| | Molecular Biology Evidence of the neuron-restrictive silencer factor (NRSF) interaction with Sp3 and its synergic repression to the mu opioid receptor (MOR) gene Chun Sung Kim, Hack Sun Choi, Cheol Kyu Hwang, Kyu Young Song, Byung-Kwon Lee, Ping-Yee Law, Li-Na Wei, and Horace H. Loh PMCID: PMC1702488 Molecular dysfunction associated with the human mitochondrial 3302A>G mutation in the MTTL1 (mt-tRNALeu(UUR)) gene Katharina Maniura-Weber, Mark Helm, Katrin Engemann, Sabrina Eckertz, Myriam Möllers, Matthias Schauen, Armine Hayrapetyan, Jürgen-Christoph von Kleist-Retzow, Robert N. Lightowlers, Laurence A. Bindoff, and Rudolf J. Wiesner PMCID: PMC1702489 Template properties of mutagenic cytosine analogues in reverse transcription Tetsuya Suzuki, Kei Moriyama, Chie Otsuka, David Loakes, and Kazuo Negishi PMCID: PMC1702492 Transcriptional regulation of the cyclin-dependent kinase inhibitor 1A (p21) gene by NFI in proliferating human cells Stéphane Ouellet, François Vigneault, Maryse Lessard, Steeve Leclerc, Régen Drouin, and Sylvain L. Guérin PMCID: PMC1702497 The Agrobacterium VirE3 effector protein: a potential plant transcriptional activator Fernando M. García-Rodríguez, Barbara Schrammeijer, and Paul J. J. Hooykaas PMCID: PMC1702499 c-Fos is required for excision repair of UV-light induced DNA lesions by triggering the re-synthesis of XPF Markus Christmann, Maja T. Tomicic, Judith Origer, Dorthe Aasland, and Bernd Kaina PMCID: PMC1702502 Mutations in the MutSα interaction interface of MLH1 can abolish DNA mismatch repair Guido Plotz, Christoph Welsch, Luis Giron-Monzon, Peter Friedhoff, Mario Albrecht, Albrecht Piiper, Ricardo M. Biondi, Thomas Lengauer, Stefan Zeuzem, and Jochen Raedle PMCID: PMC1747184 Brn-3b enhances the pro-apoptotic effects of p53 but not its induction of cell cycle arrest by cooperating in trans-activation of bax expression Vishwanie S. Budhram-Mahadeo, Samantha Bowen, Sonia Lee, Christina Perez-Sanchez, Elizabeth Ensor, Peter J. Morris, and David S. Latchman PMCID: PMC1751550 Hypervariability within the Rifin, Stevor and Pfmc-2TM superfamilies in Plasmodium falciparum Catherine Lavazec, Sohini Sanyal, and Thomas J. Templeton PMCID: PMC1751529 RNA Self-splicing of a group IIC intron: 5′ exon recognition and alternative 5′ splicing events implicate the stem–loop motif of a transcriptional terminator Navtej Toor, Aaron R. Robart, Joshua Christianson, and Steven Zimmerly PMCID: PMC1702495 Cellular delivery of small interfering RNA by a non-covalently attached cell-penetrating peptide: quantitative analysis of uptake and biological effect Sandra Veldhoen, Sandra D. Laufer, Alexander Trampe, and Tobias Restle PMCID: PMC1747183 The splicing regulators Tra and Tra2 are unusually potent activators of pre-mRNA splicing Kathryn S. Sciabica and Klemens J. Hertel PMCID: PMC1747189 Structural Biology Sequence-dependent gating of an ion channel by DNA hairpin molecules Veronica S. DeGuzman, Clarence C. Lee, David W. Deamer, and Wenonah A. Vercoutere PMCID: PMC1702491 Sequence-dependent formation of intrastrand crosslink products from the UVB irradiation of duplex DNA containing a 5-bromo-2′-deoxyuridine or 5-bromo-2′-deoxycytidine Yu Zeng and Yinsheng Wang PMCID: PMC1702501 Structure of human MRG15 chromo domain and its binding to Lys36-methylated histone H3 Peng Zhang, Jiamu Du, Bingfa Sun, Xianchi Dong, Guoliang Xu, Jinqiu Zhou, Qingqiu Huang, Qun Liu, Quan Hao, and Jianping Ding PMCID: PMC1747190 Electrostatic free energy landscapes for nucleic acid helix assembly Zhi-Jie Tan and Shi-Jie Chen PMCID: PMC1751542 A new modified thrombin binding aptamer containing a 5′–5′ inversion of polarity site Luigi Martino, Ada Virno, Antonio Randazzo, Antonella Virgilio, Veronica Esposito, Concetta Giancola, Mariarosaria Bucci, Giuseppe Cirino, and Luciano Mayol PMCID: PMC1751544 X-ray crystallographic study of DNA duplex cross-linking: simultaneous binding to two d(CGTACG)2 molecules by a