucleosome Positioning Potential in pericentromeric Chromosome Regions

Viya B. Fedoseyeva , Alexander A. Alexandrov

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Nucleosome [Mis]Positioning, Chromatin Folding and a Computational Karyotype

Victoria Bamburg, William Johnston, James Liman, James Solow, and Thomas C. Bishop

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Packaging Trinucleotide Repeats: The effect of CAG/CTG Repeats On Nucleosome Formation

Vilma Medrano , Sarah Delaney

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The synergy between DNA and nucleosomes in chromatin

Nicolas Clauvelin , Wilma K. Olson

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Binding and transactivation by the tumor suppression protein p53 is encoded in the differential structural properties of its response elements

Tali E. Haran, Alon Senitzki, Jenia Sharav, Itai Beno , Karin Rosenthal, Jennifer J. Jordan, Daniel Menendez , Michael A. Resnick

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Distinct nucleosome organization around p53 response elements associated with cell cycle arrest and apoptosis

Feng Cui , Victor B. Zhurkin

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EMSA detection of p53 sequence non-specific binding on PCR produced human DNA analogues

Jiri Cerven, Pavla Bazantova, Petr Pecinka, Barbora Chvatalova, and Marie Brazdova

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High-resolution crystal structures of p53 mutants and their interaction with DNA

Haim Rozenberg , Yael Diskin-Posner, Amir Eldar , Zippora Shakked

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Hoogsteen or not Hoogsteen? Iodine-125 radioprobing of the p53-induced DNA deformations

Igor G. Panyutin, Valery N. Karamychev, Ronald D. Neumann, Sharlyn Mazur, Ettore Appella, Difei Wang, Victor B. Zhurkin

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QM-MM simulations on p53-DNA complex: Comparison of DNA-binding property between cancer and their rescue mutants

Shruti Koulgi , Archana Achalere , Neeru Sharma , Uddhavesh Sonavane , Rajendra Joshi

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Shifting interfaces: changes in protein-protein and protein-DNA interfaces probed via molecular dynamics

Lacra Negureanu , Freddie Salsbury Jr.

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Architectural role of HMO1 in bending, bridging and compacting DNA

Divakaran Murugesapillai, Micah J. McCauley, Ran Huo , Molly H. Nelson Holte, L. James Maher III, Nathan E. Israeloff , Mark C. Williams

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Covariation between homeodomains and the DNA shape of their binding sites provides new insights into protein-DNA recognition

Iris Dror , Tianyin Zhou, Yael Mandel-Gutfreund, Remo Rohs

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Deconvoluting the recognition of DNA shape from DNA sequence

Namiko Abe, Matthew Slattery, Iris Dror, Remo Rohs, Barry Honig, and Richard S. Mann

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DNA Binding Studies of Large Antiviral Polyamides

Elena Vasilieva, Gaofei He, Kevin J. Koeller, G. Davis Harris, Cynthia M. Dupureur,, James K. Bashkin

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Electrostatic properties of bacterial DNA and promoter predictions

Evgenia A. Temlyakova, Timur R. Dzhelyadin, Svetlana G. Kamzolova, Anatoly A. Sorokin

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Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape

Raluca Gordan, Ning Shen, Iris Dror, Tianyin Zhou, John Horton, Remo Rohs, Martha L. Bulyk

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Get into shape: new insights into the broadly observed mechanism of DNA shape readout and its relation to genetic variation

Ana C. D. Machado , Tianyin Zhou, Remo Rohs

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Molecular dynamics approach for DNA duplex thermal stability prediction

Alexander Lomzov, Yury Vorobjev, Dmitryi Pyshnyi

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Novel geometric approaches to uniquely characterize DNA binding interfaces

Yael Mandel-Gutfreund

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OnTheFly Database – Structural Basis to Study TF’s DNA-Binding Specificity

Shula Shazman, Jie Chen, Hunjoong Lee, Peng Liu, Richard Mann, Barry Honig

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Protein-DNA Binding and Breathing Dynamics of DNA

Boian S. Alexandrov, Kim Ø. Rasmussen, Alan R. Bishop, Anny Usheva

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Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

