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Previous Next 		Contents: Volume 34, Number 20, November 2006   [Index by Author] 

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To see an article, click its [Full Text] or [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.

Chemistry Back

Xiaohua Peng, Hong Li, and Frank Seela
pH-Dependent mismatch discrimination of oligonucleotide duplexes containing 2'-deoxytubercidin and 2- or 7-substituted derivatives: protonated base pairs formed between 7-deazapurines and cytosine
Nucleic Acids Research Advance Access published on October 27, 2006
Nucl. Acids Res. 2006 34: 5987-6000; doi:10.1093/nar/gkl719 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Computational Biology Back

Brian T. Naughton, Eugene Fratkin, Serafim Batzoglou, and Douglas L. Brutlag
A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites
Nucleic Acids Research Advance Access published on October 13, 2006
Nucl. Acids Res. 2006 34: 5730-5739; doi:10.1093/nar/gkl585 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Derrick E. Fouts
Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences
Nucleic Acids Research Advance Access published on October 24, 2006
Nucl. Acids Res. 2006 34: 5839-5851; doi:10.1093/nar/gkl732 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alexander E. Vinogradov
‘Genome design’ model and multicellular complexity: golden middle
Nucleic Acids Research Advance Access published on October 24, 2006
Nucl. Acids Res. 2006 34: 5906-5914; doi:10.1093/nar/gkl773 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tu Minh Phuong, Chuong B. Do, Robert C. Edgar, and Serafim Batzoglou
Multiple alignment of protein sequences with repeats and rearrangements
Nucleic Acids Research Advance Access published on October 26, 2006
Nucl. Acids Res. 2006 34: 5932-5942; doi:10.1093/nar/gkl511 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Uwe Ohler
Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction
Nucleic Acids Research Advance Access published on October 26, 2006
Nucl. Acids Res. 2006 34: 5943-5950; doi:10.1093/nar/gkl608 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yi-Kuo Yu, E. Michael Gertz, Richa Agarwala, Alejandro A. Schäffer, and Stephen F. Altschul
Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches
Nucleic Acids Research Advance Access published on October 26, 2006
Nucl. Acids Res. 2006 34: 5966-5973; doi:10.1093/nar/gkl731 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ivaylo Ivanov, Brian R. Chapados, J. Andrew McCammon, and John A. Tainer
Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications
Nucleic Acids Research Advance Access published on October 27, 2006
Nucl. Acids Res. 2006 34: 6023-6033; doi:10.1093/nar/gkl744 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Genomics Back

Francisco J. Silva, Eugeni Belda, and Santiago E. Talens
Differential annotation of tRNA genes with anticodon CAT in bacterial genomes
Nucleic Acids Research Advance Access published on October 27, 2006
Nucl. Acids Res. 2006 34: 6015-6022; doi:10.1093/nar/gkl739 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology Back

