Nucleic Acids Research

Survey and Summary:

Scott K. Silverman

In vitro selection, characterization, and application of deoxyribozymes that cleave RNA
Nucl. Acids Res. 2005 33: 6151-6163; doi:10.1093/nar/gki930 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Articles:

Peter D. Karp, Christos A. Ouzounis, Caroline Moore-Kochlacs, Leon Goldovsky, Pallavi Kaipa, Dag Ahrén, Sophia Tsoka, Nikos Darzentas, Victor Kunin, and Núria López-Bigas

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
Nucl. Acids Res. 2005 33: 6083-6089; doi:10.1093/nar/gki892 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kevin F. Bryant, J. Colin Cox, Hongming Wang, James M. Hogle, Andrew D. Ellington, and Donald M. Coen

Binding of herpes simplex virus-1 US11 to specific RNA sequences
Nucl. Acids Res. 2005 33: 6090-6100; doi:10.1093/nar/gki919 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Sunir Malla, Felix Dafhnis-Calas, John F. Y. Brookfield, Margaret C. M. Smith, and William R. A. Brown

Rearranging the centromere of the human Y chromosome with C31 integrase
Nucl. Acids Res. 2005 33: 6101-6113; doi:10.1093/nar/gki922 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Xingyuan Li, Zhili He, and Jizhong Zhou

Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation
Nucl. Acids Res. 2005 33: 6114-6123; doi:10.1093/nar/gki914 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Taras Shevchuk, Leo Kretzner, Kristofer Munson, John Axume, Jarrod Clark, Olga V. Dyachenko, Marie Caudill, Yaroslav Buryanov, and Steven S. Smith

Transgene-induced CCWGG methylation does not alter CG methylation patterning in human kidney cells
Nucl. Acids Res. 2005 33: 6124-6136; doi:10.1093/nar/gki920 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jeong-Hoon Kim, Young-Hoon Kang, Hyo-Jin Kang, Do-Hyung Kim, Gi-Hyuck Ryu, Min-Jung Kang, and Yeon-Soo Seo

In vivo and in vitro studies of Mgs1 suggest a link between genome instability and Okazaki fragment processing
Nucl. Acids Res. 2005 33: 6137-6150; doi:10.1093/nar/gki900 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Richard A. Notebaart, Martijn A. Huynen, Bas Teusink, Roland J. Siezen, and Berend Snel

Correlation between sequence conservation and the genomic context after gene duplication
Nucl. Acids Res. 2005 33: 6164-6171; doi:10.1093/nar/gki913 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Zehua Chen and Thomas D. Schneider

Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases
Nucl. Acids Res. 2005 33: 6172-6187; doi:10.1093/nar/gki915 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Antonella Virgilio, Veronica Esposito, Antonio Randazzo, Luciano Mayol, and Aldo Galeone

8-Methyl-2'-deoxyguanosine incorporation into parallel DNA quadruplex structures
Nucl. Acids Res. 2005 33: 6188-6195; doi:10.1093/nar/gki924 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Yoke W. Kow, Gaobin Bao, Brenda Minesinger, Sue Jinks-Robertson, Wolfram Siede, Yu Lin Jiang, and Marc M. Greenberg

Mutagenic effects of abasic and oxidized abasic lesions in Saccharomyces cerevisiae
Nucl. Acids Res. 2005 33: 6196-6202; doi:10.1093/nar/gki926 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Linus Sandegren, David Nord, and Britt-Marie Sjöberg

SegH and Hef: two novel homing endonucleases whose genes replace the mobC and mobE genes in several T4-related phages
Nucl. Acids Res. 2005 33: 6203-6213; doi:10.1093/nar/gki932 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Esther Marco, Ana Negri, F. Javier Luque, and Federico Gago

Role of stacking interactions in the binding sequence preferences of DNA bis-intercalators: insight from thermodynamic integration free energy simulations
Nucl. Acids Res. 2005 33: 6214-6224; doi:10.1093/nar/gki916 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Chudi Guan and Sanjay Kumar

A single catalytic domain of the junction-resolving enzyme T7 endonuclease I is a non-specific nicking endonuclease
Nucl. Acids Res. 2005 33: 6225-6234; doi:10.1093/nar/gki921 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yasunari Ogihara, Yukiko Yamazaki, Koji Murai, Akira Kanno, Toru Terachi, Takashi Shiina, Naohiko Miyashita, Shuhei Nasuda, Chiharu Nakamura, Naoki Mori, Shigeo Takumi, Minoru Murata, Satoshi Futo, and Koichiro Tsunewaki

Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome
Nucl. Acids Res. 2005 33: 6235-6250; doi:10.1093/nar/gki925 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Gary LeRoy, Robert Carroll, Saw Kyin, Masayuki Seki, and Michael D. Cole

