| | Articles Variation in the strength of selected codon usage bias among bacteria Paul M. Sharp, Elizabeth Bailes, Russell J. Grocock, John F. Peden, and R. Elizabeth Sockett PMCID: PMC549432 Recognition of the spliceosomal branch site RNA helix on the basis of surface and electrostatic features Darui Xu, Nancy L. Greenbaum, and Marcia O. Fenley PMCID: PMC549433 Evolutionarily conserved human targets of adenosine to inosine RNA editing Erez Y. Levanon, Martina Hallegger, Yaron Kinar, Ronen Shemesh, Kristina Djinovic-Carugo, Gideon Rechavi, Michael F. Jantsch, and Eli Eisenberg PMCID: PMC549564 Translation of the first upstream ORF in the hepatitis B virus pregenomic RNA modulates translation at the core and polymerase initiation codons Augustine Chen, Y. F. Kao, and Chris M. Brown PMCID: PMC549565 The effect of chemical modifications on the thermal stability of different G-quadruplex-forming oligonucleotides Barbara Saccà, Laurent Lacroix, and Jean-Louis Mergny PMCID: PMC549566 Separation of mutation avoidance and antirecombination functions in an Escherichia coli mutS mutant Melissa A. Calmann, Anetta Nowosielska, and M. G. Marinus PMCID: PMC549567 Enhanced RNA cleavage within bulge-loops by an artificial ribonuclease Irina L. Kuznetsova, Marina A. Zenkova, Hans J. Gross, and Valentin V. Vlassov PMCID: PMC549568 Structure and RNA binding of the third KH domain of poly(C)-binding protein 1 M. Sidiqi, J. A. Wilce, J. P. Vivian, C. J. Porter, A. Barker, P. J. Leedman, and M. C. J. Wilce PMCID: PMC549569 Human base excision repair enzymes apurinic/apyrimidinic endonuclease1 (APE1), DNA polymerase β and poly(ADP-ribose) polymerase 1: interplay between strand-displacement DNA synthesis and proofreading exonuclease activity Maria V. Sukhanova, Svetlana N. Khodyreva, Natalia A. Lebedeva, Rajendra Prasad, Samuel H. Wilson, and Olga I. Lavrik PMCID: PMC549570 Oxidative damage in telomeric DNA disrupts recognition by TRF1 and TRF2 Patricia L. Opresko, Jinshui Fan, Shamika Danzy, David M. Wilson, III, and Vilhelm A. Bohr PMCID: PMC549571 Target-dependent on/off switch increases ribozyme fidelity Lucien Junior Bergeron and Jean-Pierre Perreault PMCID: PMC549572 Selective inhibition of HIV-1 reverse transcriptase-associated ribonuclease H activity by hydroxylated tropolones Scott R. Budihas, Inna Gorshkova, Sergei Gaidamakov, Antony Wamiru, Marion K. Bona, Michael A. Parniak, Robert J. Crouch, James B. McMahon, John A. Beutler, and Stuart F. J. Le Grice PMCID: PMC552956 The contribution of phosphate–phosphate repulsions to the free energy of DNA bending Kevin Range, Evelyn Mayaan, L. J. Maher, III, and Darrin M. York PMCID: PMC552960 Molecular characterization of Drosophila NELF Chwen-Huey Wu, Chanhyo Lee, Ruopeng Fan, Meghan J. Smith, Yuki Yamaguchi, Hiroshi Handa, and David S. Gilmour PMCID: PMC552961 Vertebrate DNA damage tolerance requires the C-terminus but not BRCT or transferase domains of REV1 Anna-Laura Ross, Laura J. Simpson, and Julian E. Sale PMCID: PMC552965 Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis Angie M. Cheng, Mike W. Byrom, Jeffrey Shelton, and Lance P. Ford PMCID: PMC552951 Leaky ribosomal scanning in mammalian genomes: significance of histone H4 alternative translation in vivo Elisheva Smith, Todd E. Meyerrose, Thomas Kohler, Malka Namdar-Attar, Natti Bab, Olga Lahat, Tommy Noh, Jingjing Li, Mazen W. Karaman, Joseph G. Hacia, Ting T. Chen, Jan A. Nolta, Ralph Müller, Itai Bab, and Baruch Frenkel PMCID: PMC552952 A family of RS domain proteins with novel subcellular localization and trafficking Steven J. Kavanagh, Thomas C. Schulz, Philippa Davey, Charles Claudianos, Carrie Russell, and Peter D. Rathjen PMCID: PMC552957 RGG-boxes of the EWS oncoprotein repress a range of transcriptional activation domains Deepa Alex and Kevin A. W. Lee PMCID: PMC552958 Human pol II promoter prediction: time series descriptors and machine learning Rajeev Gangal and Pankaj Sharma PMCID: PMC552959 α2(I) collagen gene regulation by protein kinase C signaling in human dermal fibroblasts Masatoshi Jinnin, Hironobu Ihn, Kenichi Yamane, Yoshihiro Mimura, Yoshihide Asano, and Kunihiko Tamaki PMCID: PMC552962 Mithramycin forms a stable dimeric complex by chelating with Fe(II): DNA-interacting characteristics, cellular permeation and cytotoxicity Ming-Hon Hou and Andrew H.