Nucleic Acids Research

Articles:

Pawel Mackiewicz, Jolanta Zakrzewska-Czerwinska, Anna Zawilak, Miroslaw R. Dudek, and Stanislaw Cebrat

Where does bacterial replication start? Rules for predicting the oriC region
Nucl. Acids Res. 2004 32: 3781-3791; doi:10.1093/nar/gkh699 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Christopher J. Nulf and David Corey

Intracellular inhibition of hepatitis C virus (HCV) internal ribosomal entry site (IRES)-dependent translation by peptide nucleic acids (PNAs) and locked nucleic acids (LNAs)
Nucl. Acids Res. 2004 32: 3792-3798; doi:10.1093/nar/gkh706 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Carine Meignin, Bernard Dastugue, and Chantal Vaury

Intercellular communication between germ line and somatic line is utilized to control the transcription of ZAM, an endogenous retrovirus from Drosophila melanogaster
Nucl. Acids Res. 2004 32: 3799-3806; doi:10.1093/nar/gkh708 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hassan M. Fathallah-Shaykh, Bin He, Li-Juan Zhao, and Aamir Badruddin

Mathematical algorithm for discovering states of expression from direct genetic comparison by microarrays
Nucl. Acids Res. 2004 32: 3807-3814; doi:10.1093/nar/gkh718 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Shuichi Hoshika, Noriaki Minakawa, and Akira Matsuda

Synthesis and physical and physiological properties of 4'-thioRNA: application to post-modification of RNA aptamer toward NF-B
Nucl. Acids Res. 2004 32: 3815-3825; doi:10.1093/nar/gkh705 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Gary B. Fogel, Dana G. Weekes, Gabor Varga, Ernst R. Dow, Harry B. Harlow, Jude E. Onyia, and Chen Su

Discovery of sequence motifs related to coexpression of genes using evolutionary computation
Nucl. Acids Res. 2004 32: 3826-3835; doi:10.1093/nar/gkh713 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Dimitri Semizarov, Paul Kroeger, and Stephen Fesik

siRNA-mediated gene silencing: a global genome view
Nucl. Acids Res. 2004 32: 3836-3845; doi:10.1093/nar/gkh714 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Jyoti N. Athanikar, Richard M. Badge, and John V. Moran

A YY1-binding site is required for accurate human LINE-1 transcription initiation
Nucl. Acids Res. 2004 32: 3846-3855; doi:10.1093/nar/gkh698 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Roderick T. Hori, Shuping Xu, Xianyuan Hu, and Sung Pyo

TFIIB-facilitated recruitment of preinitiation complexes by a TAF-independent mechanism
Nucl. Acids Res. 2004 32: 3856-3863; doi:10.1093/nar/gkh711 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Stéphane Labialle, Guila Dayan, Landry Gayet, Dominique Rigal, Joël Gambrelle, and Loris G. Baggetto

New invMED1 element cis-activates human multidrug-related MDR1 and MVP genes, involving the LRP130 protein
Nucl. Acids Res. 2004 32: 3864-3876; doi:10.1093/nar/gkh722 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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

Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase
Nucl. Acids Res. 2004 32: 3877-3886; doi:10.1093/nar/gkh701 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

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

Sequence-specific artificial ribonucleases. I. Bis-imidazole-containing oligonucleotide conjugates prepared using precursor-based strategy
Nucl. Acids Res. 2004 32: 3887-3897; doi:10.1093/nar/gkh702 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Edit Tímár, Gergely Groma, Antal Kiss, and Pál Venetianer

Changing the recognition specificity of a DNA-methyltransferase by in vitro evolution
Nucl. Acids Res. 2004 32: 3898-3903; doi:10.1093/nar/gkh724 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

T. S. Kumarevel, S. C. B. Gopinath, S. Nishikawa, H. Mizuno, and P. K. R. Kumar

Identification of important chemical groups of the hut mRNA for HutP interactions that regulate the hut operon in Bacillus subtilis
Nucl. Acids Res. 2004 32: 3904-3912; doi:10.1093/nar/gkh725 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Monika E. Mysiak, P. Elly Holthuizen, and Peter C. van der Vliet

The adenovirus priming protein pTP contributes to the kinetics of initiation of DNA replication
Nucl. Acids Res. 2004 32: 3913-3920; doi:10.1093/nar/gkh726 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Primo Schär, Margaret Fäsi, and Rolf Jessberger

SMC1 coordinates DNA double-strand break repair pathways
Nucl. Acids Res. 2004 32: 3921-3929; doi:10.1093/nar/gkh716 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Victor V. Zinoviev, S. I. Yakishchik, Alexey A. Evdokimov, Ernst G. Malygin, and Stanley Hattman

Symmetry elements in DNA structure important for recognition/methylation by DNA [amino]-methyltransferases
Nucl. Acids Res. 2004 32: 3930-3934; doi:10.1093/nar/gkh712 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Duen-Yi Huang, Yuan-Yeh Kuo, Jiann-Shiun Lai, Yutaka Suzuki, Sumio Sugano, and Zee-Fen Chang

GATA-1 and NF-Y cooperate to mediate erythroid-specific transcription of Gfi-1B gene
Nucl. Acids Res. 2004 32: 3935-3946; doi:10.1093/nar/gkh719 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Karen L. Posey, Vassiliki Koufopanou, Austin Burt, and Frederick S. Gimble

