| | Molecular Biology A balance between NF-Y and p53 governs the pro- and anti-apoptotic transcriptional response Paolo Benatti, Valentina Basile, Daniele Merico, Luca Isaia Fantoni, Enrico Tagliafico, and Carol Imbriano PMCID: PMC2275158 Transcription regulation of the type II restriction-modification system AhdI Ekaterina Bogdanova, Marko Djordjevic, Ioanna Papapanagiotou, Tomasz Heyduk, Geoff Kneale, and Konstantin Severinov PMCID: PMC2275141 Insights into the selective activation of alternatively used splice acceptors by the human immunodeficiency virus type-1 bidirectional splicing enhancer Corinna Asang, Ilona Hauber, and Heiner Schaal PMCID: PMC2275126 Regulation of the MAD1 promoter by G-CSF Kan Jiang, Nadine Hein, Kolja Eckert, Juliane Lüscher-Firzlaff, and Bernhard Lüscher PMCID: PMC2275144 Regulation of the human AP-endonuclease (APE1/Ref-1) expression by the tumor suppressor p53 in response to DNA damage Amira Zaky, Carlos Busso, Tadahide Izumi, Ranajoy Chattopadhyay, Ahmad Bassiouny, Sankar Mitra, and Kishor K. Bhakat PMCID: PMC2275136 Primary T-lymphocytes rescue the replication of HIV-1 DIS RNA mutants in part by facilitating reverse transcription Kate L. Jones, Secondo Sonza, and Johnson Mak PMCID: PMC2275147 Histone H1 functions as a stimulatory factor in backup pathways of NHEJ Bustanur Rosidi, Minli Wang, Wenqi Wu, Aparna Sharma, Huichen Wang, and George Iliakis PMCID: PMC2275134 Functional relevance of novel p300-mediated lysine 314 and 315 acetylation of RelA/p65 Christine Buerki, Karin M. Rothgiesser, Taras Valovka, Heather R. Owen, Hubert Rehrauer, Monika Fey, William S. Lane, and Michael O. Hottiger PMCID: PMC2275151 Functional analysis of the zinc finger and activation domains of Glis3 and mutant Glis3(NDH1) Ju Youn Beak, Hong Soon Kang, Yong-Sik Kim, and Anton M. Jetten PMCID: PMC2275160 Spliceosomal introns as tools for genomic and evolutionary analysis Manuel Irimia and Scott William Roy PMCID: PMC2275149 Interaction of p21CDKN1A with PCNA regulates the histone acetyltransferase activity of p300 in nucleotide excision repair Ornella Cazzalini, Paola Perucca, Monica Savio, Daniela Necchi, Livia Bianchi, Lucia A. Stivala, Bernard Ducommun, A. Ivana Scovassi, and Ennio Prosperi PMCID: PMC2275133 Analysis of transcription factor interactions in osteoblasts using competitive chromatin immunoprecipitation Hernan Roca and Renny T. Franceschi PMCID: PMC2275161 Role of ATM in the telomere response to the G-quadruplex ligand 360A Gaëlle Pennarun, Christine Granotier, Françoise Hoffschir, Eliane Mandine, Denis Biard, Laurent R. Gauthier, and François D. Boussin PMCID: PMC2275132 RNA Sequence-function relationships provide new insight into the cleavage site selectivity of the 8–17 RNA-cleaving deoxyribozyme Kenny Schlosser, Jimmy Gu, Lauren Sule, and Yingfu Li PMCID: PMC2275145 rRNA mutants in the yeast peptidyltransferase center reveal allosteric information networks and mechanisms of drug resistance Rasa Rakauskaitė and Jonathan D. Dinman PMCID: PMC2275155 Proton-guided movements of tRNA within the Leishmania mitochondrial RNA import complex Sudarshana Basu, Saikat Mukherjee, and Samit Adhya PMCID: PMC2275131 Deadenylation-independent stage-specific mRNA degradation in Leishmania Simon Haile, Aurélien Dupé, and Barbara Papadopoulou PMCID: PMC2275140 Analysis of adenovirus VA RNAI structure and stability using compensatory base pair modifications Veronica K. Coventry and Graeme L. Conn PMCID: PMC2275154 Pentamidine binds to tRNA through non-specific hydrophobic interactions and inhibits aminoacylation and translation Tao Sun and Yi Zhang PMCID: PMC2275129 Structural Biology Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(CGCGAATTCGCG) Koen