| | Molecular Biology The second AT-hook of the architectural transcription factor HMGA2 is determinant for nuclear localization and function Giacomo Cattaruzzi, Sandro Altamura, Michela A. Tessari, Alessandra Rustighi, Vincenzo Giancotti, Carlo Pucillo, and Guidalberto Manfioletti PMCID: PMC1874589 Elevating the levels of Sox2 in embryonal carcinoma cells and embryonic stem cells inhibits the expression of Sox2:Oct-3/4 target genes Brian Boer, Janel Kopp, Sunil Mallanna, Michelle Desler, Harini Chakravarthy, Phillip J. Wilder, Cory Bernadt, and Angie Rizzino PMCID: PMC1874607 Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression Sangyong Lim, Jiae Yun, Hyunjin Yoon, Chehwee Park, Boowon Kim, Byeonghwa Jeon, Dongho Kim, and Sangryeol Ryu PMCID: PMC1874608 Switched alternative splicing of oncogene CoAA during embryonal carcinoma stem cell differentiation Zheqiong Yang, Yang Sui, Shiqin Xiong, Sean S. Liour, Andrew C. Phillips, and Lan Ko PMCID: PMC1874587 Involvement of chromatin and histone deacetylation in SV40  T antigen transcription regulation Ester Valls, Noemí Blanco-García, Naiara Aquizu, David Piedra, Conchi Estarás, Xavier de la Cruz, and Marian A. Martínez-Balbás PMCID: PMC1874590 Tat competes with HEXIM1 to increase the active pool of P-TEFb for HIV-1 transcription Matjaz Barboric, Jasper H. N. Yik, Nadine Czudnochowski, Zhiyuan Yang, Ruichuan Chen, Xavier Contreras, Matthias Geyer, B. Matija Peterlin, and Qiang Zhou PMCID: PMC1874611 Role of GAC63 in transcriptional activation mediated by β-catenin Yong-Heng Chen, Catherine K. Yang, Meng Xia, Chen-Yin Ou, and Michael R. Stallcup PMCID: PMC1874623 Cancer-derived p53 mutants suppress p53-target gene expression—potential mechanism for gain of function of mutant p53 Faina Vikhanskaya, Ming Kei Lee, Marco Mazzoletti, Massimo Broggini, and Kanaga Sabapathy PMCID: PMC1874625 RNA Alternative splicing and bioinformatic analysis of human U12-type introns Wen-Cheng Chang, Yung-Chia Chen, Kuo-Ming Lee, and Woan-Yuh Tarn PMCID: PMC1874599 An improved definition of the RNA-binding specificity of SECIS-binding protein 2, an essential component of the selenocysteine incorporation machinery A. Cléry, V. Bourguignon-Igel, C. Allmang, A. Krol, and C. Branlant PMCID: PMC1874613 Studies on the function of the riboregulator 6S RNA from E. coli: RNA polymerase binding, inhibition of in vitro transcription and synthesis of RNA-directed de novo transcripts Nina Gildehaus, Thomas Neußer, Reinhild Wurm, and Rolf Wagner PMCID: PMC1874619 Mg2+-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis Andrei Yu. Kobitski, Alexander Nierth, Mark Helm, Andres Jäschke, and G. Ulrich Nienhaus PMCID: PMC1874616 In vivo and in vitro investigation of bacterial type B RNase P interaction with tRNA 3′-CCA Barbara Wegscheid and Roland K. Hartmann PMCID: PMC1874595 Structural Biology Pressure dissociation of integration host factor–DNA complexes reveals flexibility-dependent structural variation at the protein–DNA interface Donald F. Senear, Vira Tretyachenko-Ladokhina, Michael L. Opel, Kimberly A. Aeling, G. Wesley Hatfield, Laurie M. Franklin, Reuben C. Darlington, and J.B. Alexander Ross PMCID: PMC1874591 Crystal structure of the left-handed archaeal RadA helical filament: identification of a functional motif for controlling quaternary structures and enzymatic functions of RecA family proteins Li-Tzu Chen, Tzu-Ping Ko, Yuan-Chih Chang, Kuei-An Lin, Chia-Seng Chang, Andrew H.-J. Wang, and Ting-Fang Wang PMCID: PMC1874592 Novel protein fold discovered in the PabI family of restriction enzymes Ken-ichi Miyazono, Miki Watanabe, Jan Kosinski, Ken Ishikawa, Masayuki Kamo, Tatsuya Sawasaki, Koji Nagata, Janusz M. Bujnicki, Yaeta Endo, Masaru Tanokura, and Ichizo Kobayashi PMCID: PMC1874622 Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules Ella Czarina Magat Juan, Jiro Kondo, Takeshi Kurihara, Takanori Ito, Yoshihito Ueno, Akira Matsuda, and Akio Takénaka PMCID: PMC1874594 Biophysical studies of DNA modified with conformationally constrained nucleotides: comparison of 2′-exo (north) and 3′-exo (south) ‘locked’ templates Melissa Maderia, Shilpa Shenoy, Que N. Van, Victor E. Marquez, and Joseph J. Barchi, Jr PMCID: PMC1895885 Nucleocapsid protein-mediated maturation of dimer initiation complex of full-length SL1 stemloop of HIV-1: sequence effects and mechanism of RNA refolding Anwer Mujeeb, Nikolai B. Ulyanov, Stefanos Georgantis, Ivan Smirnov, Janet Chung, Tristram G. Parslow, and Thomas L. James PMCID: PMC1874624 Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically Magdalena