| | Articles Where does bacterial replication start? Rules for predicting the oriC region Paweł Mackiewicz, Jolanta Zakrzewska-Czerwińska, Anna Zawilak, Mirosław R. Dudek, and Stanisław Cebrat PMCID: PMC506792 Intracellular inhibition of hepatitis C virus (HCV) internal ribosomal entry site (IRES)-dependent translation by peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) Christopher J. Nulf and David Corey PMCID: PMC506796 Intercellular communication between germ line and somatic line is utilized to control the transcription of ZAM, an endogenous retrovirus from Drosophila melanogaster Carine Meignin, Bernard Dastugue, and Chantal Vaury PMCID: PMC506797 Mathematical algorithm for discovering states of expression from direct genetic comparison by microarrays Hassan M. Fathallah-Shaykh, Bin He, Li-Juan Zhao, and Aamir Badruddin PMCID: PMC506804 Synthesis and physical and physiological properties of 4′-thioRNA: application to post-modification of RNA aptamer toward NF-κB Shuichi Hoshika, Noriaki Minakawa, and Akira Matsuda PMCID: PMC506795 Discovery of sequence motifs related to coexpression of genes using evolutionary computation Gary B. Fogel, Dana G. Weekes, Gabor Varga, Ernst R. Dow, Harry B. Harlow, Jude E. Onyia, and Chen Su PMCID: PMC506801 siRNA-mediated gene silencing: a global genome view Dimitri Semizarov, Paul Kroeger, and Stephen Fesik PMCID: PMC506802 A YY1-binding site is required for accurate human LINE-1 transcription initiation Jyoti N. Athanikar, Richard M. Badge, and John V. Moran PMCID: PMC506791 TFIIB-facilitated recruitment of preinitiation complexes by a TAF-independent mechanism Roderick T. Hori, Shuping Xu, Xianyuan Hu, and Sung Pyo PMCID: PMC506799 New invMED1 element cis-activates human multidrug-related MDR1 and MVP genes, involving the LRP130 protein Stéphane Labialle, Guila Dayan, Landry Gayet, Dominique Rigal, Joël Gambrelle, and Loris G. Baggetto PMCID: PMC506807 Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase John R. Horton, Gary Ratner, Nilesh K. Banavali, Niu Huang, Yongseok Choi, Martin A. Maier, Victor E. Marquez, Alexander D. MacKerell, Jr, and Xiaodong Cheng PMCID: PMC506793 Sequence-specific artificial ribonucleases. I. Bis-imidazole-containing oligonucleotide conjugates prepared using precursor-based strategy Natalia G. Beloglazova, Martin M. Fabani, Marina A. Zenkova, Elena V. Bichenkova, Nikolai N. Polushin, Vladimir V. Sil'nikov, Kenneth T. Douglas, and Valentin V. Vlassov PMCID: PMC506794 Changing the recognition specificity of a DNA-methyltransferase by in vitro evolution Edit Tímár, Gergely Groma, Antal Kiss, and Pál Venetianer PMCID: PMC506809 Identification of important chemical groups of the hut mRNA for HutP interactions that regulate the hut operon in Bacillus subtilis T. S. Kumarevel, S. C. B. Gopinath, S. Nishikawa, H. Mizuno, and P. K. R. Kumar PMCID: PMC506810 The adenovirus priming protein pTP contributes to the kinetics of initiation of DNA replication Monika E. Mysiak, P. Elly Holthuizen, and Peter C. van der Vliet PMCID: PMC506811 SMC1 coordinates DNA double-strand break repair pathways Primo Schär, Margaret Fäsi, and Rolf Jessberger PMCID: PMC506803 Symmetry elements in DNA structure important for recognition/methylation by DNA [amino]-methyltransferases Victor V. Zinoviev, S. I. Yakishchik, Alexey A. Evdokimov, Ernst G. Malygin, and Stanley Hattman PMCID: PMC506800 GATA-1 and NF-Y cooperate to mediate erythroid-specific transcription of Gfi-1B gene Duen-Yi Huang, Yuan-Yeh Kuo, Jiann-Shiun Lai, Yutaka Suzuki, Sumio Sugano, and Zee-Fen Chang PMCID: PMC506805 Evolution of divergent DNA recognition specificities in VDE homing endonucleases from two yeast species Karen L. Posey, Vassiliki Koufopanou, Austin Burt, and