Jie Wang, Jiali Zhuang, Sowmya Iyer, Xin Lin, Troy W. Whitfield, Melissa C. Greven, Brian G. Pierce, Xianjun Dong, Anshul Kundaje, Yong Cheng, Oliver J. Rando, Ewan Birney, Richard M. Myers, William S. Noble, Michael Snyder, Zhiping Weng

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Structural Studies of Rolling Circle Replication Initiator Proteins

Stephen B. Carr, Lauren B. Mecia, Alice J. Stelfox, Simon E.V. Phillips, Christopher D. Thomas

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Thermodynamic and Kinetic Studies of Trinucleotide Repeat (TNR) DNA

Ji Huang , Sarah Delaney

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A new approach in determining the rigidity of nucleic acids and polymers

Anton V. Sergeev, Natalia V. Lekontseva , Alexander A. Timchenko , Igor N. Serdyuk

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A new series of biologically active DNA minor groove binders based on bisbenzimidazole and benzimidazole-pyrrole motives

Alexander A. Ivanov, Olga Yu. Susova, Victor I. Salyanov, Kirill I. Kirsanov, Alexei L. Zhuze

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Application of Differential Scanning Calorimetry to Measure the Differential Binding of Ions, Water and Protons in the Unfolding of DNA Molecules

Chris M. Olson , Irine Khutsishvili, Sarah E. Johnson, Calliste Reiling, Luis A. Marky

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Bistable Regime of Adsorption of Ligands on a Macromolecule Induced by an External Noise

Valeri B. Arakelyan, Sos V. Harutyunyan, Vardan K. Andriasyan, Hakob V. Arakelyan

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Characterization and differentiation of binding modes of water-soluble porphyrins at complexation with DNA

Vigen G.Barkhudaryan, Gayane V.Ananyan, Yeva B.Dalyan

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Comparison of Monovalent and Divalent Ion Distributions around a DNA Duplex with Molecular Dynamic Simulation and Poisson-Boltzmann Approach

Timothy J. Robbins, Yongmei Wang

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Computational mapping reveals effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde.

Bohnuud T, Beglov D, Ngan CH, Zerbe B, Hall DR, Brenke R, Vajda S, Frank-Kamenetskii MD, and Kozakov D

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Intra-Accumbens Injection of a Dopamine Aptamer Abates MK-801-Induced Cognitive Dysfunction in a Model of Schizophrenia

Erin M. McConnell , Matthew R. Holahan , Dan Madularu , Ryan Walsh , Maria C. DeRosa

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Kinetics of DNA overstretching: Melting vs B-to-S transition

Micah J. McCauley , Ioulia Rouzina , Mark C.Williams

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Novel Interpretation of the Isotherms of Multimodal Ligands Binding with DNA

Poghos O. Vardevanyan, Valeri B. Arakelyan, Ara P. Antonyan, Zhanna H. Mukhaelyan, Lilit A. Hambardzumyan, Armen T. Karapetian

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PPC Measurements of Unfolding Volumes of DNA Stem-Loop Motifs

Irine Khutshivilli, Iztok Prislan, Luis A. Marky

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Spectroscopic Investigation of Methylene Blue Binding to DNA

Poghos O. Vardevanyan, Ara P. Antonyan, Marine A. Parsadanyan, Mariam A. Shahinyan, Lilit A. Hambrdzumyan, Mikayel V. Minasyants, Armen T. Karapetian

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Study of the Stacking of DNA Homoassociates by the Extended Cluster Approach

Victor I. Danilov , Vladimir V. Dailidonis

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Study on Electron Transfer Through RNA/DNA Duplex Using Pyrene and 5-Bromouracil As an Electron Donor and Acceptor Pair

Tadao Takada , Kenji Maie, Yumiko Otsuka, Tomohiro Saeki, Yuta Takamatsu, Mitsunobu Nakamura, Kazushige Yamana

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Targeting Intramolecular DNA Structures with Complementary Strands

Calliste Reiling , Sarah E. Johnson, Hui-Ting Lee, Luis A. Marky

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The impact of active metabolites obtained from saffron on H1- Oligonucleotide interaction

Reyhane Hoshyar , S. Zahra Bathaie

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The Investigation of Hoechst 33258 Interaction with DNA in Aqueous Solutions of Dimethylsulfoxide

Poghos O. Vardevanyan , Ara P. Antonyan, Karen Yu. Amirbekyan, Shiraz A.Markarian

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