Nucleic Acids Research

Articles:

Sally Richards, Su-Ting Liu, Alokes Majumdar, Ji-Lan Liu, Rodney S. Nairn, Michel Bernier, Veronica Maher, and Michael M. Seidman

Triplex targeted genomic crosslinks enter separable deletion and base substitution pathways
Nucl. Acids Res. 2005 33: 5382-5393; doi:10.1093/nar/gki851 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jinmai Jiang, Eun Joo Lee, Yuriy Gusev, and Thomas D. Schmittgen

Real-time expression profiling of microRNA precursors in human cancer cell lines
Nucl. Acids Res. 2005 33: 5394-5403; doi:10.1093/nar/gki863 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Sara Diaz-Trivino, María del Mar Castellano, María de la Paz Sanchez, Elena Ramirez-Parra, Bénédicte Desvoyes, and Crisanto Gutierrez

The genes encoding Arabidopsis ORC subunits are E2F targets and the two ORC1 genes are differently expressed in proliferating and endoreplicating cells
Nucl. Acids Res. 2005 33: 5404-5414; doi:10.1093/nar/gki854 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zhiyu Li, Hiroshi Hiasa, and Russell DiGate

Bacillus cereus DNA topoisomerase I and III: purification, characterization and complementation of Escherichia coli TopoIII activity
Nucl. Acids Res. 2005 33: 5415-5425; doi:10.1093/nar/gki846 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Marcin P. Klejman, Xuemei Zhao, Frederik M. A. van Schaik, Winship Herr, and H. Th. Marc Timmers

Mutational analysis of BTAF1–TBP interaction: BTAF1 can rescue DNA-binding defective TBP mutants
Nucl. Acids Res. 2005 33: 5426-5436; doi:10.1093/nar/gki850 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jordan T. Shin, James R. Priest, Ivan Ovcharenko, Amy Ronco, Rachel K. Moore, C. Geoffrey Burns, and Calum A. MacRae

Human-zebrafish non-coding conserved elements act in vivo to regulate transcription
Nucl. Acids Res. 2005 33: 5437-5445; doi:10.1093/nar/gki853 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Delphine T. Marie-Egyptienne, Maria Antonietta Cerone, J. Arturo Londoño-Vallejo, and Chantal Autexier

A human-Tetrahymena pseudoknot chimeric telomerase RNA reconstitutes a nonprocessive enzyme in vitro that is defective in telomere elongation
Nucl. Acids Res. 2005 33: 5446-5457; doi:10.1093/nar/gki848 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jesper Christensen, Paul Cloos, Ulla Toftegaard, David Klinkenberg, Adrian P. Bracken, Emmanuelle Trinh, Mel Heeran, Luisa Di Stefano, and Kristian Helin

Characterization of E2F8, a novel E2F-like cell-cycle regulated repressor of E2F-activated transcription
Nucl. Acids Res. 2005 33: 5458-5470; doi:10.1093/nar/gki855 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Muriel Canalia and Jean Louis Leroy

Structure, internal motions and association–dissociation kinetics of the i-motif dimer of d(5mCCTCACTCC)
Nucl. Acids Res. 2005 33: 5471-5481; doi:10.1093/nar/gki843 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Irene Majerfeld and Michael Yarus

A diminutive and specific RNA binding site for L-tryptophan
Nucl. Acids Res. 2005 33: 5482-5493; doi:10.1093/nar/gki861 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Thirumananseri Kumarevel, Hiroshi Mizuno, and Penmetcha K. R. Kumar

Characterization of the metal ion binding site in the anti-terminator protein, HutP, of Bacillus subtilis
Nucl. Acids Res. 2005 33: 5494-5502; doi:10.1093/nar/gki868 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Richard Bishop, Trushar Shah, Roger Pelle, David Hoyle, Terry Pearson, Lee Haines, Andrew Brass, Helen Hulme, Simon P. Graham, Evans L. N. Taracha, Simon Kanga, Charles Lu, Brian Hass, Jennifer Wortman, Owen White, Malcolm J. Gardner, Vishvanath Nene, and Etienne P. de Villiers

Analysis of the transcriptome of the protozoan Theileria parva using MPSS reveals that the majority of genes are transcriptionally active in the schizont stage
Nucl. Acids Res. 2005 33: 5503-5511; doi:10.1093/nar/gki818 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Alexander Churbanov, Igor B. Rogozin, Vladimir N. Babenko, Hesham Ali, and Eugene V. Koonin

Evolutionary conservation suggests a regulatory function of AUG triplets in 5'-UTRs of eukaryotic genes
Nucl. Acids Res. 2005 33: 5512-5520; doi:10.1093/nar/gki847 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Merja Matilainen, Marjo Malinen, Katri Saavalainen, and Carsten Carlberg