Prabhat K. Mandal, Kamal Rawal, Ram Ramaswamy, Alok Bhattacharya, and Sudha Bhattacharya
Identification of insertion hot spots for non-LTR retrotransposons: computational and biochemical application to Entamoeba histolytica
Nucleic Acids Research Advance Access published on October 13, 2006
Nucl. Acids Res. 2006 34: 5752-5763; doi:10.1093/nar/gkl710 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Christina A. Kowalczyk, Alissa M. Anderson, Maria Arce-Larreta, and Douglas L. Chalker
The germ line limited M element of Tetrahymena is targeted for elimination from the somatic genome by a homology-dependent mechanism
Nucleic Acids Research Advance Access published on October 19, 2006
Nucl. Acids Res. 2006 34: 5778-5789; doi:10.1093/nar/gkl699 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jaakko L. O. Pohjoismäki, Sjoerd Wanrooij, Anne K. Hyvärinen, Steffi Goffart, Ian J. Holt, Johannes N. Spelbrink, and Howard T. Jacobs
Alterations to the expression level of mitochondrial transcription factor A, TFAM, modify the mode of mitochondrial DNA replication in cultured human cells
Nucleic Acids Research Advance Access published on October 24, 2006
Nucl. Acids Res. 2006 34: 5815-5828; doi:10.1093/nar/gkl703 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Violeta Cordón-Preciado, Sandra Ufano, and Avelino Bueno
Limiting amounts of budding yeast Rad53 S-phase checkpoint activity results in increased resistance to DNA alkylation damage
Nucleic Acids Research Advance Access published on October 24, 2006
Nucl. Acids Res. 2006 34: 5852-5862; doi:10.1093/nar/gkl741 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Curtis Anderson, Heath Catoe, and Rudolf Werner
MIR-206 regulates connexin43 expression during skeletal muscle development
Nucleic Acids Research Advance Access published on October 24, 2006
Nucl. Acids Res. 2006 34: 5863-5871; doi:10.1093/nar/gkl743 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Suparna Laha, Shankar Prasad Das, Sujata Hajra, Soumitra Sau, and Pratima Sinha
The budding yeast protein Chl1p is required to preserve genome integrity upon DNA damage in S-phase
Nucleic Acids Research Advance Access published on October 24, 2006
Nucl. Acids Res. 2006 34: 5880-5891; doi:10.1093/nar/gkl749 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Evan Diamond, Melanie Amen, Qiaoyan Hu, Herbert M. Espinoza, and Brad A. Amendt
Functional interactions between Dlx2 and lymphoid enhancer factor regulate Msx2
Nucleic Acids Research Advance Access published on October 26, 2006
Nucl. Acids Res. 2006 34: 5951-5965; doi:10.1093/nar/gkl689 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Dujin Zhou, Jing jing Ye, Yuping Li, Ki Lui, and Shiuan Chen
The molecular basis of the interaction between the proline-rich SH3-binding motif of PNRC and estrogen receptor alpha
Nucleic Acids Research Advance Access published on October 26, 2006
Nucl. Acids Res. 2006 34: 5974-5986; doi:10.1093/nar/gkl764 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Andrew D. S. Cameron and Rosemary J. Redfield
Non-canonical CRP sites control competence regulons in Escherichia coli and many other {gamma}-proteobacteria
Nucleic Acids Research Advance Access published on October 26, 2006
Nucl. Acids Res. 2006 34: 6001-6014; doi:10.1093/nar/gkl734 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nicole Fouché, Sezgin Özgür, Debasmita Roy, and Jack D. Griffith
Replication fork regression in repetitive DNAs
Nucleic Acids Research Advance Access published on October 28, 2006
Nucl. Acids Res. 2006 34: 6044-6050; doi:10.1093/nar/gkl757 [Abstract] [Print PDF][Screen PDF]  

Nucleic Acid Enzymes Back

Zhiwan Dong and Alan E. Tomkinson
ATM mediates oxidative stress-induced dephosphorylation of DNA ligase III{alpha}
Nucleic Acids Research Advance Access published on October 12, 2006
Nucl. Acids Res. 2006 34: 5721-5279; doi:10.1093/nar/gkl705 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Bartosz Brzezicha, Marcin Schmidt, Izabela Makalowska, Artur Jarmolowski, Joanna Pienkowska, and Zofia Szweykowska-Kulinska
Identification of human tRNA:m5C methyltransferase catalysing intron-dependent m5C formation in the first position of the anticodon of the Formula
Nucleic Acids Research Advance Access published on October 27, 2006
Nucl. Acids Res. 2006 34: 6034-6043; doi:10.1093/nar/gkl765 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Elisa Longás, Miguel de Vega, José M. Lázaro, and Margarita Salas
Functional characterization of highly processive protein-primed DNA polymerases from phages Nf and GA-1, endowed with a potent strand displacement capacity
Nucleic Acids Research Advance Access published on October 28, 2006
Nucl. Acids Res. 2006 34: 6051-6063; doi:10.1093/nar/gkl769 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

