| | Survey and Summary Molecular models for the tissue specificity of DNA mismatch repair-deficient carcinogenesis Elizabeth C. Chao and Steven M. Lipkin PMCID: PMC1361617 Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling Vigdis Nygaard and Eivind Hovig PMCID: PMC1363777 Articles Coordinated changes of histone modifications and HDAC mobilization regulate the induction of MHC class II genes by Trichostatin A Manolis Gialitakis, Androniki Kretsovali, Charalampos Spilianakis, Lara Kravariti, Jörg Mages, Reinhard Hoffmann, Antonis K. Hatzopoulos, and Joseph Papamatheakis PMCID: PMC1360741 HelF, a putative RNA helicase acts as a nuclear suppressor of RNAi but not antisense mediated gene silencing Blagovesta Popova, Markus Kuhlmann, Andrea Hinas, Fredrik Söderbom, and Wolfgang Nellen PMCID: PMC1360742 A new anti conformation for N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) allows Watson–Crick pairing in the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) Lihua Wang and Suse Broyde PMCID: PMC1360743 Engineering a rare-cutting restriction enzyme: genetic screening and selection of NotI variants James C. Samuelson, Richard D. Morgan, Jack S. Benner, Toby E. Claus, Stephanie L. Packard, and Shuang-yong Xu PMCID: PMC1360745 Dimerization of the bacterial RsrI N6-adenine DNA methyltransferase Chad B. Thomas and Richard I. Gumport PMCID: PMC1361615 Structure of the Tetrahymena thermophila telomerase RNA helix II template boundary element Rebecca J. Richards, Carla A. Theimer, L. David Finger, and Juli Feigon PMCID: PMC1360744 Crystal structure determination and site-directed mutagenesis of the Pyrococcus abyssi aCBF5–aNOP10 complex reveal crucial roles of the C-terminal domains of both proteins in H/ACA sRNP activity Xavier Manival, Christophe Charron, Jean-Baptiste Fourmann, François Godard, Bruno Charpentier, and Christiane Branlant PMCID: PMC1361308 The dicistronic RNA from the mouse LINE-1 retrotransposon contains an internal ribosome entry site upstream of each ORF: implications for retrotransposition Patrick Wai-Lun Li, Jinfang Li, Stephanie L. Timmerman, Les A. Krushel, and Sandra L. Martin PMCID: PMC1361618 Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions Romina Oliva, Luigi Cavallo, and Anna Tramontano PMCID: PMC1361619 Haploinsufficiency of the Mus81–Eme1 endonuclease activates the intra-S-phase and G2/M checkpoints and promotes rereplication in human cells Takashi Hiyama, Mari Katsura, Takashi Yoshihara, Mari Ishida, Aiko Kinomura, Tetsuji Tonda, Toshimasa Asahara, and Kiyoshi Miyagawa PMCID: PMC1360746 TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase David H. Ardell and Siv G. E. Andersson PMCID: PMC1363771 Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos Eva Freyhult, Vincent Moulton, and David H. Ardell PMCID: PMC1363773 Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae Xueping Yu, Jimmy Lin, Tomohiro Masuda, Noriko Esumi, Donald J. Zack, and Jiang Qian PMCID: PMC1361616 Mechanisms of transcriptional repression of cell-cycle G2/M promoters by p63 Barbara Testoni and Roberto Mantovani PMCID: PMC1363772 DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion John R. Horton, Xing Zhang, Robert Maunus, Zhe Yang, Geoffrey G. Wilson, Richard J. Roberts, and Xiaodong Cheng PMCID: PMC1363774 Formation of the G-quadruplex and i-motif structures in retinoblastoma susceptibility genes (Rb) Yan Xu and Hiroshi Sugiyama PMCID: PMC1361614 Transcriptional activators in yeast Björn Titz, Sindhu Thomas, Seesandra V. Rajagopala, Tomoko Chiba, Takashi Ito, and Peter Uetz PMCID: PMC1361621 Core requirements for glmS ribozyme self-cleavage reveal a putative pseudoknot structure Garrett A. Soukup PMCID: PMC1361622 Roles for Gcn5p and Ada2p in transcription and nucleotide excision repair at the Saccharomyces cerevisiae MET16 gene J. A. Ferreiro, N. G. Powell, N. Karabetsou, J. Mellor, and R. Waters PMCID: PMC1363778 Identification of post-transcriptionally regulated Xenopus tropicalis maternal mRNAs by microarray Antoine Graindorge, Raphaël Thuret, Nicolas Pollet, H. Beverley Osborne, and Yann Audic PMCID: PMC1361620 tRNA properties help shape codon pair preferences in open reading