| | Articles SURVEY AND SUMMARY: Structures of trinucleotide repeats in human transcripts and their functional implications Anna Jasinska, Gracjan Michlewski, Mateusz de Mezer, Krzysztof Sobczak, Piotr Kozlowski, Marek Napierala, and Wlodzimierz J. Krzyzosiak PMCID: PMC206467 RNA structure of trinucleotide repeats associated with human neurological diseases Krzysztof Sobczak, Mateusz de Mezer, Gracjan Michlewski, Jacek Krol, and Wlodzimierz J. Krzyzosiak PMCID: PMC206466 Requirements for selective recruitment of Ets proteins and activation of mb-1/Ig-α gene transcription by Pax-5 (BSAP) Holly Maier, Rachel Ostraat, Sarah Parenti, Daniel Fitzsimmons, Lawrence J. Abraham, Colin W. Garvie, and James Hagman PMCID: PMC206479 Using pyrene-labeled HIV-1 TAR to measure RNA–small molecule binding Kenneth F. Blount and Yitzhak Tor PMCID: PMC206455 Vanillins—a novel family of DNA-PK inhibitors Stephen Durant and Peter Karran PMCID: PMC206453 GLIS3, a novel member of the GLIS subfamily of Krüppel-like zinc finger proteins with repressor and activation functions Yong-Sik Kim, Gen Nakanishi, Mark Lewandoski, and Anton M. Jetten PMCID: PMC206473 A requirement for PARP-1 for the assembly or stability of XRCC1 nuclear foci at sites of oxidative DNA damage Sherif F. El-Khamisy, Mitsuko Masutani, Hiroshi Suzuki, and Keith W. Caldecott PMCID: PMC206461 Characterization of the RNA motif responsible for the specific interaction of potato spindle tuber viroid RNA (PSTVd) and the tomato protein Virp1 Mariyana Gozmanova, Michela Alessandra Denti, Ivan Nikiforov Minkov, Mina Tsagris, and Martin Tabler PMCID: PMC206474 Biochemical characterization of the kink-turn RNA motif Shigeyoshi Matsumura, Yoshiya Ikawa, and Tan Inoue PMCID: PMC206460 Allosteric regulation of tRNA import: interactions between tRNA domains at the inner membrane of Leishmania mitochondria Srikanta Goswami, Saibal Chatterjee, Suvendra Nath Bhattacharyya, Sudarshana Basu, and Samit Adhya PMCID: PMC206471 Characterization of AP lyase activities of Saccharomyces cerevisiae Ntg1p and Ntg2p: implications for biological function Kellen L. Meadows, Binwei Song, and Paul W. Doetsch PMCID: PMC206450 The human checkpoint Rad protein Rad17 is chromatin-associated throughout the cell cycle, localizes to DNA replication sites, and interacts with DNA polymerase ε Sean M. Post, Alan E. Tomkinson, and Eva Y.-H. P. Lee PMCID: PMC206465 Genome-scale design of PCR primers and long oligomers for DNA microarrays Stefan A. Haas, Marc Hild, Anthony P. H. Wright, Torsten Hain, Driss Talibi, and Martin Vingron PMCID: PMC206452 EXCAVATOR: a computer program for efficiently mining gene expression data Dong Xu, Victor Olman, Li Wang, and Ying Xu PMCID: PMC206478 Thermodynamics of the binding of Thermus aquaticus DNA polymerase to primed-template DNA Kausiki Datta and Vince J. LiCata PMCID: PMC206472 Thermodynamic and kinetic stability of intermolecular triple helices containing different proportions of C+·GC and T·AT triplets Peter L. James, Tom Brown, and Keith R. Fox PMCID: PMC206477 Global mapping of nucleic acid conformational space: dinucleoside monophosphate conformations and transition pathways among conformational classes Gregory E. Sims and Sung-Hou Kim PMCID: PMC206451 PANDORA: keyword-based analysis of protein sets by integration of annotation sources Noam Kaplan, Avishay Vaaknin, and Michal Linial PMCID: PMC206469 hMSH2 expression is driven by AP1-dependent regulation through phorbol-ester exposure Odile Humbert, Ikbel Achour, Dominique Lautier, Guy Laurent, and Bernard Salles PMCID: PMC206476 Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences Qiang Xu and Christopher Lee PMCID: PMC206480 RNAi-mediated depletion of the 15 KH domain protein, vigilin, induces death of dividing and non-dividing human cells but does not initially inhibit protein synthesis Kathryn M. Goolsby and David J. Shapiro PMCID: PMC206468 Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies Brian J. Haas, Arthur L. Delcher, Stephen M. Mount, Jennifer R. Wortman, Roger K. Smith, Jr, Linda I. Hannick, Rama Maiti, Catherine M. Ronning, Douglas B. Rusch, Christopher D. Town, Steven L. Salzberg, and Owen White PMCID: PMC206470 Advanced computational techniques for re-sequencing DNA with polymerase signaling assay arrays Itsik Pe’er, Naama Arbili, Yi Liu, Colby Enck, Craig A. Gelfand, and Ron Shamir PMCID: PMC206457 Evaluation of gene expression measurements from commercial microarray platforms Paul K. Tan, Thomas J. Downey, Edward L. Spitznagel, Jr, Pin Xu, Dadin Fu, Dimiter S. Dimitrov, Richard A. Lempicki, Bruce M. Raaka, and Margaret C. Cam PMCID: PMC206463 3′-Modified oligonucleotides by reverse DNA synthesis Christopher D. Claeboe, Rong Gao, and Sidney M. Hecht PMCID: PMC206447 Long-distance radical cation reactions in DNA three-way junctions: inter-arm interaction and migration through the junction U. Santhosh and Gary B. Schuster PMCID: PMC206456 In vitro selection of molecular beacons Manjula Rajendran and Andrew D. Ellington PMCID: PMC206464 Modulation of drug sensitivity in yeast cells by the ATP-binding domain of human DNA topoisomerase IIα Nathalie Vilain, Monika Tsai-Pflugfelder, Audrey Benoit, Susan M. Gasser, and Didier Leroy PMCID: PMC206448 Enhanced gene activation by Notch and BMP signaling cross-talk Takumi Takizawa, Wataru Ochiai, Kinichi Nakashima, and Tetsuya Taga PMCID: PMC206475 The DNA and RNA specificity of eilatin Ru(II) complexes as compared to eilatin and ethidium bromide Nathan W. Luedtke, Judy S. Hwang, Eileen Nava, Dalia Gut, Moshe Kol, and Yitzhak Tor PMCID: PMC206458 dsRBM1 and a proline-rich domain of RNA helicase A can form a composite binder to recognize a specific dsDNA Ming-Lung Hung, Ping Chao, and Kung-Yao Chang PMCID: PMC206459 G-quartets direct assembly of HIV-1 nucleocapsid protein along single-stranded DNA Sébastien Lyonnais, Robert J. Gorelick, Jean-Louis Mergny, Eric Le Cam, and Gilles Mirambeau PMCID: PMC206446 Structure–function relationships of the initiation complex of HIV-1 reverse transcription: the case of mutant viruses using tRNAHis as primer Mickaël Rigourd, Valérie Goldschmidt, Fabienne Brulé, Casey D. Morrow, Bernard Ehresmann, Chantal Ehresmann, and Roland Marquet PMCID: PMC206454 Selective inhibitory DNA aptamers of the human RNase H1 Frédéric Pileur, Marie-Line Andreola, Eric Dausse, Justine Michel, Serge Moreau, Hirofumi Yamada, Sergei A. Gaidamakov, Robert J. Crouch, Jean-Jacques Toulmé, and Christian Cazenave PMCID: PMC206449 Integrated transcriptome analysis of the cellular mechanisms associated with Ha-ras-dependent malignant transformation of the human breast epithelial MCF7 cell line Franck Gadal, Christophe Bozic, Céline Pillot-Brochet, Sophie Malinge, Sarah Wagner, Aurélie Le Cam, Laurent Buffat, Michel Crepin, and François Iris PMCID: PMC206462 NAR Methods Online A microarray-based high throughput molecular marker genotyping method: the tagged microarray marker (TAM) approach Andrew J. Flavell, Viacheslav N. Bolshakov, Allan Booth, Runchun Jing, Joanne Russell, T. H. Noel Ellis, and Peter Isaac PMCID: PMC206481 A non-parametric model for transcription factor binding sites Oliver D. King and Frederick P. Roth PMCID: PMC206482 Real-time closed tube single nucleotide polymorphism (SNP) quantification in pooled samples by quencher extension (QEXT) Knut Rudi and Askild L. Holck PMCID: PMC206483 DNA display for in vitro selection of diverse peptide libraries Masato Yonezawa, Nobuhide Doi, Yuko Kawahashi, Toru Higashinakagawa, and Hiroshi Yanagawa PMCID: PMC206484 PNA microarrays for hybridisation of unlabelled DNA samples Ole Brandt, Julia Feldner, Achim Stephan, Markus Schröder, Martina Schnölzer, Heinrich F. Arlinghaus, Jörg D. Hoheisel, and Anette Jacob PMCID: PMC206485 Reconstitution of an efficient thymidine salvage pathway in Saccharomyces cerevisiae Laurence Vernis, Jure Piskur, and John F. X. Diffley PMCID: PMC206486 |
