| | Survey and Summary The diverse superfamily of lysine acetyltransferases and their roles in leukemia and other diseases Xiang-Jiao Yang PMCID: PMC384351 Articles Biochemical characterization of the mitochondrial tRNASer(UCN) T7511C mutation associated with nonsyndromic deafness Xiaoming Li, Nathan Fischel-Ghodsian, Faina Schwartz, Qingfeng Yan, Rick A. Friedman, and Min-Xin Guan PMCID: PMC373379 Site-resolved stabilization of a DNA triple helix by magnesium ions Daniel Coman and Irina M. Russu PMCID: PMC373380 Identification of a direct Dlx homeodomain target in the developing mouse forebrain and retina by optimization of chromatin immunoprecipitation Qing-Ping Zhou, Trung Ngoc Le, Xiangguo Qiu, Virginia Spencer, Jimmy de Melo, Guoyan Du, Margot Plews, Mario Fonseca, Jian Min Sun, James R. Davie, and David D. Eisenstat PMCID: PMC373381 A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: determinants of gene silencing for use in cell-based screens Andrew C. Hsieh, Ronghai Bo, Judith Manola, Francisca Vazquez, Olivia Bare, Anastasia Khvorova, Stephen Scaringe, and William R. Sellers PMCID: PMC373385 Inhibitors of protein synthesis identified by a high throughput multiplexed translation screen Olivia Novac, Anne-Sophie Guenier, and Jerry Pelletier PMCID: PMC373382 Kinetic and thermodynamic characterization of the RNA-cleaving 8-17 deoxyribozyme Maria Bonaccio, Alfredo Credali, and Alessio Peracchi PMCID: PMC373389 Pre-steady-state kinetics shows differences in processing of various DNA lesions by Escherichia coli formamidopyrimidine-DNA glycosylase Vladimir V. Koval, Nikita A. Kuznetsov, Dmitry O. Zharkov, Alexander A. Ishchenko, Kenneth T. Douglas, Georgy A. Nevinsky, and Olga S. Fedorova PMCID: PMC373384 Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference Kumiko Ui-Tei, Yuki Naito, Fumitaka Takahashi, Takeshi Haraguchi, Hiroko Ohki-Hamazaki, Aya Juni, Ryu Ueda, and Kaoru Saigo PMCID: PMC373388 Statistical analysis of over-represented words in human promoter sequences Leonardo Mariño-Ramírez, John L. Spouge, Gavin C. Kanga, and David Landsman PMCID: PMC373387 The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1 David A. Rasko, Jacques Ravel, Ole Andreas Økstad, Erlendur Helgason, Regina Z. Cer, Lingxia Jiang, Kelly A. Shores, Derrick E. Fouts, Nicolas J. Tourasse, Samuel V. Angiuoli, James Kolonay, William C. Nelson, Anne-Brit Kolstø, Claire M. Fraser, and Timothy D. Read PMCID: PMC373394 The effect of manganese(II) on DNA structure: electronic and vibrational circular dichroism studies A. M. Polyanichko, V. V. Andrushchenko, E. V. Chikhirzhina, V. I. Vorob'ev, and H. Wieser PMCID: PMC373386 Phosphatidyl inositol 3-kinase-like serine/threonine protein kinases (PIKKs) are required for DNA damage-induced phosphorylation of the 32 kDa subunit of replication protein A at threonine 21 Wesley D. Block, Yaping Yu, and Susan P. Lees-Miller PMCID: PMC373400 A mutation in polynucleotide phosphorylase from Escherichia coli impairing RNA binding and degradosome stability Maria Elena Regonesi, Federica Briani, Andrea Ghetta, Sandro Zangrossi, Daniela Ghisotti, Paolo Tortora, and Gianni Dehò PMCID: PMC373403 Mycobacterium tuberculosis Rv2118c codes for a single-component homotetrameric m1A58 tRNA methyltransferase U. Varshney, V. Ramesh, A. Madabushi, R. Gaur, H. S. Subramanya, and U. L. RajBhandary PMCID: PMC373377 RBD-1, a nucleolar RNA-binding protein, is essential for Caenorhabditis elegans early development through 18S ribosomal RNA processing Eiko Saijou, Toshinobu Fujiwara, Toshinobu Suzaki, Kunio Inoue, and Hiroshi Sakamoto PMCID: PMC373399 The importance of intrinsic disorder for protein phosphorylation Lilia M. Iakoucheva, Predrag Radivojac, Celeste J. Brown, Timothy R. O'Connor, Jason G. Sikes, Zoran Obradovic, and A. Keith Dunker PMCID: PMC373391 Biased distribution of DNA uptake sequences towards