Regulation of multiple insulin-like growth factor binding protein genes by 1,25-dihydroxyvitamin D₃
Nucl. Acids Res. 2005 33: 5521-5532; doi:10.1093/nar/gki872 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Miao Sun, Laurence D. Hurst, Gordon G. Carmichael, and Jianjun Chen

Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts
Nucl. Acids Res. 2005 33: 5533-5543; doi:10.1093/nar/gki852 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material][Supplementary Material] [Request Permissions]  

Krisana Asano, Daisuke Kurita, Kazuma Takada, Takayuki Konno, Akira Muto, and Hyouta Himeno

Competition between trans-translation and termination or elongation of translation
Nucl. Acids Res. 2005 33: 5544-5552; doi:10.1093/nar/gki871 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Amitava Adhikary, Aramice Y. S. Malkhasian, Sean Collins, Jessica Koppen, David Becker, and Michael D. Sevilla

UVA-visible photo-excitation of guanine radical cations produces sugar radicals in DNA and model structures
Nucl. Acids Res. 2005 33: 5553-5564; doi:10.1093/nar/gki857 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Chao Cheng and Lei M. Li

Sub-array normalization subject to differentiation
Nucl. Acids Res. 2005 33: 5565-5573; doi:10.1093/nar/gki844 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alon Magen and Gil Ast

The importance of being divisible by three in alternative splicing
Nucl. Acids Res. 2005 33: 5574-5582; doi:10.1093/nar/gki858 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sangita Phadtare and Konstantin Severinov

Nucleic acid melting by Escherichia coli CspE
Nucl. Acids Res. 2005 33: 5583-5590; doi:10.1093/nar/gki859 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

N. S. Singh, G. Das, A. Seshadri, R. Sangeetha, and U. Varshney

Evidence for a role of initiation factor 3 in recycling of ribosomal complexes stalled on mRNAs in Escherichia coli
Nucl. Acids Res. 2005 33: 5591-5601; doi:10.1093/nar/gki864 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kelly A. Plummer, James M. Carothers, Masahiro Yoshimura, Jack W. Szostak, and Gregory L. Verdine

In vitro selection of RNA aptamers against a composite small molecule-protein surface
Nucl. Acids Res. 2005 33: 5602-5610; doi:10.1093/nar/gki867 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Michael Hiller, Klaus Huse, Matthias Platzer, and Rolf Backofen

Non-EST based prediction of exon skipping and intron retention events using Pfam information
Nucl. Acids Res. 2005 33: 5611-5621; doi:10.1093/nar/gki870 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jayati Roy Choudhury and Ulrich Bierbach

Characterization of the bisintercalative DNA binding mode of a bifunctional platinum–acridine agent
Nucl. Acids Res. 2005 33: 5622-5632; doi:10.1093/nar/gki869 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Kimberley Bruce, Fiona A. Myers, Evangelia Mantouvalou, Pascal Lefevre, Ian Greaves, Constanze Bonifer, David J. Tremethick, Alan W. Thorne, and Colyn Crane-Robinson

The replacement histone H2A.Z in a hyperacetylated form is a feature of active genes in the chicken
Nucl. Acids Res. 2005 33: 5633-5639; doi:10.1093/nar/gki874 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

A. Michael Sismour and Steven A. Benner

The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system
Nucl. Acids Res. 2005 33: 5640-5646; doi:10.1093/nar/gki873 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Myriam Möllers, Katharina Maniura-Weber, Emina Kiseljakovic, Maria Bust, Armine Hayrapetyan, Michaela Jaksch, Mark Helm, Rudolf J. Wiesner, and Jürgen-Christoph von Kleist-Retzow

A new mechanism for mtDNA pathogenesis: impairment of post-transcriptional maturation leads to severe depletion of mitochondrial tRNA^Ser(UCN) caused by T7512C and G7497A point mutations
Nucl. Acids Res. 2005 33: 5647-5658; doi:10.1093/nar/gki876 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Zhengyan Kan, Philip W. Garrett-Engele, Jason M. Johnson, and John C. Castle

Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles
Nucl. Acids Res. 2005 33: 5659-5666; doi:10.1093/nar/gki834 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Richard Pelletier, Brian T. Farrell, Juan José Miret, and Robert S. Lahue

Mechanistic features of CAG•CTG repeat contractions in cultured cells revealed by a novel genetic assay
Nucl. Acids Res. 2005 33: 5667-5676; doi:10.1093/nar/gki880 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Boris François, Rupert J. M. Russell, James B. Murray, Fareed Aboul-ela, Benoît Masquida, Quentin Vicens, and Eric Westhof

Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding
Nucl. Acids Res. 2005 33: 5677-5690; doi:10.1093/nar/gki862 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ross Overbeek, Tadhg Begley, Ralph M. Butler, Jomuna V. Choudhuri, Han-Yu Chuang, Matthew Cohoon, Valérie de Crécy-Lagard, Naryttza Diaz, Terry Disz, Robert Edwards, Michael Fonstein, Ed D. Frank, Svetlana Gerdes, Elizabeth M. Glass, Alexander Goesmann, Andrew Hanson, Dirk Iwata-Reuyl, Roy Jensen, Neema Jamshidi, Lutz Krause, Michael Kubal, Niels Larsen, Burkhard Linke, Alice C. McHardy, Folker Meyer, Heiko Neuweger, Gary Olsen, Robert Olson, Andrei Osterman, Vasiliy Portnoy, Gordon D. Pusch, Dmitry A. Rodionov, Christian Rückert, Jason Steiner, Rick Stevens, Ines Thiele, Olga Vassieva, Yuzhen Ye, Olga Zagnitko, and Veronika Vonstein

The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
Nucl. Acids Res. 2005 33: 5691-5702; doi:10.1093/nar/gki866 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Masumi Hidaka, Yasumitsu Takagi, Tomoko Y. Takano, and Mutsuo Sekiguchi

PCNA–MutS-mediated binding of MutL to replicative DNA with mismatched bases to induce apoptosis in human cells
Nucl. Acids Res. 2005 33: 5703-5712; doi:10.1093/nar/gki878 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Corrigendum:

Alexander V. Sverdlov, Igor B. Rogozin, Vladimir N. Babenko, and Eugene V. Koonin

Conservation versus parallel gains in intron evolution
Nucl. Acids Res. 2005 33: 5713; doi:10.1093/nar/gki860 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Jiajian Liu and Gary D. Stormo

Combining SELEX with quantitative assays to rapidly obtain accurate models of protein–DNA interactions
Nucl. Acids Res. 2005 33: e141; doi:10.1093/nar/gni139 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jesper Brohede, Rob Dunne, James D. McKay, and Garry N. Hannan

PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays
Nucl. Acids Res. 2005 33: e142; doi:10.1093/nar/gni142 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Arnoldo Frigessi, Mark A. van de Wiel, Marit Holden, Debbie H. Svendsrud, Ingrid K. Glad, and Heidi Lyng

Genome-wide estimation of transcript concentrations from spotted cDNA microarray data
Nucl. Acids Res. 2005 33: e143; doi:10.1093/nar/gni141 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Kang Ning, Kwok Pui Choi, Hon Wai Leong, and Louxin Zhang

A post-processing method for optimizing synthesis strategy for oligonucleotide microarrays
Nucl. Acids Res. 2005 33: e144; doi:10.1093/nar/gni147 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Timur R. Samatov, Helena V. Chetverina, and Alexander B. Chetverin

Expressible molecular colonies
Nucl. Acids Res. 2005 33: e145; doi:10.1093/nar/gni153 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Irina V. Smolina, Vadim V. Demidov, Viatcheslav A. Soldatenkov, Sergey G. Chasovskikh, and Maxim D. Frank-Kamenetskii

End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes
Nucl. Acids Res. 2005 33: e146; doi:10.1093/nar/gni151 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ee Tsin Wong, John L Kolman, Yao-Cheng Li, Larry D Mesner, Wolfgang Hillen, Christian Berens, and Geoffrey M Wahl

Reproducible doxycycline-inducible transgene expression at specific loci generated by Cre-recombinase mediated cassette exchange
Nucl. Acids Res. 2005 33: e147; doi:10.1093/nar/gni145 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Zhiyong Yang, Howard J. Edenberg, and Ronald L. Davis

Isolation of mRNA from specific tissues of Drosophila by mRNA tagging
Nucl. Acids Res. 2005 33: e148; doi:10.1093/nar/gni149 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Nader Ghebranious, Lynn Ivacic, Jamie Mallum, and Charles Dokken

Detection of ApoE E2, E3 and E4 alleles using MALDI-TOF mass spectrometry and the homogeneous mass-extend technology
Nucl. Acids Res. 2005 33: e149; doi:10.1093/nar/gni155 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Takaaki Kojima, Yoshiaki Takei, Miharu Ohtsuka, Yasuaki Kawarasaki, Tsuneo Yamane, and Hideo Nakano

PCR amplification from single DNA molecules on magnetic beads in emulsion: application for high-throughput screening of transcription factor targets
Nucl. Acids Res. 2005 33: e150; doi:10.1093/nar/gni143 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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