| | Articles Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals Mitsuteru Nakao, Roberto A. Barrero, Yuri Mukai, Chie Motono, Makiko Suwa, and Kenta Nakai PMCID: PMC1087780 Characterization of the DNA-binding domain and identification of the active site residue in the ‘Gyr A’ half of Leishmania donovani topoisomerase II Tanushri Sengupta, Mandira Mukherjee, Rakhee Das, Aditi Das, and Hemanta K. Majumder PMCID: PMC1087781 Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability Paul M. Harrison, Deyou Zheng, Zhaolei Zhang, Nicholas Carriero, and Mark Gerstein PMCID: PMC1087782 Independent binding sites of small protein B onto transfer-messenger RNA during trans-translation Laurent Metzinger, Marc Hallier, and Brice Felden PMCID: PMC1087783 Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments Aurélie Lescoute, Neocles B. Leontis, Christian Massire, and Eric Westhof PMCID: PMC1087784 The requirement of yeast replication origins for pre-replication complex proteins is modulated by transcription Conrad A. Nieduszynski, J. Julian Blow, and Anne D. Donaldson PMCID: PMC1087785 Dissecting eukaryotic translation and its control by ribosome density mapping Yoav Arava, F. Edward Boas, Patrick O. Brown, and Daniel Herschlag PMCID: PMC1087779 A benchmark of multiple sequence alignment programs upon structural RNAs Paul P. Gardner, Andreas Wilm, and Stefan Washietl PMCID: PMC1087786 Regulation of the human cyclin C gene via multiple vitamin D3-responsive regions in its promoter Lasse Sinkkonen, Marjo Malinen, Katri Saavalainen, Sami Väisänen, and Carsten Carlberg PMCID: PMC1087898 Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides Koen Nauwelaerts, Eveline Lescrinier, Gert Sclep, and Piet Herdewijn PMCID: PMC1087899 Studies on Escherichia coli RNase P RNA with Zn2+ as the catalytic cofactor Simona Cuzic and Roland K. Hartmann PMCID: PMC1088067 Repair of cyclobutane pyrimidine dimers or dimethylsulfate damage in DNA is identical in normal or telomerase-immortalized human skin fibroblasts Steven E. Bates, Ning Ye Zhou, Laura E. Federico, Liqun Xia, and Timothy R. O'Connor PMCID: PMC1087900 Selenocysteine insertion directed by the 3′-UTR SECIS element in Escherichia coli Dan Su, Yehua Li, and Vadim N. Gladyshev PMCID: PMC1087901 U1 small nuclear RNP from Trypanosoma brucei: a minimal U1 snRNA with unusual protein components Zsofia Palfi, Bernd Schimanski, Arthur Günzl, Stephan Lücke, and Albrecht Bindereif PMCID: PMC1087902 Activity of Lac repressor anchored to the Escherichia coli inner membrane Boris Görke, Jana Reinhardt, and Bodo Rak PMCID: PMC1088070 XRCC1 is required for DNA single-strand break repair in human cells Reto Brem and Janet Hall PMCID: PMC1088068 Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons Sarath Chandra Janga, Julio Collado-Vides, and Gabriel Moreno-Hagelsieb PMCID: PMC1088069 Inhibition of double-strand break non-homologous end-joining by cisplatin adducts in human cell extracts C. P. Diggle, J. Bentley, M. A. Knowles, and A. E. Kiltie PMCID: PMC1088968 Modulating DNA bending affects NodD-mediated transcriptional control in Rhizobium leguminosarum Xiao-Chun Chen, Jie Feng, Bi-He Hou, Feng-Qing Li, Qiang Li, and Guo-Fan Hong PMCID: PMC1088969 How many clones need to be sequenced from a single forensic or ancient DNA sample in order to determine a reliable consensus sequence? Mim A. Bower, Matthew Spencer, Shuichi Matsumura, R. Ellen R. Nisbet, and Christopher J. Howe PMCID: PMC1088305 The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure Sylvia Tobé, Thomas Heams, Jacques Vergne, Guy Hervé, and Marie-Christine Maurel PMCID: PMC1088306 Alternative polyadenylation of cyclooxygenase-2 Tyra Hall-Pogar, Haibo Zhang, Bin Tian, and