Nucleic Acids Research

Survey and Summary:

Louis Levinger, Mario Mörl, and Catherine Florentz

Mitochondrial tRNA 3' end metabolism and human disease
Nucl. Acids Res. 2004 32: 5430-5441; doi:10.1093/nar/gkh884 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Michael Y. Galperin and Eugene V. Koonin

‘Conserved hypothetical’ proteins: prioritization of targets for experimental study
Nucl. Acids Res. 2004 32: 5452-5463; doi:10.1093/nar/gkh885 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Articles:

Aaron R. Ellison, Joan Lofing, and Grant A. Bitter

Human MutL homolog (MLH1) function in DNA mismatch repair: a prospective screen for missense mutations in the ATPase domain
Nucl. Acids Res. 2004 32: 5321-5338; doi:10.1093/nar/gkh855 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Tatsuo Nunoshiba, Rikiya Ishida, Michi Sasaki, Shigenori Iwai, Yusaku Nakabeppu, and Kazuo Yamamoto

A novel Nudix hydrolase for oxidized purine nucleoside triphosphates encoded by ORFYLR151c (PCD1 gene) in Saccharomyces cerevisiae
Nucl. Acids Res. 2004 32: 5339-5348; doi:10.1093/nar/gkh868 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nolwenn Le Meur, Guillaume Lamirault, Audrey Bihouée, Marja Steenman, Hélène Bédrine-Ferran, Raluca Teusan, Gérard Ramstein, and Jean J. Léger

A dynamic, web-accessible resource to process raw microarray scan data into consolidated gene expression values: importance of replication
Nucl. Acids Res. 2004 32: 5349-5358; doi:10.1093/nar/gkh870 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Yujian He, Ronald D. Neumann, and Igor G. Panyutin

Intramolecular quadruplex conformation of human telomeric DNA assessed with ¹²⁵I-radioprobing
Nucl. Acids Res. 2004 32: 5359-5367; doi:10.1093/nar/gkh875 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Dragan Marinkovic, Tatjana Marinkovic, Eniko Kokai, Thomas Barth, Peter Möller, and Thomas Wirth

Identification of novel Myc target genes with a potential role in lymphomagenesis
Nucl. Acids Res. 2004 32: 5368-5378; doi:10.1093/nar/gkh877 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Benjamin Guglielmi, Nynke L. van Berkum, Benjamin Klapholz, Theo Bijma, Muriel Boube, Claire Boschiero, Henri-Marc Bourbon, Frank C. P. Holstege, and Michel Werner

A high resolution protein interaction map of the yeast Mediator complex
Nucl. Acids Res. 2004 32: 5379-5391; doi:10.1093/nar/gkh878 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Sarath Chandra Janga and Gabriel Moreno-Hagelsieb

Conservation of adjacency as evidence of paralogous operons
Nucl. Acids Res. 2004 32: 5392-5397; doi:10.1093/nar/gkh882 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Panagiotis Panopoulos, John Dresios, and Dennis Synetos

Biochemical evidence of translational infidelity and decreased peptidyltransferase activity by a sarcin/ricin domain mutation of yeast 25S rRNA
Nucl. Acids Res. 2004 32: 5398-5408; doi:10.1093/nar/gkh860 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Xiaochuan Zhou, Shiying Cai, Ailing Hong, Qimin You, Peilin Yu, Nijing Sheng, Onnop Srivannavit, Seema Muranjan, Jean Marie Rouillard, Yongmei Xia, Xiaolin Zhang, Qin Xiang, Renuka Ganesh, Qi Zhu, Anna Matejko, Erdogan Gulari, and Xiaolian Gao

Microfluidic PicoArray synthesis of oligodeoxynucleotides and simultaneous assembling of multiple DNA sequences
Nucl. Acids Res. 2004 32: 5409-5417; doi:10.1093/nar/gkh879 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Mathias Brännvall, Ema Kikovska, and Leif A. Kirsebom

Cross talk between the +73/294 interaction and the cleavage site in RNase P RNA mediated cleavage
Nucl. Acids Res. 2004 32: 5418-5429; doi:10.1093/nar/gkh883 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Claire L. Middleton, Joanne L. Parker, Derek J. Richard, Malcolm F. White, and Charles S. Bond

Substrate recognition and catalysis by the Holliday junction resolving enzyme Hje
Nucl. Acids Res. 2004 32: 5442-5451; doi:10.1093/nar/gkh869 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Angela C. Spencer and Linda L. Spremulli