bis(9-aminoacridine-4-carboxamide) derivative Nicholas H. Hopcroft, Anna L. Brogden, Mark Searcey, and Christine J. Cardin PMCID: PMC1751537 3D structure of Thermus aquaticus single-stranded DNA–binding protein gives insight into the functioning of SSB proteins Roman Fedorov, Gregor Witte, Claus Urbanke, Dietmar J. Manstein, and Ute Curth PMCID: PMC1761420 Survey and Summary The interaction networks of structured RNAs A. Lescoute and E. Westhof PMCID: PMC1747187 Genomics The natural history of the WRKY–GCM1 zinc fingers and the relationship between transcription factors and transposons M. Madan Babu, Lakshminarayan M. Iyer, S. Balaji, and L. Aravind PMCID: PMC1702500 Chemistry Fabrication and characterization of RNA aptamer microarrays for the study of protein–aptamer interactions with SPR imaging Yuan Li, Hye Jin Lee, and Robert M. Corn PMCID: PMC1702490 Use of thermolytic protective groups to prevent G-tetrad formation in CpG ODN type D: structural studies and immunomodulatory activity in primates Montserrat Puig, Andrzej Grajkowski, Malgorzata Boczkowska, Cristina Ausín, Serge L. Beaucage, and Daniela Verthelyi PMCID: PMC1702498 Methods Online A bichromatic fluorescent reporter for cell-based screens of alternative splicing James P. Orengo, Donnie Bundman, and Thomas A. Cooper PMCID: PMC1669726 A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences Julianne Smith, Sylvestre Grizot, Sylvain Arnould, Aymeric Duclert, Jean-Charles Epinat, Patrick Chames, Jesús Prieto, Pilar Redondo, Francisco J. Blanco, Jerónimo Bravo, Guillermo Montoya, Frédéric Pâques, and Philippe Duchateau PMCID: PMC1702487 Development of a novel site-specific mutagenesis assay using MALDI-ToF MS (SSMA-MS) Keith I. E. McLuckie, John H. Lamb, Jatinderpal K. Sandhu, Helen L. Pearson, Karen Brown, Peter B. Farmer, and Donald J. L. Jones PMCID: PMC1761429 Absolute enrichment: gene set enrichment analysis for homeostatic systems Vishal Saxena, Dennis Orgill, and Isaac Kohane PMCID: PMC1702493 Rapid detection of similarity in protein structure and function through contact metric distances Andreas Martin Lisewski and Olivier Lichtarge PMCID: PMC1702494 Computational Biology Identification of degenerate motifs using position restricted selection and hybrid ranking combination Chien-Hua Peng, Jeh-Ting Hsu, Yun-Sheng Chung, Yen-Jen Lin, Wei-Yuan Chow, D. Frank Hsu, and Chuan Yi Tang PMCID: PMC1702486 Amino acid residue doublet propensity in the protein–RNA interface and its application to RNA interface prediction Oanh T. P. Kim, Kei Yura, and Nobuhiro Go PMCID: PMC1761430 Sequence comparison by sequence harmony identifies subtype-specific functional sites Walter Pirovano, K. Anton Feenstra, and Jaap Heringa PMCID: PMC1702503 Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments Omar J. Jabado, Gustavo Palacios, Vishal Kapoor, Jeffrey Hui, Neil Renwick, Junhui Zhai, Thomas Briese, and W. Ian Lipkin PMCID: PMC1747188 Nucleic Acid Enzymes Activation of RegB endoribonuclease by S1 ribosomal protein requires an 11 nt conserved sequence Sylvain Durand, Graziella Richard, Marco Bisaglia, Soumaya Laalami, François Bontems, and Marc Uzan PMCID: PMC1702504 Inhibition of BACH1 (FANCJ) helicase by backbone discontinuity is overcome by increased motor ATPase or length of loading strand Rigu Gupta, Sudha Sharma, Kevin M. Doherty, Joshua A. Sommers, Sharon B. Cantor, and Robert M. Brosh, Jr PMCID: PMC1751539 Selection and cloning of poly(rC)-binding protein 2 and Raf kinase inhibitor protein RNA activators of 2′,5′-oligoadenylate synthetase from prostate cancer cells Ross J. Molinaro, Babal Kant Jha, Krishnamurthy Malathi, Sooryanarayana Varambally, Arul M. Chinnaiyan, and Robert H. Silverman PMCID: PMC1751551 Corrigendum Nucleic Acids Res. 2006 December; 34(22): 6718. doi: 10.1093/nar/gkl1020.PMCID: PMC1828438 Corrects: James J. Yun, et al. Genomic DNA functions as a universal external standard in quantitative real-time PCR. Nucleic Acids Res. 2006; 34(12): e85. |