Frederick S. Gimble PMCID: PMC506816 Synthesis and processing of tRNA-related SINE transcripts in Arabidopsis thaliana Thierry Pélissier, Cécile Bousquet-Antonelli, Laurence Lavie, and Jean-Marc Deragon PMCID: PMC506818 Heat capacity changes in RNA folding: application of perturbation theory to hammerhead ribozyme cold denaturation Peter J. Mikulecky and Andrew L. Feig PMCID: PMC506808 The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome Jeremy Leipzig, Pavel Pevzner, and Steffen Heber PMCID: PMC506815 Role of DNA polymerase η in the bypass of abasic sites in yeast cells Bo Zhao, Zhongwen Xie, Huiyun Shen, and Zhigang Wang PMCID: PMC506798 Gene trap as a tool for genome annotation and analysis of X chromosome inactivation in human embryonic stem cells Sujoy K. Dhara and Nissim Benvenisty PMCID: PMC506821 Poly(ADP-ribose) polymerase 1 regulates both the exonuclease and helicase activities of the Werner syndrome protein Cayetano von Kobbe, Jeanine A. Harrigan, Valérie Schreiber, Patrick Stiegler, Jason Piotrowski, Lale Dawut, and Vilhelm A. Bohr PMCID: PMC506806 AdoMet radical proteins—from structure to evolution—alignment of divergent protein sequences reveals strong secondary structure element conservation Yvain Nicolet and Catherine L. Drennan PMCID: PMC506812 Quantitative modeling of DNA–protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor Tsz-Kwong Man, Joshua SungWoo Yang, and Gary D. Stormo PMCID: PMC506813 Integron integrase binds to bulged hairpin DNA Carolina Johansson, Masood Kamali-Moghaddam, and Lars Sundström PMCID: PMC506814 High salt solution structure of a left-handed RNA double helix Mariusz Popenda, Jan Milecki, and Ryszard W. Adamiak PMCID: PMC506817 Origin of the intrinsic rigidity of DNA Janine B. Mills and Paul J. Hagerman PMCID: PMC506819 Enhanced nucleic acid binding to ATP-bound hepatitis C virus NS3 helicase at low pH activates RNA unwinding Angela M. I. Lam, Ryan S. Rypma, and David N. Frick PMCID: PMC506820 Cleavage of deoxyoxanosine-containing oligodeoxyribonucleotides by bacterial endonuclease V Thomas M. Hitchcock, Honghai Gao, and Weiguo Cao PMCID: PMC506822 Single amino acid changes in AspRS reveal alternative routes for expanding its tRNA repertoire in vivo Franck Martin, Sharief Barends, and Gilbert Eriani PMCID: PMC506823 NAR Methods Online Protein–DNA footprinting by endcapped duplex oligodeoxyribonucleotides Pei-Sze Ng and Donald E. Bergstrom PMCID: PMC506826 New separation-free assay technique for SNPs using two-photon excitation fluorometry Jonne Vaarno, Emmi Ylikoski, Niko J. Meltola, Juhani T. Soini, Pekka Hänninen, Riitta Lahesmaa, and Aleksi E. Soini PMCID: PMC506825 Atelocollagen-mediated synthetic small interfering RNA delivery for effective gene silencing in vitro and in vivo Yoshiko Minakuchi, Fumitaka Takeshita, Nobuyoshi Kosaka, Hideo Sasaki, Yusuke Yamamoto, Makiko Kouno, Kimi Honma, Shunji Nagahara, Koji Hanai, Akihiko Sano, Takashi Kato, Masaaki Terada, and Takahiro Ochiya PMCID: PMC506824 Detection of protein–DNA interaction with a DNA probe: distinction between single-strand and double-strand DNA–protein interaction Changill Ban, Suhman Chung, Deog-Su Park, and Yoon-Bo Shim PMCID: PMC506829 Transcriptionally competent chromatin assembled with exogenous histones in a yeast whole cell extract Antonio Rodríguez-Campos, Ronald Koop, Susanna Faraudo, and Miguel Beato PMCID: PMC506827 Detecting single DNA copy number variations in complex genomes using one nanogram of starting DNA and BAC-array CGH Marine Guillaud-Bataille, Alexander Valent, Pascal Soularue, Christine Perot, Maria-del-Mar Inda, Aline Receveur, Sadek Smaïli, Hugues Roest Crollius, Jean Bénard, Alain Bernheim, Xavier Gidrol, and Gisèle Danglot PMCID: PMC506828 |
