Nucleic Acids Research

Survey and Summary:

David Loakes

SURVEY AND SUMMARY: The applications of universal DNA base analogues
Nucl. Acids Res. 2001 29: 2437-2447; doi:10.1093/nar/29.12.2437 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Articles:

Marie-Claire Daugeron, Fabienne Mauxion, and Bertrand Séraphin

The yeast POP2 gene encodes a nuclease involved in mRNA deadenylation
Nucl. Acids Res. 2001 29: 2448-2455; doi:10.1093/nar/29.12.2448 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Naoko Karino, Yoshihito Ueno, and Akira Matsuda

Synthesis and properties of oligonucleotides containing 5-formyl-2'-deoxycytidine: in vitro DNA polymerase reactions on DNA templates containing 5-formyl-2'-deoxycytidine
Nucl. Acids Res. 2001 29: 2456-2463; doi:10.1093/nar/29.12.2456 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Alexander Bucka and Andrzej Stasiak

RecA-mediated strand exchange traverses substitutional heterologies more easily than deletions or insertions
Nucl. Acids Res. 2001 29: 2464-2470; doi:10.1093/nar/29.12.2464 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Tsz-Kwong Man and Gary D. Stormo

Non-independence of Mnt repressor–operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay
Nucl. Acids Res. 2001 29: 2471-2478; doi:10.1093/nar/29.12.2471 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Julian P. Venables, Matteo Ruggiu, and Howard J. Cooke

The RNA-binding specificity of the mouse Dazl protein
Nucl. Acids Res. 2001 29: 2479-2483; doi:10.1093/nar/29.12.2479 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Jean-Claude Farré and Alejandro Araya

Gene expression in isolated plant mitochondria: high fidelity of transcription, splicing and editing of a transgene product in electroporated organelles
Nucl. Acids Res. 2001 29: 2484-2491; doi:10.1093/nar/29.12.2484 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Lauren S. Higgins, Caroline Besnier, and Huimin Kong

The nicking endonuclease N.BstNBI is closely related to Type IIs restriction endonucleases MlyI and PleI
Nucl. Acids Res. 2001 29: 2492-2501; doi:10.1093/nar/29.12.2492 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Evelyne Myslinski, Jean-Christophe Amé, Alain Krol, and Philippe Carbon

An unusually compact external promoter for RNA polymerase III transcription of the human H1RNA gene
Nucl. Acids Res. 2001 29: 2502-2509; doi:10.1093/nar/29.12.2502 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Elong Lin, Sue-Wen Lin, and Alan Lin

The participation of 5S rRNA in the co-translational formation of a eukaryotic 5S ribonucleoprotein complex
Nucl. Acids Res. 2001 29: 2510-2516; doi:10.1093/nar/29.12.2510 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Heng-Bin Wang and Yi Zhang

Mi2, an auto-antigen for dermatomyositis, is an ATP-dependent nucleosome remodeling factor
Nucl. Acids Res. 2001 29: 2517-2521; doi:10.1093/nar/29.12.2517 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Elena Cubero, Ramon Güimil-García, F. Javier Luque, Ramon Eritja, and Modesto Orozco

The effect of amino groups on the stability of DNA duplexes and triplexes based on purines derived from inosine
Nucl. Acids Res. 2001 29: 2522-2534; doi:10.1093/nar/29.12.2522 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Alita J. Lyons, J. Robin Lytle, Jordi Gomez, and Hugh D. Robertson

Hepatitis C virus internal ribosome entry site RNA contains a tertiary structural element in a functional domain of stem–loop II
Nucl. Acids Res. 2001 29: 2535-2541; doi:10.1093/nar/29.12.2535 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sarit Cohen and Marcel Mechali

A novel cell-free system reveals a mechanism of circular DNA formation from tandem repeats
Nucl. Acids Res. 2001 29: 2542-2548; doi:10.1093/nar/29.12.2542 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

George C. Tseng, Min-Kyu Oh, Lars Rohlin, James C. Liao, and Wing Hung Wong

Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects
Nucl. Acids Res. 2001 29: 2549-2557; doi:10.1093/nar/29.12.2549 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Emiko L. Kreklau, Melissa Limp-Foster, Naili Liu, Yi Xu, Mark R. Kelley, and Leonard C. Erickson

A novel fluorometric oligonucleotide assay to measure O ⁶-methylguanine DNA methyltransferase, methylpurine DNA glycosylase, 8-oxoguanine DNA glycosylase and abasic endonuclease activities: DNA repair status in human breast carcinoma cells overexpressing methylpurine DNA glycosylase
Nucl. Acids Res. 2001 29: 2558-2566; doi:10.1093/nar/29.12.2558 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Brian D. Lang, Ai-min Li, Heather D. Black-Brewster, and Judith L. Fridovich-Keil

The brefeldin A resistance protein Bfr1p is a component of polyribosome-associated mRNP complexes in yeast
Nucl. Acids Res. 2001 29: 2567-2574; doi:10.1093/nar/29.12.2567 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Aaron L. Kabb, Lisa M. Oppegard, Bruce A. McKenzie, and Gregory J. Connell