frames J. Ross Buchan, Lorna S. Aucott, and Ian Stansfield PMCID: PMC1363775 Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer Sarah L. Williams, Laura K. Parkhurst, and Lawrence J. Parkhurst PMCID: PMC1369283 Poly(ADP-RIBOSE) polymerase-1 (Parp-1) antagonizes topoisomerase I-dependent recombination stimulation by P53 Cindy Baumann, Gisa S. Boehden, Alexander Bürkle, and Lisa Wiesmüller PMCID: PMC1363779 Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102 Zhengchang Su, Fenglou Mao, Phuongan Dam, Hongwei Wu, Victor Olman, Ian T. Paulsen, Brian Palenik, and Ying Xu PMCID: PMC1363776 Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space Russell L. Marsden, David Lee, Michael Maibaum, Corin Yeats, and Christine A. Orengo PMCID: PMC1373602 Methods Online Accurate quantification of DNA methylation using combined bisulfite restriction analysis coupled with the Agilent 2100 Bioanalyzer platform Romulo Martin Brena, Herbert Auer, Karl Kornacker, Björn Hackanson, Aparna Raval, John C. Byrd, and Christoph Plass PMCID: PMC1361623 SNP genotyping using alkali cleavage of RNA/DNA chimeras and MALDI time-of-flight mass spectrometry Florence Mauger, Olivier Jaunay, Valérie Chamblain, Fred Reichert, Keith Bauer, Ivo G. Gut, and David H. Gelfand PMCID: PMC1369287 Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation Srinivasan Yegnasubramanian, Xiaohui Lin, Michael C. Haffner, Angelo M. DeMarzo, and William G. Nelson PMCID: PMC1363782 Expression of Cre recombinase during transient phage infection permits efficient marker removal in Streptomyces Gholam Khodakaramian, Sarah Lissenden, Bertolt Gust, Laura Moir, Paul A. Hoskisson, Keith F. Chater, and Margaret C. M. Smith PMCID: PMC1363781 Isolation of a site-specifically modified RNA from an unmodified transcript Ya-Ming Hou, Zhi Li, and Howard Gamper PMCID: PMC1363780 BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies Milan Fedurco, Anthony Romieu, Scott Williams, Isabelle Lawrence, and Gerardo Turcatti PMCID: PMC1363783 A translation control reporter system (TCRS) for the analysis of translationally controlled processes in the vertebrate cell Volker Wiesenthal, Achim Leutz, and Cornelis F. Calkhoven PMCID: PMC1363784 Diels-Alder cycloadditions in water for the straightforward preparation of peptide–oligonucleotide conjugates Vicente Marchán, Samuel Ortega, Daniel Pulido, Enrique Pedroso, and Anna Grandas PMCID: PMC1369286 High-throughput trapping of secretory pathway genes in mouse embryonic stem cells Silke De-Zolt, Frank Schnütgen, Claudia Seisenberger, Jens Hansen, Melanie Hollatz, Thomas Floss, Patricia Ruiz, Wolfgang Wurst, and Harald von Melchner PMCID: PMC1369290 On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes Lukas M. Wick, Jean Marie Rouillard, Thomas S. Whittam, Erdogan Gulari, James M. Tiedje, and Syed A. Hashsham PMCID: PMC1369288 Affinity selection of DNA-binding protein complexes using mRNA display Seiji Tateyama, Kenichi Horisawa, Hideaki Takashima, Etsuko Miyamoto-Sato, Nobuhide Doi, and Hiroshi Yanagawa PMCID: PMC1369289 Corrigendum Structure-specific binding of MeCP2 to four-way junction DNA through its methyl CpG-binding domain Teca Calcagno Galvão and Jean O. Thomas PMCID: PMC1369285 Corrects: Teca Calcagno Galvão, et al. Structure-specific binding of MeCP2 to four-way junction DNA through its methyl CpG-binding domain. Nucleic Acids Res. 2005; 33(20): 6603–6609. Errata Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides Robert J. Fisher, Matthew J. Fivash, Andrew G. Stephen, Nathan A. Hagan, Shilpa R. Shenoy, Maxine V. Medaglia, Lindsey R. Smith, Karen M. Worthy, John T. Simpson, Robert Shoemaker, Karen L. McNitt, Donald G. Johnson, Catherine V. Hixson, Robert J. Gorelick, Daniele Fabris, Louis E. Henderson, and Alan Rein PMCID: PMC1369284 Corrects: Robert J. Fisher, et al. Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides. Nucleic Acids Res. 2006; 34(2): 472–484. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix Peter Yakovchuk, Ekaterina Protozanova, and Maxim D. Frank-Kamenetskii PMCID: PMC1373690 Corrects: Peter Yakovchuk, et al. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res. 2006; 34(2): 564–574. |