Kaus-Drobek, Honorata Czapinska, Monika Sokołowska, Gintautas Tamulaitis, Roman H. Szczepanowski, Claus Urbanke, Virginijus Siksnys, and Matthias Bochtler PMCID: PMC1874612 Survey and Summary Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protists to humans: close to 300 cases reveal remarkable diversity despite underlying conservation Ivaylo P. Ivanov and John F. Atkins PMCID: PMC1874602 Genomics Impaired expression of NER gene network in sporadic solid tumors Mauro A. A. Castro, José C. M. Mombach, Rita M. C. de Almeida, and José C. F. Moreira PMCID: PMC1874609 Beyond the 3′ end: experimental validation of extended transcript isoforms Virginie Moucadel, Fabrice Lopez, Takeshi Ara, Philippe Benech, and Daniel Gautheret PMCID: PMC1874610 EST assembly supported by a draft genome sequence: an analysis of the Chlamydomonas reinhardtii transcriptome Monica Jain, Jeff Shrager, Elizabeth H. Harris, Renee Halbrook, Arthur R. Grossman, Charles Hauser, and Olivier Vallon PMCID: PMC1874618 Chemistry Mechanism of the formation of DNA–protein cross-links by antitumor cisplatin Kateřina Chválová, Viktor Brabec, and Jana Kašpárková PMCID: PMC1874601 Methods Online Visualizing the proteome of Escherichia coli: an efficient and versatile method for labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes Rory M. Watt, Jing Wang, Meikid Leong, Hsiang-fu Kung, Kathryn S.E. Cheah, Depei Liu, Antoine Danchin, and Jian-Dong Huang PMCID: PMC1874593 Motif programming: a microgene-based method for creating synthetic proteins containing multiple functional motifs Hirohide Saito, Tamiko Minamisawa, and Kiyotaka Shiba PMCID: PMC1874597 Rapid coupling of Surface Plasmon Resonance (SPR and SPRi) and ProteinChip™ based mass spectrometry for the identification of proteins in nucleoprotein interactions Emeline Bouffartigues, Hervé Leh, Marielle Anger-Leroy, Sylvie Rimsky, and Malcolm Buckle PMCID: PMC1874600 Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene Jong-Yoon Chun, Kyoung-Joong Kim, In-Taek Hwang, Yun-Jee Kim, Dae-Hoon Lee, In-Kyoung Lee, and Jong-Kee Kim PMCID: PMC1874606 Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation Tomasz K. Wojdacz and Alexander Dobrovic PMCID: PMC1874596 Quantitative surface-enhanced resonance Raman scattering of phthalocyanine-labelled oligonucleotides A. Macaskill, A. A. Chernonosov, V. V. Koval, E. A. Lukyanets, O. S. Fedorova, W. E. Smith, K. Faulds, and D. Graham PMCID: PMC1874604 Vectors for co-expression of an unrestricted number of proteins Christoph Scheich, Daniel Kümmel, Dimitri Soumailakakis, Udo Heinemann, and Konrad Büssow PMCID: PMC1874614 SNP discovery by mismatch-targeting of Mu transposition Luisa Orsini, Maria Pajunen, Ilkka Hanski, and Harri Savilahti PMCID: PMC1874615 A versatile ligation-independent cloning method suitable for high-throughput expression screening applications Nick S. Berrow, David Alderton, Sarah Sainsbury, Joanne Nettleship, Rene Assenberg, Nahid Rahman, David I. Stuart, and Raymond J. Owens PMCID: PMC1874605 A synthetic luxCDABE gene cluster optimized for expression in high-GC bacteria Arryn Craney, Tobias Hohenauer, Ye Xu, Naveen Kumar Navani, Yingfu Li, and Justin Nodwell PMCID: PMC1874620 Computational Biology Codon conservation in the influenza A virus genome defines RNA packaging signals Julia R. Gog, Emmanuel Dos Santos Afonso, Rosa M. Dalton, India Leclercq, Laurence Tiley, Debra Elton, Johann C. von Kirchbach, Nadia Naffakh, Nicolas Escriou, and Paul Digard PMCID: PMC1874621 QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data Stefano Colella, Christopher Yau, Jennifer M. Taylor, Ghazala Mirza, Helen Butler, Penny Clouston, Anne S. Bassett, Anneke Seller, Christopher C. Holmes, and Jiannis Ragoussis PMCID: PMC1874617 Nucleic Acid Enzymes Controlling the motor activity of a transcription-repair coupling factor: autoinhibition and the role of RNA polymerase Abigail J. Smith, Mark D. Szczelkun, and Nigel J. Savery PMCID: PMC1874598 The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis Jana Sefcikova, Maryna V. Krasovska, Jiří Šponer, and Nils G. Walter PMCID: PMC1874588 USER™ friendly DNA engineering and cloning method by uracil excision Jurate Bitinaite, Michelle Rubino, Kamini Hingorani Varma, Ira Schildkraut, Romualdas Vaisvila, and Rita Vaiskunaite PMCID: PMC1874603 Corrigendum G-quadruplexes in promoters throughout the human genome Julian L. Huppert and Shankar Balasubramanian PMCID: PMC1874626 Corrects: Julian L. Huppert, et al. G-quadruplexes in promoters throughout the human genome. Nucleic Acids Res. 2007 January; 35(2): 406–413. |
