Nucleic Acids Research

Articles:

Peter Sandin, L. Marcus Wilhelmsson, Per Lincoln, Vicki E. C. Powers, Tom Brown, and Bo Albinsson

Fluorescent properties of DNA base analogue tC upon incorporation into DNA — negligible influence of neighbouring bases on fluorescence quantum yield
Nucl. Acids Res. 2005 33: 5019-5025; doi:10.1093/nar/gki790 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Meenakshi Roy, Qiang Xu, and Christopher Lee

Evidence that public database records for many cancer-associated genes reflect a splice form found in tumors and lack normal splice forms
Nucl. Acids Res. 2005 33: 5026-5033; doi:10.1093/nar/gki792 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Stephan Steigele and Kay Nieselt

Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes
Nucl. Acids Res. 2005 33: 5034-5044; doi:10.1093/nar/gki804 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

M. Angeles Freire-Picos, Shankarling Krishnamurthy, Zu-Wen Sun, and Michael Hampsey

Evidence that the Tfg1/Tfg2 dimer interface of TFIIF lies near the active center of the RNA polymerase II initiation complex
Nucl. Acids Res. 2005 33: 5045-5052; doi:10.1093/nar/gki825 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jinhua Wang, Philip J. Smith, Adrian R. Krainer, and Michael Q. Zhang

Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes
Nucl. Acids Res. 2005 33: 5053-5062; doi:10.1093/nar/gki810 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jonatha M. Gott, Neeta Parimi, and Ralf Bundschuh

Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs
Nucl. Acids Res. 2005 33: 5063-5072; doi:10.1093/nar/gki820 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

In-Youb Chang, Soo-Hyun Kim, Hyun-Ju Cho, Do Young Lee, Mi-Hwa Kim, Myung-Hee Chung, and Ho Jin You

Human AP endonuclease suppresses DNA mismatch repair activity leading to microsatellite instability
Nucl. Acids Res. 2005 33: 5073-5081; doi:10.1093/nar/gki829 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Elzbieta Kierzek, Anna Ciesielska, Karol Pasternak, David H. Mathews, Douglas H. Turner, and Ryszard Kierzek

The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes
Nucl. Acids Res. 2005 33: 5082-5093; doi:10.1093/nar/gki789 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Peter Macpherson, Flavia Barone, Giovanni Maga, Filomena Mazzei, Peter Karran, and Margherita Bignami

8-Oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutS
Nucl. Acids Res. 2005 33: 5094-5105; doi:10.1093/nar/gki813 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Paola Favaretto, Arjun Bhutkar, and Temple F. Smith

Constraining ribosomal RNA conformational space
Nucl. Acids Res. 2005 33: 5106-5111; doi:10.1093/nar/gki805 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Marcel Freund, Martin J. Hicks, Carolin Konermann, Marianne Otte, Klemens J. Hertel, and Heiner Schaal

Extended base pair complementarity between U1 snRNA and the 5' splice site does not inhibit splicing in higher eukaryotes, but rather increases 5' splice site recognition
Nucl. Acids Res. 2005 33: 5112-5119; doi:10.1093/nar/gki824 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ela Sharin, Aleks Schein, Hagit Mann, Yitzhak Ben-Asouli, and Nayef Jarrous

RNase P: role of distinct protein cofactors in tRNA substrate recognition and RNA-based catalysis
Nucl. Acids Res. 2005 33: 5120-5132; doi:10.1093/nar/gki828 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sriram Kanvah and Gary B. Schuster

The sacrificial role of easily oxidizable sites in the protection of DNA from damage
Nucl. Acids Res. 2005 33: 5133-5138; doi:10.1093/nar/gki801 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

C. Lux, H. Albiez, R. D. Chapman, M. Heidinger, M. Meininghaus, R. Brack-Werner, A. Lang, M. Ziegler, T. Cremer, and D. Eick

Transition from initiation to promoter proximal pausing requires the CTD of RNA polymerase II
Nucl. Acids Res. 2005 33: 5139-5144; doi:10.1093/nar/gki802 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nina Y. Sidorova, Shakir Muradymov, and Donald C. Rau

Trapping DNA–protein binding reactions with neutral osmolytes for the analysis by gel mobility shift and self-cleavage assays
Nucl. Acids Res. 2005 33: 5145-5155; doi:10.1093/nar/gki808 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zhengchang Su, Victor Olman, Fenglou Mao, and Ying Xu