-J. Wang PMCID: PMC552963 Amino-functionalized DNA: the properties of C5-amino-alkyl substituted 2′-deoxyuridines and their application in DNA triplex formation John A. Brazier, Takayuki Shibata, John Townsley, Brian F. Taylor, Elaine Frary, Nicholas H. Williams, and David M. Williams PMCID: PMC552953 Enzymatic properties of the Caenorhabditis elegans Dna2 endonuclease/helicase and a species-specific interaction between RPA and Dna2 Do-Hyung Kim, Kyoung-Hwa Lee, Jeong-Hoon Kim, Gi-Hyuck Ryu, Sung-Ho Bae, Byung-Chul Lee, Kyeong-Yeop Moon, Si-Myung Byun, Hyeon-Sook Koo, and Yeon-Soo Seo PMCID: PMC552954 Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs Samuela Pasquali, Hin Hark Gan, and Tamar Schlick PMCID: PMC552955 metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella John W. Pinney, Martin W. Shirley, Glenn A. McConkey, and David R. Westhead PMCID: PMC552966 Cadmium inhibits mismatch repair by blocking the ATPase activity of the MSH2–MSH6 complex Sreeparna Banerjee and Hernan Flores-Rozas PMCID: PMC552968 Methods Online A high-throughput screening of genes that encode proteins transported into the endoplasmic reticulum in mammalian cells Takeaki Ozawa, Kengo Nishitani, Yusuke Sako, and Yoshio Umezawa PMCID: PMC549573 Selection of functional human antibodies from retroviral display libraries Johannes H. Urban, Richard M. Schneider, Marta Compte, Carsten Finger, Klaus Cichutek, Luis Álvarez-Vallina, and Christian J. Buchholz PMCID: PMC549574 Simple and highly efficient BAC recombineering using galK selection Søren Warming, Nina Costantino, Donald L. Court, Nancy A. Jenkins, and Neal G. Copeland PMCID: PMC549575 Novel cyanine-AMP conjugates for efficient 5′ RNA fluorescent labeling by one-step transcription and replacement of [γ-32P]ATP in RNA structural investigation Na Li, Changjun Yu, and Faqing Huang PMCID: PMC549576 Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS Mathias Ehrich, Sebastian Böcker, and Dirk van den Boom PMCID: PMC549577 Screening of retroviral cDNA libraries for factors involved in protein phosphorylation in signaling cascades J. Stitz, P. O. Krutzik, and G. P. Nolan PMCID: PMC549578 Modified branched peptides with a histidine-rich tail enhance in vitro gene transfection Qixin Leng and A. James Mixson PMCID: PMC549579 Targeted ‘knockdown’ of spliceosome function in mammalian cells Nathalie Matter and Harald König PMCID: PMC549580 A multipurpose vector system for the screening of libraries in bacteria, insect and mammalian cells and expression in vivo Olli H. Laitinen, Kari J. Airenne, Vesa P. Hytönen, Erik Peltomaa, Anssi J. Mähönen, Thomas Wirth, Miia M. Lind, Kari A. Mäkelä, Pyry I. Toivanen, Diana Schenkwein, Tommi Heikura, Henri R. Nordlund, Markku S. Kulomaa, and Seppo Ylä-Herttuala PMCID: PMC549581 An efficient system to establish multiple embryonic stem cell lines carrying an inducible expression unit Shinji Masui, Daisuke Shimosato, Yayoi Toyooka, Rika Yagi, Kazue Takahashi, and Hitoshi Niwa PMCID: PMC552969 Tagging genes with cassette-exchange sites Gilda Cobellis, Giancarlo Nicolaus, Mariangela Iovino, Antonio Romito, Emanuele Marra, Manlio Barbarisi, Marco Sardiello, Francesco P. Di Giorgio, Nicola Iovino, Massimo Zollo, Andrea Ballabio, and Riccardo Cortese PMCID: PMC552971 Development of an automated in vitro selection protocol to obtain RNA-based aptamers: identification of a biostable substance P antagonist Dirk Eulberg, Klaus Buchner, Christian Maasch, and Sven Klussmann PMCID: PMC552970 Corrigendum Sam68 is absolutely required for Rev function and HIV-1 production Suhasini Modem, Kameswara R. Badri, Thomas C. Holland, and Thipparthi R. Reddy PMCID: PMC552981 Corrects: Suhasini Modem, et al. Sam68 is absolutely required for Rev function and HIV-1 production. Nucleic Acids Res. 2005; 33(3): 873–879. Erratum Rapid creation of BAC-based human artifical chromosome vectors by transposition with synthetic alpha-satellite arrays Joydeep Basu, Gregory Stromberg, George Compitello, Huntington F. Willard, and Gil Van Bokkelen PMCID: PMC552980 Corrects: Joydeep Basu, et al. Rapid creation of BAC-based human artificial chromosome vectors by transposition with synthetic alpha-satellite arrays. Nucleic Acids Res. 2005; 33(2): 587–596. |
