| | Articles Contextual interactions determine whether the Drosophila homeodomain protein, Vnd, acts as a repressor or activator Zhongxin Yu, Li-Jyun Syu, and Dervla M. Mellerick PMCID: PMC546129 Regulation of androgen receptor and histone deacetylase 1 by Mdm2-mediated ubiquitylation Luke Gaughan, Ian R. Logan, David E. Neal, and Craig N. Robson PMCID: PMC546130 Synthesis, cellular uptake and HIV-1 Tat-dependent trans-activation inhibition activity of oligonucleotide analogues disulphide-conjugated to cell-penetrating peptides John J. Turner, Andrey A. Arzumanov, and Michael J. Gait PMCID: PMC546131 New insights into DNA triplexes: residual twist and radial difference as measures of base triplet non-isomorphism and their implication to sequence-dependent non-uniform DNA triplex R. Thenmalarchelvi and N. Yathindra PMCID: PMC546132 Multi-class cancer classification by total principal component regression (TPCR) using microarray gene expression data Yongxi Tan, Leming Shi, Weida Tong, and Charles Wang PMCID: PMC546133 DNA-binding properties of ARID family proteins Antonia Patsialou, Deborah Wilsker, and Elizabeth Moran PMCID: PMC546134 Kinetics of tetramolecular quadruplexes Jean-Louis Mergny, Anne De Cian, Amar Ghelab, Barbara Saccà, and Laurent Lacroix PMCID: PMC546136 Significant expansion of exon-bordering protein domains during animal proteome evolution Mingyi Liu, Heiko Walch, Shaoping Wu, and Andrei Grigoriev PMCID: PMC546140 Effects of camptothecin on double-strand break repair by non-homologous end-joining in DNA mismatch repair-deficient human colorectal cancer cell lines Sandrine Jacob, Catherine Miquel, Alain Sarasin, and Françoise Praz PMCID: PMC546142 Translation of stable hepadnaviral mRNA cleavage fragments induced by the action of phosphorothioate-modified antisense oligodeoxynucleotides Peter Hasselblatt, Birgit Hockenjos, Christian Thoma, Hubert E. Blum, and Wolf-Bernhard Offensperger PMCID: PMC546143 A precise DNA bend angle is essential for the function of the phage ![[var phi]](corehtml/pmc/pmcents/x03C6.gif) 29 transcriptional regulator Laura Pérez-Lago, Margarita Salas, and Ana Camacho PMCID: PMC546135 Isolation and characterization of a thermostable RNA ligase 1 from a Thermus scotoductus bacteriophage TS2126 with good single-stranded DNA ligation properties Thorarinn Blondal, Audur Thorisdottir, Unnur Unnsteinsdottir, Sigridur Hjorleifsdottir, Arnthor Ævarsson, Sveinn Ernstsson, Olafur H. Fridjonsson, Sigurlaug Skirnisdottir, Jon Oskar Wheat, Anna Gudny Hermannsdottir, Snorri Th. Sigurdsson, Gudmundur O. Hreggvidsson, Albert Vernon Smith, and Jakob K. Kristjansson PMCID: PMC546137 Condensation of oligonucleotides assembled into nicked and gapped duplexes: potential structures for oligonucleotide delivery Tumpa Sarkar, Christine C. Conwell, Lilia C. Harvey, Catherine T. Santai, and Nicholas V. Hud PMCID: PMC546144 Differential activation of DNA-PK based on DNA strand orientation and sequence bias Katherine S. Pawelczak, Brooke J. Andrews, and John J. Turchi PMCID: PMC546145 MAP2: multiple alignment of syntenic genomic sequences Liang Ye and Xiaoqiu Huang PMCID: PMC546147 Functional roles of carboxylate residues comprising the DNA polymerase active site triad of Ty3 reverse transcriptase Arkadiusz Bibillo, Daniela Lener, George J. Klarmann, and Stuart F. J. Le Grice PMCID: PMC546138 Site-specific labeling of the ribosome for single-molecule spectroscopy Magdalena Dorywalska, Scott C. Blanchard, Ruben L. Gonzalez, Jr, Harold D. Kim, Steven Chu, and Joseph D. Puglisi PMCID: PMC546139 The RNA ligands for mouse proline-rich RNA-binding