Comparative genomics analysis of NtcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis
Nucl. Acids Res. 2005 33: 5156-5171; doi:10.1093/nar/gki817 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Scott A. Kinzy, Kelvin Caban, and Paul R. Copeland

Characterization of the SECIS binding protein 2 complex required for the co-translational insertion of selenocysteine in mammals
Nucl. Acids Res. 2005 33: 5172-5180; doi:10.1093/nar/gki826 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

J. Lesley Brown, Daniel J. Grau, Sarah K. DeVido, and Judith A. Kassis

An Sp1/KLF binding site is important for the activity of a Polycomb group response element from the Drosophila engrailed gene
Nucl. Acids Res. 2005 33: 5181-5189; doi:10.1093/nar/gki827 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ko-Fan Chen, Yen-Yu Lai, H. Sunny Sun, and Shaw-Jenq Tsai

Transcriptional repression of human cad gene by hypoxia inducible factor-1
Nucl. Acids Res. 2005 33: 5190-5198; doi:10.1093/nar/gki839 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Raul Alvarez-Venegas and Zoya Avramova

Methylation patterns of histone H3 Lys 4, Lys 9 and Lys 27 in transcriptionally active and inactive Arabidopsis genes and in atx1 mutants
Nucl. Acids Res. 2005 33: 5199-5207; doi:10.1093/nar/gki830 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Amélie E. Coudert, Laurence Pibouin, Brigitte Vi-Fane, Bethan L. Thomas, Mary Macdougall, Anuradha Choudhury, Benoît Robert, Paul T. Sharpe, Ariane Berdal, and Frédéric Lezot

Expression and regulation of the Msx1 natural antisense transcript during development
Nucl. Acids Res. 2005 33: 5208-5218; doi:10.1093/nar/gki831 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Justin K. Ichida, Allen Horhota, Keyong Zou, Larry W. McLaughlin, and Jack W. Szostak

High fidelity TNA synthesis by Therminator polymerase
Nucl. Acids Res. 2005 33: 5219-5225; doi:10.1093/nar/gki840 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nina J. Oparina, Olga V. Kalinina, Mikhail S. Gelfand, and Lev L. Kisselev

Common and specific amino acid residues in the prokaryotic polypeptide release factors RF1 and RF2: possible functional implications
Nucl. Acids Res. 2005 33: 5226-5234; doi:10.1093/nar/gki841 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

D. H. Crouch, F. Fisher, S. A. La Rocca, C. R. Goding, and D. A. F. Gillespie

Viral mutations enhance the Max binding properties of the vMyc b-HLH-LZ domain
Nucl. Acids Res. 2005 33: 5235-5242; doi:10.1093/nar/gki832 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Dilip K. Nag, Michael Fasullo, Zheng Dong, and Ashlie Tronnes

Inverted repeat-stimulated sister-chromatid exchange events are RAD1-independent but reduced in a msh2 mutant
Nucl. Acids Res. 2005 33: 5243-5249; doi:10.1093/nar/gki835 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nerea Beguiristain, Hugh D. Robertson, and Jordi Gómez

RNase III cleavage demonstrates a long range RNA: RNA duplex element flanking the hepatitis C virus internal ribosome entry site
Nucl. Acids Res. 2005 33: 5250-5261; doi:10.1093/nar/gki822 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Lori H. Conlan, Matthew J. Stanger, Kenji Ichiyanagi, and Marlene Belfort

Localization, mobility and fidelity of retrotransposed Group II introns in rRNA genes
Nucl. Acids Res. 2005 33: 5262-5270; doi:10.1093/nar/gki819 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Céline René, Magali Taulan, Florence Iral, Julien Doudement, Aurore L'Honoré, Catherine Gerbon, Jacques Demaille, Mireille Claustres, and Marie-Catherine Romey

Binding of serum response factor to cystic fibrosis transmembrane conductance regulator CArG-like elements, as a new potential CFTR transcriptional regulation pathway
Nucl. Acids Res. 2005 33: 5271-5290; doi:10.1093/nar/gki837 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