Carol S. Lutz PMCID: PMC1088970 A mathematical and computational framework for quantitative comparison and integration of large-scale gene expression data Christopher E. Hart, Lucas Sharenbroich, Benjamin J. Bornstein, Diane Trout, Brandon King, Eric Mjolsness, and Barbara J. Wold PMCID: PMC1092273 In vitro selection to identify determinants in tRNA for Bacillus subtilis tyrS T box antiterminator mRNA binding Hamid Fauzi, Karen D. Jack, and Jennifer V. Hines PMCID: PMC1090546 An SOS-regulated operon involved in damage-inducible mutagenesis in Caulobacter crescentus Rodrigo S. Galhardo, Raquel P. Rocha, Marilis V. Marques, and Carlos F. M. Menck PMCID: PMC1092274 Molecular haplotyping by linking emulsion PCR: analysis of paraoxonase 1 haplotypes and phenotypes James G. Wetmur, Madhu Kumar, Li Zhang, Caroline Palomeque, Sylvan Wallenstein, and Jia Chen PMCID: PMC1092276 Exploration of factors driving incorporation of unnatural dNTPS into DNA by Klenow fragment (DNA polymerase I) and DNA polymerase α Kristi Kincaid, Jeff Beckman, Aleksandra Zivkovic, Randall L. Halcomb, Joachim W. Engels, and Robert D. Kuchta PMCID: PMC1090547 The highly conserved glutamic acid 791 of Rpb2 is involved in the binding of NTP and Mg(B) in the active center of human RNA polymerase II Marie-France Langelier, Dania Baali, Vincent Trinh, Jack Greenblatt, Jacques Archambault, and Benoit Coulombe PMCID: PMC1092279 Binding of pRNA to the N-terminal 14 amino acids of connector protein of bacteriophage phi29 Feng Xiao, Wulf-Dieter Moll, Songchuan Guo, and Peixuan Guo PMCID: PMC1092275 ZAC, LIT1 (KCNQ1OT1) and p57KIP2 (CDKN1C) are in an imprinted gene network that may play a role in Beckwith–Wiedemann syndrome Takahiro Arima, Tetsuya Kamikihara, Toshirou Hayashida, Kiyoko Kato, Toshiaki Inoue, Yasuaki Shirayoshi, Mitsuo Oshimura, Hidenobu Soejima, Tunehiro Mukai, and Norio Wake PMCID: PMC1097765 The third helix of the homeodomain of paired class homeodomain proteins acts as a recognition helix both for DNA and protein interactions Jack-Ansgar Bruun, Ernst Ivan Simon Thomassen, Kurt Kristiansen, Garth Tylden, Turid Holm, Ingvild Mikkola, Geir Bjørkøy, and Terje Johansen PMCID: PMC1092277 DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway Bram van den Broek, Maarten C. Noom, and Gijs J. L. Wuite PMCID: PMC1092278 Identification of brassinosteroid-related genes by means of transcript co-response analyses Janina Lisso, Dirk Steinhauser, Thomas Altmann, Joachim Kopka, and Carsten Müssig PMCID: PMC1110741 Clustering and conservation patterns of human microRNAs Yael Altuvia, Pablo Landgraf, Gila Lithwick, Naama Elefant, Sébastien Pfeffer, Alexei Aravin, Michael J. Brownstein, Thomas Tuschl, and Hanah Margalit PMCID: PMC1110742 Nucleoside diphosphate kinase from Mycobacterium tuberculosis cleaves single strand DNA within the human c-myc promoter in an enzyme-catalyzed reaction Praveen Kumar, Anjali Verma, Adesh Kumar Saini, Puneet Chopra, Pradip K. Chakraborti, Yogendra Singh, and Shantanu Chowdhury PMCID: PMC1097768 Regulation of ribonucleotide reductase M2 expression by the upstream AUGs Zizheng Dong, Yang Liu, and Jian-Ting Zhang PMCID: PMC1097769 Common patterns in type II restriction enzyme binding sites Svetlana Nikolajewa, Andreas Beyer, Maik Friedel, Jens Hollunder, and Thomas Wilhelm PMCID: PMC1097771 The recent transfer of a homing endonuclease gene Peik Haugen, Odd-Gunnar Wikmark, Anna Vader, Dag H. Coucheron, Eva Sjøttem, and Steinar D. Johansen PMCID: PMC1110740 Chromatin assembly factor Asf1p-dependent occupancy of the SAS histone acetyltransferase complex at the silent mating-type locus HMLα Shigehiro Osada, Mitsumasa Kurita, Jun-ichi Nishikawa, and Tsutomu Nishihara PMCID: PMC1110739 RNR1, a 3′–5′ exoribonuclease belonging to the RNR superfamily, catalyzes 3′ maturation of chloroplast ribosomal RNAs in Arabidopsis thaliana