Identification of RecQL1 as a Holliday junction processing enzyme in human cell lines
Nucl. Acids Res. 2005 33: 6251-6257; doi:10.1093/nar/gki929 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Norman E. Watkins, Jr and John SantaLucia, Jr

Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes
Nucl. Acids Res. 2005 33: 6258-6267; doi:10.1093/nar/gki918 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Mitsuoki Kawano, Gisela Storz, B. Sridhar Rao, Judah L. Rosner, and Robert G. Martin

Detection of low-level promoter activity within open reading frame sequences of Escherichia coli
Nucl. Acids Res. 2005 33: 6268-6276; doi:10.1093/nar/gki928 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Constanze Baranek, Elisabeth Sock, and Michael Wegner

The POU protein Oct-6 is a nucleocytoplasmic shuttling protein
Nucl. Acids Res. 2005 33: 6277-6286; doi:10.1093/nar/gki947 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Eli S. Groban, Martha B. Johnson, Poopak Banky, Peta-Gaye G. Burnett, Georgina L. Calderon, Erica C. Dwyer, Shakierah N. Fuller, Biniam Gebre, Leah M. King, Ila N. Sheren, Lindi D. Von Mutius, Thomas M. O'Gara, and Charles M. Lovett

Binding of the Bacillus subtilis LexA protein to the SOS operator
Nucl. Acids Res. 2005 33: 6287-6295; doi:10.1093/nar/gki939 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Noriaki Shimizu, Fumie Kamezaki, and Shiho Shigematsu

Tracking of microinjected DNA in live cells reveals the intracellular behavior and elimination of extrachromosomal genetic material
Nucl. Acids Res. 2005 33: 6296-6307; doi:10.1093/nar/gki946 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ahmed Fadiel, Ifeanyi Anidi, and Kenneth D. Eichenbaum

Farm animal genomics and informatics: an update
Nucl. Acids Res. 2005 33: 6308-6318; doi:10.1093/nar/gki931 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Joseph Schacherer, Jacky de Montigny, Anne Welcker, Jean-Luc Souciet, and Serge Potier

Duplication processes in Saccharomyces cerevisiae haploid strains
Nucl. Acids Res. 2005 33: 6319-6326; doi:10.1093/nar/gki941 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Francesca Di Felice, Francesco Cioci, and Giorgio Camilloni

FOB1 affects DNA topoisomerase I in vivo cleavages in the enhancer region of the Saccharomyces cerevisiae ribosomal DNA locus
Nucl. Acids Res. 2005 33: 6327-6337; doi:10.1093/nar/gki950 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Irmtraud M. Meyer and István Miklós

Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs
Nucl. Acids Res. 2005 33: 6338-6348; doi:10.1093/nar/gki923 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

M. Fahad Khalid, Masad J. Damha, Stewart Shuman, and Beate Schwer

Structure–function analysis of yeast RNA debranching enzyme (Dbr1), a manganese-dependent phosphodiesterase
Nucl. Acids Res. 2005 33: 6349-6360; doi:10.1093/nar/gki934 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

J. Zhou, S. Krueger, and S. K. Gregurick

A coarse graining approach to determine nucleic acid structures from small angle neutron scattering profiles in solution
Nucl. Acids Res. 2005 33: 6361-6371; doi:10.1093/nar/gki936 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Claudia D. Borgeson and Marie-Laure Samson

Shared RNA-binding sites for interacting members of the Drosophila ELAV family of neuronal proteins
Nucl. Acids Res. 2005 33: 6372-6383; doi:10.1093/nar/gki942 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Klaas W. Mulder, G. Sebastiaan Winkler, and H. Th. Marc Timmers

DNA damage and replication stress induced transcription of RNR genes is dependent on the Ccr4–Not complex
Nucl. Acids Res. 2005 33: 6384-6392; doi:10.1093/nar/gki938 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Marie J. Lucey, Dongsheng Chen, Jorge Lopez-Garcia, Stephen M. Hart, Fladia Phoenix, Rajai Al-Jehani, John P. Alao, Roger White, Karin B. Kindle, Régine Losson, Pierre Chambon, Malcolm G. Parker, Primo Schär, David M. Heery, Lakjaya Buluwela, and Simak Ali

T:G mismatch-specific thymine-DNA glycosylase (TDG) as a coregulator of transcription interacts with SRC1 family members through a novel tyrosine repeat motif
Nucl. Acids Res. 2005 33: 6393-6404; doi:10.1093/nar/gki940 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Markus Kuhlmann, Branimira E. Borisova, Markus Kaller, Pontus Larsson, Dirk Stach, Jianbo Na, Ludwig Eichinger, Frank Lyko, Victor Ambros, Fredrik Söderbom, Christian Hammann, and Wolfgang Nellen