A mRNA determinant of gRNA-directed kinetoplastid editing
Nucl. Acids Res. 2001 29: 2575-2580; doi:10.1093/nar/29.12.2575 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

T. A. Thanaraj and Francis Clark

Human GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions
Nucl. Acids Res. 2001 29: 2581-2593; doi:10.1093/nar/29.12.2581 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hendrik Huthoff and Ben Berkhout

Mutations in the TAR hairpin affect the equilibrium between alternative conformations of the HIV-1 leader RNA
Nucl. Acids Res. 2001 29: 2594-2600; doi:10.1093/nar/29.12.2594 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Iaroslav Kuzmine, Philip A. Gottlieb, and Craig T. Martin

Structure in nascent RNA leads to termination of slippage transcription by T7 RNA polymerase
Nucl. Acids Res. 2001 29: 2601-2606; doi:10.1093/nar/29.12.2601 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

John Besemer, Alexandre Lomsadze, and Mark Borodovsky

GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
Nucl. Acids Res. 2001 29: 2607-2618; doi:10.1093/nar/29.12.2607 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Philip R. Hardwidge and L. James Maher

Experimental evaluation of the Liu–Beveridge dinucleotide step model of DNA structure
Nucl. Acids Res. 2001 29: 2619-2625; doi:10.1093/nar/29.12.2619 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Edward Timofeev and Andrei Mirzabekov

Binding specificity and stability of duplexes formed by modified oligonucleotides with a 4096-hexanucleotide microarray
Nucl. Acids Res. 2001 29: 2626-2634; doi:10.1093/nar/29.12.2626 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Garry W. Buchko, Chang-Shung Tung, Kathleen McAteer, Nancy G. Isern, Leonard D. Spicer, and Michael A. Kennedy

DNA–XPA interactions: a ³¹P NMR and molecular modeling study of dCCAATAACC association with the minimal DNA-binding domain (M98–F219) of the nucleotide excision repair protein XPA
Nucl. Acids Res. 2001 29: 2635-2643; doi:10.1093/nar/29.12.2635 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yi Zhang and Michael J. Leibowitz

Folding of the group I intron ribozyme from the 26S rRNA gene of Candida albicans
Nucl. Acids Res. 2001 29: 2644-2653; doi:10.1093/nar/29.12.2644 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Alexander S. Krylov, Olga A. Zasedateleva, Dmitry V. Prokopenko, Josette Rouviere-Yaniv, and Andrei D. Mirzabekov

Massive parallel analysis of the binding specificity of histone-like protein HU to single- and double-stranded DNA with generic oligodeoxyribonucleotide microchips
Nucl. Acids Res. 2001 29: 2654-2660; doi:10.1093/nar/29.12.2654 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Matthias Wagner, Christiane Fingerhut, Hans J. Gross, and Astrid Schön

The first phytoplasma RNase P RNA provides new insights into the sequence requirements of this ribozyme
Nucl. Acids Res. 2001 29: 2661-2665; doi:10.1093/nar/29.12.2661 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yesong Gu and A-Lien Lu

Differential DNA recognition and glycosylase activity of the native human MutY homolog (hMYH) and recombinant hMYH expressed in bacteria
Nucl. Acids Res. 2001 29: 2666-2674; doi:10.1093/nar/29.12.2666 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

NAR Methods Online:

Alberto Piccin, Ahmad Salameh, Clara Benna, Federica Sandrelli, Gabriella Mazzotta, Mauro Zordan, Ezio Rosato, Charalambos P. Kyriacou, and Rodolfo Costa

Efficient and heritable functional knock-out of an adult phenotype in Drosophila using a GAL4-driven hairpin RNA incorporating a heterologous spacer
Nucl. Acids Res. 2001 29: e55; doi:10.1093/nar/29.12.e55 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Stanislaw J. Kaczmarczyk and Jeffrey E. Green

A single vector containing modified cre recombinase and LOX recombination sequences for inducible tissue-specific amplification of gene expression
Nucl. Acids Res. 2001 29: e56; doi:10.1093/nar/29.12.e56 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yuri Yu. Kusov, Gocha Shatirishvili, Georgy Dzagurov, and Verena Gauss-Müller

A new G-tailing method for the determination of the poly(A) tail length applied to hepatitis A virus RNA
Nucl. Acids Res. 2001 29: e57; doi:10.1093/nar/29.12.e57 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kandiah Jeyaseelan, Donghui Ma, and Arunmozhiarasi Armugam

Real-time detection of gene promoter activity: quantitation of toxin gene transcription
Nucl. Acids Res. 2001 29: e58; doi:10.1093/nar/29.12.e58 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Warren P. Voth, James D. Richards, Janet M. Shaw, and David J. Stillman

Yeast vectors for integration at the HO locus
Nucl. Acids Res. 2001 29: e59; doi:10.1093/nar/29.12.e59 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Elliott H. Margulies, Sharon L. R. Kardia, and Jeffrey W. Innis

Identification and prevention of a GC content bias in SAGE libraries
Nucl. Acids Res. 2001 29: e60; doi:10.1093/nar/29.12.e60 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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