Thomas J. Bollenbach, Heike Lange, Ryan Gutierrez, Mathieu Erhardt, David B. Stern, and Dominique Gagliardi PMCID: PMC1110743 Methods Online Diagnostic application of padlock probes—multiplex detection of plant pathogens using universal microarrays Marianna Szemes, Peter Bonants, Marjanne de Weerdt, Johan Baner, Ulf Landegren, and Cor D. Schoen PMCID: PMC1087788 Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments Fredrik Dahl, Mats Gullberg, Johan Stenberg, Ulf Landegren, and Mats Nilsson PMCID: PMC1087789 PieceMaker: selection of DNA fragments for selector-guided multiplex amplification Johan Stenberg, Fredrik Dahl, Ulf Landegren, and Mats Nilsson PMCID: PMC1087790 Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines Cora Mund, Verena Beier, Peter Bewerunge, Michael Dahms, Frank Lyko, and Jörg D. Hoheisel PMCID: PMC1087791 Suppression of vascular endothelial growth factor expression at the transcriptional and post-transcriptional levels Heung-Sun Kwon, Hyun-Chul Shin, and Jin-Soo Kim PMCID: PMC1087787 In situ oligonucleotide synthesis on poly(dimethylsiloxane): a flexible substrate for microarray fabrication Matthew J. Moorcroft, Wouter R. A. Meuleman, Steven G. Latham, Thomas J. Nicholls, Ryan D. Egeland, and Edwin M. Southern PMCID: PMC1088307 Production of viral vectors using recombinase-mediated cassette exchange Masakazu Nakano, Kazuhiko Odaka, Yuzuka Takahashi, Masakazu Ishimura, Izumu Saito, and Yumi Kanegae PMCID: PMC1090444 Molecular beacons with a homo-DNA stem: improving target selectivity Caroline Crey-Desbiolles, Dae-Ro Ahn, and Christian J. Leumann PMCID: PMC1090445 Using a microfluidic device for 1 μl DNA microarray hybridization in 500 s Cheng-Wey Wei, Ji-Yen Cheng, Chih-Ting Huang, Meng-Hua Yen, and Tai-Horng Young PMCID: PMC1110744 Proof of concept for microarray-based detection of DNA-binding oncogenes in cell extracts Tanja Egener, Emmanuelle Roulet, Marc Zehnder, Philipp Bucher, and Nicolas Mermod PMCID: PMC1110745 Corrigenda Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays Yee Leng Yap, Maria P. Wong, Xue Wu Zhang, David Hernandez, Robin Gras, David K. Smith, and Antoine Danchin PMCID: PMC1097766 Corrects: Yee Leng Yap, et al. Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays. Nucleic Acids Res. 2005; 33(1): 409–421. Conditional and inducible transgene expression in mice through the combinatorial use of Cre-mediated recombination and tetracycline induction Gusztav Belteki, Jody Haigh, Nikolett Kabacs, Katharina Haigh, Karen Sison, Frank Costantini, Jeff Whitsett, Susan E. Quaggin, and Andras Nagy PMCID: PMC1097767 Corrects: Gusztav Belteki, et al. Conditional and inducible transgene expression in mice through the combinatorial use of Cre-mediated recombination and tetracycline induction. Nucleic Acids Res. 2005; 33(5): e51. Torque-limited RecA polymerization on dsDNA Thijn van der Heijden, John van Noort, Hendrikje van Leest, Roland Kanaar, Claire Wyman, Nynke Dekker, and Cees Dekker PMCID: PMC1097770 Corrects: Thijn van der Heijden, et al. Torque-limited RecA polymerization on dsDNA. Nucleic Acids Res. 2005; 33(7): 2099–2105. Erratum Analysis of scanning force microscopy images of protein-induced DNA bending using simulations Remus T. Dame, Joost van Mameren, Martijn S. Luijsterburg, Monika E. Mysiak, Ana Janićijević, Grzegorz Pazdzior, Peter C. van der Vliet, Claire Wyman, and Gijs J.L. Wuite PMCID: PMC1097772 Corrects: Remus T. Dame, et al. Analysis of scanning force microscopy images of protein-induced DNA bending using simulations. Nucleic Acids Res. 2005; 33(7): e68. |