protein (mouse Prrp) contain two consensus sequences in separate loop structure Tamaki Hori, Yusuke Taguchi, Seiichi Uesugi, and Yasuyuki Kurihara PMCID: PMC546141 A large-scale analysis of mRNA polyadenylation of human and mouse genes Bin Tian, Jun Hu, Haibo Zhang, and Carol S. Lutz PMCID: PMC546146 i-motif solution structure and dynamics of the d(AACCCC) and d(CCCCAA) tetrahymena telomeric repeats Narcisse Esmaili and Jean Louis Leroy PMCID: PMC546148 GM-CSF promoter chromatin remodelling and gene transcription display distinct signal and transcription factor requirements Kate H. Brettingham-Moore, Sudha Rao, Torsten Juelich, M. Frances Shannon, and Adele F. Holloway PMCID: PMC546149 Inhibition of HIV-1 gene expression by retroviral vector-mediated small-guide RNAs that direct specific RNA cleavage by tRNase ZL Yuichiro Habu, Naoko Miyano-Kurosaki, Michiko Kitano, Yumihiko Endo, Masakazu Yukita, Shigeru Ohira, Hiroaki Takaku, Masayuki Nashimoto, and Hiroshi Takaku PMCID: PMC546152 Accuracy of structure-derived properties in simple comparative models of protein structures Suvobrata Chakravarty, Lei Wang, and Roberto Sanchez PMCID: PMC546150 Processing of a complex multiply damaged DNA site by human cell extracts and purified repair proteins Grégory Eot-Houllier, Séverine Eon-Marchais, Didier Gasparutto, and Evelyne Sage PMCID: PMC546153 Inferring combinatorial regulation of transcription in silico Nils Blüthgen, Szymon M. Kiełbasa, and Hanspeter Herzel PMCID: PMC546154 The accumulation of MMS-induced single strand breaks in G1 phase is recombinogenic in DNA polymerase β defective mammalian cells Barbara Pascucci, Maria Teresa Russo, Marco Crescenzi, Margherita Bignami, and Eugenia Dogliotti PMCID: PMC546155 Deficiency in 3′-phosphoglycolate processing in human cells with a hereditary mutation in tyrosyl-DNA phosphodiesterase (TDP1) Tong Zhou, Jae Wan Lee, Haritha Tatavarthi, James R. Lupski, Kristoffer Valerie, and Lawrence F. Povirk PMCID: PMC546157 APE1 overexpression in XRCC1-deficient cells complements the defective repair of oxidative single strand breaks but increases genomic instability Marguerite Sossou, Claudia Flohr-Beckhaus, Ina Schulz, Fayza Daboussi, Bernd Epe, and J. Pablo Radicella PMCID: PMC546158 Probing a rate-limiting step by mutational perturbation of AdoMet binding in the HhaI methyltransferase Eglė Merkienė and Saulius Klimašauskas PMCID: PMC546160 Functional domains of the Xenopus replication licensing factor Cdt1 Andrew Ferenbach, Anatoliy Li, Marta Brito-Martins, and J. Julian Blow PMCID: PMC546161 The histone deacetylase inhibitor trichostatin A alters the pattern of DNA replication origin activity in human cells Michael G. Kemp, Maloy Ghosh, Guoqi Liu, and Michael Leffak PMCID: PMC546162 Multiple promoters are a common feature of mitochondrial genes in Arabidopsis Kristina Kühn, Andreas Weihe, and Thomas Börner PMCID: PMC546163 RDE-2 interacts with MUT-7 to mediate RNA interference in Caenorhabditis elegans Bastiaan B. J. Tops, Hiroaki Tabara, Titia Sijen, Femke Simmer, Craig C. Mello, Ronald H. A. Plasterk, and René F. Ketting PMCID: PMC546165 The BRCT domain of mammalian Rev1 is involved in regulating DNA translesion synthesis Jacob G. Jansen, Anastasia Tsaalbi-Shtylik, Petra Langerak, Fabienne Calléja, Caro M. Meijers, Heinz Jacobs, and Niels de Wind PMCID: PMC546167 Comparative study of sequence-dependent hybridization kinetics in solution and on microspheres Michael M. A. Sekar, Will Bloch, and Pamela M. St John PMCID: PMC546151 Serum-deprivation stimulates cap-binding by PARN at the expense of eIF4E, consistent with the