Interaction of mitochondrial initiation factor 2 with mitochondrial fMet-tRNA
Nucl. Acids Res. 2004 32: 5464-5470; doi:10.1093/nar/gkh886 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Li-Xuan Qin, and Kathleen F. Kerr Contributing Members of the Toxicogenomics Research Consortium

Empirical evaluation of data transformations and ranking statistics for microarray analysis
Nucl. Acids Res. 2004 32: 5471-5479; doi:10.1093/nar/gkh866 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Kelly M. Kroeger, Myron F. Goodman, and Marc M. Greenberg

A comprehensive comparison of DNA replication past 2-deoxyribose and its tetrahydrofuran analog in Escherichia coli
Nucl. Acids Res. 2004 32: 5480-5485; doi:10.1093/nar/gkh873 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Mansour Akbari, Marit Otterlei, Javier Peña-Diaz, Per Arne Aas, Bodil Kavli, Nina B. Liabakk, Lars Hagen, Kohsuke Imai, Anne Durandy, Geir Slupphaug, and Hans E. Krokan

Repair of U/G and U/A in DNA by UNG2-associated repair complexes takes place predominantly by short-patch repair both in proliferating and growth-arrested cells
Nucl. Acids Res. 2004 32: 5486-5498; doi:10.1093/nar/gkh872 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kyoung-Hwa Lee, Jong-Wan Park, and Yang-Sook Chun

Non-hypoxic transcriptional activation of the aryl hydrocarbon receptor nuclear translocator in concert with a novel hypoxia-inducible factor-1alpha isoform
Nucl. Acids Res. 2004 32: 5499-5511; doi:10.1093/nar/gkh880 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mark A. Bayfield, Jill Thompson, and Albert E. Dahlberg

The A2453-C2499 wobble base pair in Escherichia coli 23S ribosomal RNA is responsible for pH sensitivity of the peptidyltransferase active site conformation
Nucl. Acids Res. 2004 32: 5512-5518; doi:10.1093/nar/gkh888 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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

Electrostatic analysis of the hepatitis C virus NS3 helicase reveals both active and allosteric site locations
Nucl. Acids Res. 2004 32: 5519-5528; doi:10.1093/nar/gkh891 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Tobias May, Hansjörg Hauser, and Dagmar Wirth

Transcriptional control of SV40 T-antigen expression allows a complete reversion of immortalization
Nucl. Acids Res. 2004 32: 5529-5538; doi:10.1093/nar/gkh887 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Andreas Ruepp, Alfred Zollner, Dieter Maier, Kaj Albermann, Jean Hani, Martin Mokrejs, Igor Tetko, Ulrich Güldener, Gertrud Mannhaupt, Martin Münsterkötter, and H. Werner Mewes

The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes
Nucl. Acids Res. 2004 32: 5539-5545; doi:10.1093/nar/gkh894 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Jana Kasparkova, Miroslav Fojta, Nicholas Farrell, and Viktor Brabec

Differential recognition by the tumor suppressor protein p53 of DNA modified by the novel antitumor trinuclear platinum drug BBR3464 and cisplatin
Nucl. Acids Res. 2004 32: 5546-5552; doi:10.1093/nar/gkh896 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Poonam Malik and J. Barklie Clements

Protein kinase CK2 phosphorylation regulates the interaction of Kaposi's sarcoma-associated herpesvirus regulatory protein ORF57 with its multifunctional partner hnRNP K
Nucl. Acids Res. 2004 32: 5553-5569; doi:10.1093/nar/gkh876 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Claudette L. Doe, Fekret Osman, Julie Dixon, and Matthew C. Whitby

DNA repair by a Rad22–Mus81-dependent pathway that is independent of Rhp51
Nucl. Acids Res. 2004 32: 5570-5581; doi:10.1093/nar/gkh853 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Lina Piesiniene, Lidija Truncaite, Aurelija Zajanckauskaite, and Rimas Nivinskas

The sequences and activities of RegB endoribonucleases of T4-related bacteriophages
Nucl. Acids Res. 2004 32: 5582-5595; doi:10.1093/nar/gkh892 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

K. Hashiguchi, J. A. Stuart, N. C. de Souza-Pinto, and V. A. Bohr

The C-terminal O helix of human Ogg1 is essential for 8-oxoguanine DNA glycosylase activity: the mitochondrial ß-Ogg1 lacks this domain and does not have glycosylase activity
Nucl. Acids Res. 2004 32: 5596-5608; doi:10.1093/nar/gkh863 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Alexandros G. Georgakilas, Paula V. Bennett, David M. Wilson, III, and Betsy M. Sutherland