genome maintenance genes Tonje Davidsen, Einar A. Rødland, Karin Lagesen, Erling Seeberg, Torbjørn Rognes, and Tone Tønjum PMCID: PMC373393 Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica Joel A. Malek, Jamey M. Wierzbowski, Wei Tao, Stephanie A. Bosak, David J. Saranga, Lynn Doucette-Stamm, Douglas R. Smith, Paul J. McEwan, and Kevin J. McKernan PMCID: PMC373392 Physical and functional interaction of the archaeal single-stranded DNA-binding protein SSB with RNA polymerase Derek J. Richard, Stephen D. Bell, and Malcolm F. White PMCID: PMC373395 Structure–function correlations derived from faster variants of a RNA ligase deoxyribozyme Tracey K. Prior, Daniel R. Semlow, Amber Flynn-Charlebois, Imran Rashid, and Scott K. Silverman PMCID: PMC373398 Interactions among CII protein, RNA polymerase and the λ PRE promoter: contacts between RNA polymerase and the –35 region of PRE are identical in the presence and absence of CII protein Michael T. Marr, Jeffrey W. Roberts, Susan E. Brown, Matthew Klee, and Gary N. Gussin PMCID: PMC373397 Atypical archaeal tRNA pyrrolysine transcript behaves towards EF-Tu as a typical elongator tRNA Anne Théobald-Dietrich, Magali Frugier, Richard Giegé, and Joëlle Rudinger-Thirion PMCID: PMC373401 A thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+/Na+ ions Carmen Cáceres, Glenford Wright, Catherine Gouyette, Gary Parkinson, and Juan A. Subirana PMCID: PMC373404 Assembly of the replication initiation complex on SV40 origin DNA Daniel T. Simmons, Dahai Gai, Rebekah Parsons, Amanda Debes, and Rupa Roy PMCID: PMC373383 The inhibition of the human cholesterol 7α-hydroxylase gene (CYP7A1) promoter by fibrates in cultured cells is mediated via the liver x receptor α and peroxisome proliferator-activated receptor α heterodimer G. Franck Gbaguidi and Luis B. Agellon PMCID: PMC373396 Translesion synthesis of acetylaminofluorene-dG adducts by DNA polymerase ζ is stimulated by yeast Rev1 protein Dongyu Guo, Zhongwen Xie, Huiyun Shen, Bo Zhao, and Zhigang Wang PMCID: PMC373411 Analysis and recognition of 5′ UTR intron splice sites in human pre-mRNA E. Eden and S. Brunak PMCID: PMC373407 Psoralen interstrand cross-link repair is specifically altered by an adjacent triple-stranded structure F. Guillonneau, A. L. Guieysse, S. Nocentini, C. Giovannangeli, and D. Praseuth PMCID: PMC373402 Enhanced gene silencing of HIV-1 specific siRNA using microRNA designed hairpins Daniel Boden, Oliver Pusch, Rebecca Silbermann, Fred Lee, Lynne Tucker, and Bharat Ramratnam PMCID: PMC373410 Overexpression of phage-type RNA polymerase RpoTp in tobacco demonstrates its role in chloroplast transcription by recognizing a distinct promoter type Karsten Liere, Daniela Kaden, Pal Maliga, and Thomas Börner PMCID: PMC373414 Relevance of UP elements for three strong Bacillus subtilis phage ![[var phi]](corehtml/pmc/pmcents/x03C6.gif) 29 promoters Wilfried J. J. Meijer and Margarita Salas PMCID: PMC373416 Identification of NH…N hydrogen bonds by magic angle spinning solid state NMR in a double-stranded RNA associated with myotonic dystrophy Jörg Leppert, Carl R. Urbinati, Sabine Häfner, Oliver Ohlenschläger, Maurice S. Swanson, Matthias Görlach, and Ramadurai Ramachandran PMCID: PMC373415 Gene repeat expansion and contraction by spontaneous intrachromosomal homologous recombination in mammalian cells Leah R. Read, Steven J. Raynard, Ania Rukść, and Mark D. Baker PMCID: PMC373412 A novel strategy to engineer DNA polymerases for enhanced processivity and improved performance in vitro Yan Wang, Dennis E. Prosen, Li Mei, John C. Sullivan, Michael Finney, and Peter B. Vander Horn PMCID: PMC373405 A gene-specific DNA sequencing chip for exploring molecular evolutionary change Olivier Fedrigo and Gavin Naylor PMCID: PMC373378 Delineation of the mechanisms of aberrant splicing caused by two unusual intronic mutations in the RSK2 