Robeyns, Piet Herdewijn, and Luc Van Meervelt PMCID: PMC2275148 Interaction of cationic surfactants with DNA: a single-molecule study Sudhir Husale, Wilfried Grange, Marc Karle, Stephan Bürgi, and Martin Hegner PMCID: PMC2275125 Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations Vineet Pande and Lennart Nilsson PMCID: PMC2275159 Stretching and unzipping nucleic acid hairpins using a synthetic nanopore Q. Zhao, J. Comer, V. Dimitrov, S. Yemenicioglu, A. Aksimentiev, and G. Timp PMCID: PMC2275135 The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site Alexander B. Taylor, Britta Meyer, Belinda Z. Leal, Peter Kötter, Virgil Schirf, Borries Demeler, P. John Hart, Karl-Dieter Entian, and Jens Wöhnert PMCID: PMC2275143 Crystal structure of IcaR, a repressor of the TetR family implicated in biofilm formation in Staphylococcus epidermidis Wen-Yih Jeng, Tzu-Ping Ko, Chia-I Liu, Rey-Ting Guo, Chien-Liang Liu, Hui-Lin Shr, and Andrew H.-J. Wang PMCID: PMC2275139 Probing the mechanism of recognition of ssDNA by the Cdc13-DBD Aimee M. Eldridge and Deborah S. Wuttke PMCID: PMC2275150 Solution structure of stem-loop α of the hepatitis B virus post-transcriptional regulatory element Martin Schwalbe, Oliver Ohlenschläger, Aliaksandr Marchanka, Ramadurai Ramachandran, Sabine Häfner, Tilman Heise, and Matthias Görlach PMCID: PMC2275152 Chemistry Chiral introduction of positive charges to PNA for double-duplex invasion to versatile sequences Takumi Ishizuka, Junya Yoshida, Yoji Yamamoto, Jun Sumaoka, Tullia Tedeschi, Roberto Corradini, Stefano Sforza, and Makoto Komiyama PMCID: PMC2275137 Methods Online Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG) Inhan Lee, Subramanian S. Ajay, Haiming Chen, Atsushi Maruyama, Nulang Wang, Melvin G. McInnis, and Brian D. Athey PMCID: PMC2275156 Improvement of reporter activity by IRES-mediated polycistronic reporter system Hicham Bouabe, Reinhard Fässler, and Jürgen Heesemann PMCID: PMC2275123 Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry Yao Chi Chen and Carmay Lim PMCID: PMC2275128 Target accessibility and signal specificity in live-cell detection of BMP-4 mRNA using molecular beacons Won Jong Rhee, Philip J. Santangelo, Hanjoong Jo, and Gang Bao PMCID: PMC2275124 Facile SNP detection using bifunctional, cross-linking oligonucleotide probes Xiaohua Peng and Marc M. Greenberg PMCID: PMC2275146 The use of multiple displacement amplification to amplify complex DNA libraries Melissa J. Fullwood, Jack J. S. Tan, Patrick W. P. Ng, Kuo Ping Chiu, Jun Liu, Chia Lin Wei, and Yijun Ruan PMCID: PMC2275127 Performance comparison between k-tuple distance and four model-based distances in phylogenetic tree reconstruction Kuan Yang and Liqing Zhang PMCID: PMC2275138 Bisulfite sequencing Data Presentation and Compilation (BDPC) web server—a useful tool for DNA methylation analysis Christian Rohde, Yingying Zhang, Tomasz P. Jurkowski, Heinrich Stamerjohanns, Richard Reinhardt, and Albert Jeltsch PMCID: PMC2275153 Computational Biology Algorithm for prediction of tumour suppressor p53 affinity for binding sites in DNA Dmitry B. Veprintsev and Alan R. Fersht PMCID: PMC2275157 Nucleic Acid Enzymes Identification and characterization of coumestans as novel HCV NS5B polymerase inhibitors Neerja Kaushik-Basu, Alain Bopda-Waffo, Tanaji T. Talele, Amartya Basu, Paulo R. R. Costa, Alcides J. M. da Silva, Stefan G. Sarafianos, and François Noël PMCID: PMC2275130 Substitution of a residue contacting the triphosphate moiety of the incoming nucleotide increases the fidelity of yeast DNA polymerase ζ Craig A. Howell, Christine M. Kondratick, and M. Todd Washington PMCID: PMC2275142 |