Evolution of divergent DNA recognition specificities in VDE homing endonucleases from two yeast species
Nucl. Acids Res. 2004 32: 3947-3956; doi:10.1093/nar/gkh734 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Thierry Pélissier, Cécile Bousquet-Antonelli, Laurence Lavie, and Jean-Marc Deragon

Synthesis and processing of tRNA-related SINE transcripts in Arabidopsis thaliana
Nucl. Acids Res. 2004 32: 3957-3966; doi:10.1093/nar/gkh738 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Peter J. Mikulecky and Andrew L. Feig

Heat capacity changes in RNA folding: application of perturbation theory to hammerhead ribozyme cold denaturation
Nucl. Acids Res. 2004 32: 3967-3976; doi:10.1093/nar/gkh723 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Jeremy Leipzig, Pavel Pevzner, and Steffen Heber

The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome
Nucl. Acids Res. 2004 32: 3977-3983; doi:10.1093/nar/gkh731 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Bo Zhao, Zhongwen Xie, Huiyun Shen, and Zhigang Wang

Role of DNA polymerase in the bypass of abasic sites in yeast cells
Nucl. Acids Res. 2004 32: 3984-3994; doi:10.1093/nar/gkh710 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sujoy K. Dhara and Nissim Benvenisty

Gene trap as a tool for genome annotation and analysis of X chromosome inactivation in human embryonic stem cells
Nucl. Acids Res. 2004 32: 3995-4002; doi:10.1093/nar/gkh746 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Cayetano von Kobbe, Jeanine A. Harrigan, Valérie Schreiber, Patrick Stiegler, Jason Piotrowski, Lale Dawut, and Vilhelm A. Bohr

Poly(ADP-ribose) polymerase 1 regulates both the exonuclease and helicase activities of the Werner syndrome protein
Nucl. Acids Res. 2004 32: 4003-4014; doi:10.1093/nar/gkh721 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yvain Nicolet and Catherine L. Drennan

AdoMet radical proteins—from structure to evolution—alignment of divergent protein sequences reveals strong secondary structure element conservation
Nucl. Acids Res. 2004 32: 4015-4025; doi:10.1093/nar/gkh728 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Tsz-Kwong Man, Joshua SungWoo Yang, and Gary D. Stormo

Quantitative modeling of DNA–protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor
Nucl. Acids Res. 2004 32: 4026-4032; doi:10.1093/nar/gkh729 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Carolina Johansson, Masood Kamali-Moghaddam, and Lars Sundström

Integron integrase binds to bulged hairpin DNA
Nucl. Acids Res. 2004 32: 4033-4043; doi:10.1093/nar/gkh730 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mariusz Popenda, Jan Milecki, and Ryszard W. Adamiak

High salt solution structure of a left-handed RNA double helix
Nucl. Acids Res. 2004 32: 4044-4054; doi:10.1093/nar/gkh736 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Janine B. Mills and Paul J. Hagerman

Origin of the intrinsic rigidity of DNA
Nucl. Acids Res. 2004 32: 4055-4059; doi:10.1093/nar/gkh740 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Angela M. I. Lam, Ryan S. Rypma, and David N. Frick

Enhanced nucleic acid binding to ATP-bound hepatitis C virus NS3 helicase at low pH activates RNA unwinding
Nucl. Acids Res. 2004 32: 4060-4070; doi:10.1093/nar/gkh743 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Thomas M. Hitchcock, Honghai Gao, and Weiguo Cao

Cleavage of deoxyoxanosine-containing oligodeoxyribonucleotides by bacterial endonuclease V
Nucl. Acids Res. 2004 32: 4071-4080; doi:10.1093/nar/gkh747 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Franck Martin, Sharief Barends, and Gilbert Eriani

Single amino acid changes in AspRS reveal alternative routes for expanding its tRNA repertoire in vivo
Nucl. Acids Res. 2004 32: 4081-4089; doi:10.1093/nar/gkh751 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Methods Online:

Pei-Sze Ng and Donald E. Bergstrom

Protein–DNA footprinting by endcapped duplex oligodeoxyribonucleotides
Nucl. Acids Res. 2004 32: e107; doi:10.1093/nar/gnh103 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Jonne Vaarno, Emmi Ylikoski, Niko J. Meltola, Juhani T. Soini, Pekka Hänninen, Riitta Lahesmaa, and Aleksi E. Soini

New separation-free assay technique for SNPs using two-photon excitation fluorometry
Nucl. Acids Res. 2004 32: e108; doi:10.1093/nar/gnh102 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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

Atelocollagen-mediated synthetic small interfering RNA delivery for effective gene silencing in vitro and in vivo
Nucl. Acids Res. 2004 32: e109; doi:10.1093/nar/gnh093 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Changill Ban, Suhman Chung, Deog-Su Park, and Yoon-Bo Shim

Detection of protein–DNA interaction with a DNA probe: distinction between single-strand and double-strand DNA–protein interaction
Nucl. Acids Res. 2004 32: e110; doi:10.1093/nar/gnh109 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Antonio Rodríguez-Campos, Ronald Koop, Susanna Faraudo, and Miguel Beato

Transcriptionally competent chromatin assembled with exogenous histones in a yeast whole cell extract
Nucl. Acids Res. 2004 32: e111; doi:10.1093/nar/gnh107 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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

Detecting single DNA copy number variations in complex genomes using one nanogram of starting DNA and BAC-array CGH
Nucl. Acids Res. 2004 32: e112; doi:10.1093/nar/gnh108 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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