gene involved in Coffin–Lowry syndrome Maria Zeniou, Renata Gattoni, André Hanauer, and James Stévenin PMCID: PMC373406 Length-dependent structure formation in Friedreich ataxia (GAA)n·(TTC)n repeats at neutral pH V. N. Potaman, E. A. Oussatcheva, Y. L. Lyubchenko, L. S. Shlyakhtenko, S. I. Bidichandani, T. Ashizawa, and R. R. Sinden PMCID: PMC373408 ETR-3 and CELF4 protein domains required for RNA binding and splicing activity in vivo Gopal Singh, Nicolas Charlet-B., Jin Han, and Thomas A. Cooper PMCID: PMC373409 Mer1p is a modular splicing factor whose function depends on the conserved U2 snRNP protein Snu17p Marc Spingola, Javier Armisen, and Manuel Ares, Jr PMCID: PMC373413 NAR Methods Online Determination of detection and quantification limits for SNP allele frequency estimation in DNA pools using real time PCR Gerhard Schwarz, Stefan Bäumler, Annette Block, Friedrich G. Felsenstein, and Gerhard Wenzel PMCID: PMC373417 Nuclear localization signal and cell synchrony enhance gene targeting efficiency in primary fetal fibroblasts Bashir Mir and Jorge A. Piedrahita PMCID: PMC373419 Sequence saturation mutagenesis (SeSaM): a novel method for directed evolution Tuck Seng Wong, Kang Lan Tee, Berhard Hauer, and Ulrich Schwaneberg PMCID: PMC373423 Genomic shotgun array: a procedure linking large-scale DNA sequencing with regional transcript mapping Ling-Hui Li, Jian-Chiuan Li, Yung-Feng Lin, Chung-Yen Lin, Chung-Yung Chen, and Shih-Feng Tsai PMCID: PMC373421 Semiconductor nanocrystal probes for human metaphase chromosomes Yan Xiao and Peter E. Barker PMCID: PMC373420 Reliability of gene expression ratios for cDNA microarrays in multiconditional experiments with a reference design Rainer König, Danila Baldessari, Nicolas Pollet, Christof Niehrs, and Roland Eils PMCID: PMC373422 Doxycyline regulation in a single retroviral vector by an autoregulatory loop facilitates controlled gene expression in liver cells Florian Kühnel, Corinna Fritsch, Sabine Krause, Bettina Mundt, Thomas Wirth, Yasmin Paul, Nisar Peter Malek, Lars Zender, Michael Peter Manns, and Stefan Kubicka PMCID: PMC373428 Large-scale determination of the methylation status of retrotransposons in different tissues using a methylation tags approach Konstantin Khodosevich, Yuri Lebedev, and Eugene D. Sverdlov PMCID: PMC373429 Strong positional preference in the interaction of LNA oligonucleotides with DNA polymerase and proofreading exonuclease activities: implications for genotyping assays Daniel A. Di Giusto and Garry C. King PMCID: PMC373430 Surfection: a new platform for transfected cell arrays Fu-Hsiung Chang, Chien-Hsin Lee, Ming-Ta Chen, Chun-Chen Kuo, Yi-Lin Chiang, Chi-Ying Hang, and Steve Roffler PMCID: PMC373424 LSimpute: accurate estimation of missing values in microarray data with least squares methods Trond Hellem Bø, Bjarte Dysvik, and Inge Jonassen PMCID: PMC374359 Unlocking hidden genomic sequence Jonathan M. Keith, Duncan A. E. Cochran, Gita H. Lala, Peter Adams, Darryn Bryant, and Keith R. Mitchelson PMCID: PMC373418 Shuffled antibody libraries created by in vivo homologous recombination and yeast surface display Jeffrey S. Swers, Brenda A. Kellogg, and K. Dane Wittrup PMCID: PMC373425 Simple cDNA normalization using kamchatka crab duplex-specific nuclease Pavel A. Zhulidov, Ekaterina A. Bogdanova, Alex S. Shcheglov, Laura L. Vagner, George L. Khaspekov, Valery B. Kozhemyako, Mikhail V. Matz, Ella Meleshkevitch, Leonid L. Moroz, Sergey A. Lukyanov, and Dmitry A. Shagin PMCID: PMC373426 A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements Allen S. Yang, Marcos R. H. Estécio, Ketan Doshi, Yutaka Kondo, Eloiza H. Tajara, and Jean-Pierre J. Issa PMCID: PMC373427 Generating in vitro transcripts with homogenous 3′ ends using trans-acting antigenomic delta ribozyme Agnieszka Wichłacz, Michał Łęgiewicz, and Jerzy Ciesiołka PMCID: PMC373431 |