observed decrease in mRNA stability Ruth Seal, Richard Temperley, Jeffrey Wilusz, Robert N. Lightowlers, and Zofia M. A. Chrzanowska-Lightowlers PMCID: PMC546156 Plant tRNA ligases are multifunctional enzymes that have diverged in sequence and substrate specificity from RNA ligases of other phylogenetic origins Markus Englert and Hildburg Beier PMCID: PMC546159 Destabilization of tetranucleotide repeats in Haemophilus influenzae mutants lacking RnaseHI or the Klenow domain of PolI Christopher D. Bayliss, Wendy A. Sweetman, and E. Richard Moxon PMCID: PMC546164 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: PMC546166 Translocation of XRCC1 and DNA ligase IIIα from centrosomes to chromosomes in response to DNA damage in mitotic human cells Satoshi Okano, Li Lan, Alan E. Tomkinson, and Akira Yasui PMCID: PMC546168 Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d Chin-Yu Chen, Tzu-Ping Ko, Ting-Wan Lin, Chia-Cheng Chou, Chun-Jung Chen, and Andrew H.-J. Wang PMCID: PMC546169 Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality Joacim Elmén, Håkan Thonberg, Karl Ljungberg, Miriam Frieden, Majken Westergaard, Yunhe Xu, Britta Wahren, Zicai Liang, Henrik Ørum, Troels Koch, and Claes Wahlestedt PMCID: PMC546170 Methods Online Rapid, solid-phase based automated analysis of chromatin structure and transcription factor occupancy in living eukaryotic cells Richard Ingram, Hiromi Tagoh, Arthur D. Riggs, and Constanze Bonifer PMCID: PMC546173 Detection and discovery of RNA modifications using microarrays Shawna L. Hiley, Jane Jackman, Tomas Babak, Miles Trochesset, Quaid D. Morris, Eric Phizicky, and Timothy R. Hughes PMCID: PMC546174 ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes Hong-Yu Ou, Rebecca Smith, Sacha Lucchini, Jay Hinton, Roy R. Chaudhuri, Mark Pallen, Michael R. Barer, and Kumar Rajakumar PMCID: PMC546176 Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions Kae Sato, Kazuo Hosokawa, and Mizuo Maeda PMCID: PMC546178 Mapping the B-A conformational transition along plasmid DNA Karel Nejedlý, Jana Chládková, Michaela Vorlíčková, Iva Hrabcová, and Jaroslav Kypr PMCID: PMC546179 Detection and characterization of horizontal transfers in prokaryotes using genomic signature Christine Dufraigne, Bernard Fertil, Sylvain Lespinats, Alain Giron, and Patrick Deschavanne PMCID: PMC546175 Conditional UAS-targeted repression in Drosophila Alberto Pascual, Kai-Lian Huang, and Thomas Preat PMCID: PMC546177 Use of a restriction enzyme-digested PCR product as substrate for helicase assays Jae-Ho Shin, John N. Reeve, and Zvi Kelman PMCID: PMC546180 BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes Gábor E. Tusnády, István Simon, András Váradi, and Tamás Arányi PMCID: PMC546182 Covalent antibody display—an in vitro antibody-DNA library selection system Herald Reiersen, Inger Løbersli, Geir Å. Løset, Else Hvattum, Bjørg Simonsen, John E. Stacy, Duncan McGregor, Kevin FitzGerald, Martin Welschof, Ole H. Brekke, and Ole J. Marvik PMCID: PMC546181 Corrigendum HOPPSIGEN: a database of human and mouse processed pseudogenes Khelifi Adel, Durent Laurent, and Mouchiroud Dominique PMCID: PMC546172 Corrects: Khelifi Adel, et al. HOPPSIGEN: a database of human and mouse processed pseudogenes. Nucleic Acids Res. 2005 January 1; 33(Database Issue): D59–D66. Erratum FESD: a Functional Element SNPs Database in human Hyo Jin Kang, Kyoung Oak Choi, Byung-Dong Kim, Sangsoo Kim, and Young Joo Kim PMCID: PMC546171 Corrects: Hyo Jin Kang, et al. FESD: a Functional Element SNPs Database in human. Nucleic Acids Res. 2005 January 1; 33(Database Issue): D518–D522. |