Processing of bistranded abasic DNA clusters in -irradiated human hematopoietic cells
Nucl. Acids Res. 2004 32: 5609-5620; doi:10.1093/nar/gkh871 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Maxim A. Skabkin, Olga I. Kiselyova, Konstantin G. Chernov, Alexey V. Sorokin, Evgeniy V. Dubrovin, Igor V. Yaminsky, Victor D. Vasiliev, and Lev P. Ovchinnikov

Structural organization of mRNA complexes with major core mRNP protein YB-1
Nucl. Acids Res. 2004 32: 5621-5635; doi:10.1093/nar/gkh889 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kyoko Otsuki, Yuko Hayashi, Masaki Kato, Hideki Yoshida, and Masamitsu Yamaguchi

Characterization of dRFX2, a novel RFX family protein in Drosophila
Nucl. Acids Res. 2004 32: 5636-5648; doi:10.1093/nar/gkh895 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Jacqueline J. Vermeersch, Serge Christmann-Franck, Leon V. Karabashyan, Serge Fermandjian, Gilles Mirambeau, and P. Arsène Der Garabedian

Pyridoxal 5'-phosphate inactivates DNA topoisomerase IB by modifying the lysine general acid
Nucl. Acids Res. 2004 32: 5649-5657; doi:10.1093/nar/gkh897 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sara N. Richter, Ileana Menegazzo, Daniele Fabris, and Manlio Palumbo

Concerted bis-alkylating reactivity of clerocidin towards unpaired cytosine residues in DNA
Nucl. Acids Res. 2004 32: 5658-5667; doi:10.1093/nar/gkh898 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Pradeep K. Chatterjee, Leighcraft A. Shakes, Deepak K. Srivastava, Douglas M. Garland, Ken R. Harewood, Kyle J. Moore, and Jonathon S. Coren

Mutually exclusive recombination of wild-type and mutant loxP sites in vivo facilitates transposon-mediated deletions from both ends of genomic DNA in PACs
Nucl. Acids Res. 2004 32: 5668-5676; doi:10.1093/nar/gkh900 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Dilip K. Nag, Manisha Suri, and Erin K. Stenson

Both CAG repeats and inverted DNA repeats stimulate spontaneous unequal sister-chromatid exchange in Saccharomyces cerevisiae
Nucl. Acids Res. 2004 32: 5677-5684; doi:10.1093/nar/gkh901 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Smitha Antony, Jacob A. Theruvathu, P. J. Brooks, Diem-Thu Lesher, Matt Redinbo, and Yves Pommier

Enhancement of camptothecin-induced topoisomerase I cleavage complexes by the acetaldehyde adduct N²-ethyl-2'-deoxyguanosine
Nucl. Acids Res. 2004 32: 5685-5692; doi:10.1093/nar/gkh902 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Peter C. Hollenhorst, David A. Jones, and Barbara J. Graves

Expression profiles frame the promoter specificity dilemma of the ETS family of transcription factors
Nucl. Acids Res. 2004 32: 5693-5702; doi:10.1093/nar/gkh906 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Methods Online:

Martin Huber, Tai-Fen Wei, Uwe R. Müller, Phil A. Lefebvre, Sudhakar S. Marla, and Y. Paul Bao

Gold nanoparticle probe-based gene expression analysis with unamplified total human RNA
Nucl. Acids Res. 2004 32: e137; doi:10.1093/nar/gnh133 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

V. Chin, V. Valinluck, S. Magaki, and J. Ryu

KpnBI is the prototype of a new family (IE) of bacterial type I restriction-modification system
Nucl. Acids Res. 2004 32: e138; doi:10.1093/nar/gnh134 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

C. Dehainault, A. Laugé, V. Caux-Moncoutier, S. Pagès-Berhouet, F. Doz, L. Desjardins, J. Couturier, M. Gauthier-Villars, D. Stoppa-Lyonnet, and C. Houdayer

Multiplex PCR/liquid chromatography assay for detection of gene rearrangements: application to RB1 gene
Nucl. Acids Res. 2004 32: e139; doi:10.1093/nar/gnh137 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

N. H. Dekker, J. A. Abels, P. T. M. Veenhuizen, M. M. Bruinink, and C. Dekker

Joining of long double-stranded RNA molecules through controlled overhangs
Nucl. Acids Res. 2004 32: e140; doi:10.1093/nar/gnh138 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Junko Wakai, Atsuko Takagi, Masato Nakayama, Takahito Miya, Takatoshi Miyahara, Tsuyoshi Iwanaga, Shigeori Takenaka, Yasuyuki Ikeda, and Masahiko Amano

A novel method of identifying genetic mutations using an electrochemical DNA array
Nucl. Acids Res. 2004 32: e141; doi:10.1093/nar/gnh141 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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