Silencing of retrotransposons in Dictyostelium by DNA methylation and RNAi
Nucl. Acids Res. 2005 33: 6405-6417; doi:10.1093/nar/gki952 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Petr Kolosov, Ludmila Frolova, Alim Seit-Nebi, Vera Dubovaya, Artem Kononenko, Nina Oparina, Just Justesen, Alexandr Efimov, and Lev Kisselev

Invariant amino acids essential for decoding function of polypeptide release factor eRF1
Nucl. Acids Res. 2005 33: 6418-6425; doi:10.1093/nar/gki927 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yo-Chan Jeong, Jun Nakamura, Patricia B. Upton, and James A. Swenberg

Pyrimido[1,2-a]-purin-10(3H)-one, M₁G, is less prone to artifact than base oxidation
Nucl. Acids Res. 2005 33: 6426-6434; doi:10.1093/nar/gki944 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hedije Meka, Finn Werner, Suzanne C. Cordell, Silvia Onesti, and Peter Brick

Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II
Nucl. Acids Res. 2005 33: 6435-6444; doi:10.1093/nar/gki945 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fan Yang, Jian Yang, Xiaobing Zhang, Lihong Chen, Yan Jiang, Yongliang Yan, Xudong Tang, Jing Wang, Zhaohui Xiong, Jie Dong, Ying Xue, Yafang Zhu, Xingye Xu, Lilian Sun, Shuxia Chen, Huan Nie, Junping Peng, Jianguo Xu, Yu Wang, Zhenghong Yuan, Yumei Wen, Zhijian Yao, Yan Shen, Boqin Qiang, Yunde Hou, Jun Yu, and Qi Jin

Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery
Nucl. Acids Res. 2005 33: 6445-6458; doi:10.1093/nar/gki954 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Corrigendum:

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: 6459; doi:10.1093/nar/gki933 [Extract] [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: 6460; doi:10.1093/nar/gki948 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Maddalena Collini, Michele Caccia, Giuseppe Chirico, Flavia Barone, Eugenia Dogliotti, and Filomena Mazzei

Two-photon fluorescence cross-correlation spectroscopy as a potential tool for high-throughput screening of DNA repair activity
Nucl. Acids Res. 2005 33: e165; doi:10.1093/nar/gni166 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Lei Zhang, Thomas Hurek, and Barbara Reinhold-Hurek

Position of the fluorescent label is a crucial factor determining signal intensity in microarray hybridizations
Nucl. Acids Res. 2005 33: e166; doi:10.1093/nar/gni156 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Johan Ohlson, Mats Ensterö, Britt-Marie Sjöberg, and Marie Öhman

A method to find tissue-specific novel sites of selective adenosine deamination
Nucl. Acids Res. 2005 33: e167; doi:10.1093/nar/gni169 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jishan Li, Xia Chu, Yali Liu, Jian-Hui Jiang, Zhimin He, Zhiwei Zhang, Guoli Shen, and Ru-Qin Yu

A colorimetric method for point mutation detection using high-fidelity DNA ligase
Nucl. Acids Res. 2005 33: e168; doi:10.1093/nar/gni163 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jose Luis Royo, Hamid Manyani, Angel Cebolla, and Eduardo Santero

A new generation of vectors with increased induction ratios by overimposing a second regulatory level by attenuation
Nucl. Acids Res. 2005 33: e169; doi:10.1093/nar/gni168 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Dehai Liang, Yen K. Luu, Kwangsok Kim, Benjamin S. Hsiao, Michael Hadjiargyrou, and Benjamin Chu

In vitro non-viral gene delivery with nanofibrous scaffolds
Nucl. Acids Res. 2005 33: e170; doi:10.1093/nar/gni171 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nava Whiteford, Niall Haslam, Gerald Weber, Adam Prügel-Bennett, Jonathan W. Essex, Peter L. Roach, Mark Bradley, and Cameron Neylon

An analysis of the feasibility of short read sequencing
Nucl. Acids Res. 2005 33: e171; doi:10.1093/nar/gni170 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

L. D. Burgoon, J. E. Eckel-Passow, C. Gennings, D. R. Boverhof, J. W. Burt, C. J. Fong, and T. R. Zacharewski

Protocols for the assurance of microarray data quality and process control
Nucl. Acids Res. 2005 33: e172; doi:10.1093/nar/gni167 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yasuko Kamisugi, Andrew C. Cuming, and David J. Cove

Parameters determining the efficiency of gene targeting in the moss Physcomitrella patens
Nucl. Acids Res. 2005 33: e173; doi:10.1093/nar/gni172 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

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