George Dinos, Dimitrios L. Kalpaxis, Daniel N. Wilson, and Knud H. Nierhaus

Deacylated tRNA is released from the E site upon A site occupation but before GTP is hydrolyzed by EF-Tu
Nucl. Acids Res. 2005 33: 5291-5296; doi:10.1093/nar/gki833 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Benjamin Diop-Frimpong, Thazha P. Prakash, Kallanthottathil G. Rajeev, Muthiah Manoharan, and Martin Egli

Stabilizing contributions of sulfur-modified nucleotides: crystal structure of a DNA duplex with 2'-O-[2-(methoxy)ethyl]-2-thiothymidines
Nucl. Acids Res. 2005 33: 5297-5307; doi:10.1093/nar/gki823 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sybille Kempe, Hans Kestler, Andrea Lasar, and Thomas Wirth

NF-B controls the global pro-inflammatory response in endothelial cells: evidence for the regulation of a pro-atherogenic program
Nucl. Acids Res. 2005 33: 5308-5319; doi:10.1093/nar/gki836 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Mariana Yaneva, Han Li, Teresa Marple, and Paul Hasty

Non-homologous end joining, but not homologous recombination, enables survival for cells exposed to a histone deacetylase inhibitor
Nucl. Acids Res. 2005 33: 5320-5330; doi:10.1093/nar/gki821 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Duen-Yi Huang, Yuan-Yeh Kuo, and Zee-Fen Chang

GATA-1 mediates auto-regulation of Gfi-1B transcription in K562 cells
Nucl. Acids Res. 2005 33: 5331-5342; doi:10.1093/nar/gki838 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Erik Kruus, Peter Thumfort, Chao Tang, and Ned S. Wingreen

Gibbs sampling and helix-cap motifs
Nucl. Acids Res. 2005 33: 5343-5353; doi:10.1093/nar/gki842 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Isabelle Frouin, Magali Toueille, Elena Ferrari, Igor Shevelev, and Ulrich Hübscher

Phosphorylation of human DNA polymerase by the cyclin-dependent kinase Cdk2/cyclin A complex is modulated by its association with proliferating cell nuclear antigen
Nucl. Acids Res. 2005 33: 5354-5361; doi:10.1093/nar/gki845 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Michael Koeris, Lars Funke, Jay Shrestha, Alexander Rich, and Stefan Maas

Modulation of ADAR1 editing activity by Z-RNA in vitro
Nucl. Acids Res. 2005 33: 5362-5370; doi:10.1093/nar/gki849 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Brian C. Bales, Tetsuya Kodama, Yvonne N. Weledji, Marguerite Pitié, Bernard Meunier, and Marc M. Greenberg

Mechanistic studies on DNA damage by minor groove binding copper–phenanthroline conjugates
Nucl. Acids Res. 2005 33: 5371-5379; doi:10.1093/nar/gki856 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

L. Li, D. Techel, N. Gretz, and A. Hildebrandt

A novel transcriptome subtraction method for the detection of differentially expressed genes in highly complex eukaryotes
Nucl. Acids Res. 2005 33: e136; doi:10.1093/nar/gni136 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Georg W. Bornkamm, Christian Berens, Conny Kuklik-Roos, Jean-Marie Bechet, Gerhard Laux, Jürgen Bachl, Martin Korndoerfer, Martin Schlee, Michael Hölzel, Anastassia Malamoussi, Rob D. Chapman, Falk Nimmerjahn, Josef Mautner, Wolfgang Hillen, Hermann Bujard, and Jean Feuillard

Stringent doxycycline-dependent control of gene activities using an episomal one-vector system
Nucl. Acids Res. 2005 33: e137; doi:10.1093/nar/gni137 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jean-Louis Mergny, Jing Li, Laurent Lacroix, Samir Amrane, and Jonathan B. Chaires

Thermal difference spectra: a specific signature for nucleic acid structures
Nucl. Acids Res. 2005 33: e138; doi:10.1093/nar/gni134 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Young Geol Yoon and Michael D. Koob

Transformation of isolated mammalian mitochondria by bacterial conjugation
Nucl. Acids Res. 2005 33: e139; doi:10.1093/nar/gni140 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Brian D. Peyser, Rafael A. Irizarry, Carol W. Tiffany, Ou Chen, Daniel S. Yuan, Jef D. Boeke, and Forrest A. Spencer

Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools
Nucl. Acids Res. 2005 33: e140; doi:10.1093/nar/gni138 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

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