RNA Back

Flore Joli, Nadia Bouchemal, Alain Laigle, Brigitte Hartmann, and Edith Hantz
Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides
Nucleic Acids Research Advance Access published on October 13, 2006
Nucl. Acids Res. 2006 34: 5740-5751; doi:10.1093/nar/gkl617 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Caroline Gabus, Roland Ivanyi-Nagy, Julien Depollier, Alain Bucheton, Alain Pelisson, and Jean-Luc Darlix
Characterization of a nucleocapsid-like region and of two distinct primer tRNALys,2 binding sites in the endogenous retrovirus Gypsy
Nucleic Acids Research Advance Access published on October 13, 2006
Nucl. Acids Res. 2006 34: 5764-5777; doi:10.1093/nar/gkl722 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

D. Shcherbakov, M. Dontsova, M. Tribus, M. Garber, and W. Piendl
Stability of the ‘L12 stalk’ in ribosomes from mesophilic and (hyper)thermophilic Archaea and Bacteria
Nucleic Acids Research Advance Access published on October 19, 2006
Nucl. Acids Res. 2006 34: 5800-5814; doi:10.1093/nar/gkl751 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Lucía Yim, Ismaïl Moukadiri, Glenn R. Björk, and M.-Eugenia Armengod
Further insights into the tRNA modification process controlled by proteins MnmE and GidA of Escherichia coli
Nucleic Acids Research Advance Access published on October 24, 2006
Nucl. Acids Res. 2006 34: 5892-5905; doi:10.1093/nar/gkl752 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Omid R. Faridani, Abbas Nikravesh, Deo Prakash Pandey, Kenn Gerdes, and Liam Good
Competitive inhibition of natural antisense Sok-RNA interactions activates Hok-mediated cell killing in Escherichia coli
Nucleic Acids Research Advance Access published on October 25, 2006
Nucl. Acids Res. 2006 34: 5915-5922; doi:10.1093/nar/gkl750 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Victoria Portnoy and Gadi Schuster
RNA polyadenylation and degradation in different Archaea; roles of the exosome and RNase R
Nucleic Acids Research Advance Access published on October 25, 2006
Nucl. Acids Res. 2006 34: 5923-5931; doi:10.1093/nar/gkl763 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Structural Biology Back

Thomas Bentin, Georg I. Hansen, and Peter E. Nielsen
Structural diversity of target-specific homopyrimidine peptide nucleic acid–dsDNA complexes
Nucleic Acids Research Advance Access published on October 19, 2006
Nucl. Acids Res. 2006 34: 5790-5799; doi:10.1093/nar/gkl736 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Alessandro Costa, Tillmann Pape, Marin van Heel, Peter Brick, Ardan Patwardhan, and Silvia Onesti
Structural basis of the Methanothermobacter thermautotrophicus MCM helicase activity
Nucleic Acids Research Advance Access published on October 24, 2006
Nucl. Acids Res. 2006 34: 5829-5838; doi:10.1093/nar/gkl708 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Daniel J. Krosky, Mario A. Bianchet, Lauren Seiple, Suhman Chung, L. Mario Amzel, and James T. Stivers
Mimicking damaged DNA with a small molecule inhibitor of human UNG2
Nucleic Acids Research Advance Access published on October 24, 2006
Nucl. Acids Res. 2006 34: 5872-5879; doi:10.1093/nar/gkl747 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online Back

Ashraf E. K. Ibrahim, Natalie P. Thorne, Katie Baird, Nuno L. Barbosa-Morais, Simon Tavaré, V. Peter Collins, Andrew H. Wyllie, Mark J. Arends, and James D. Brenton
MMASS: an optimized array-based method for assessing CpG island methylation
Nucleic Acids Research Advance Access published on October 13, 2006
Nucl. Acids Res. 2006 34: e136; doi:10.1093/nar/gkl551 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Erik J. Slootweg, Hans J.H.G. Keller, Mark A. Hink, Jan Willem Borst, Jaap Bakker, and Arjen Schots
Fluorescent T7 display phages obtained by translational frameshift
Nucleic Acids Research Advance Access published on October 13, 2006
Nucl. Acids Res. 2006 34: e137; doi:10.1093/nar/gkl600 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nobutaka Nakashima, Tomohiro Tamura, and Liam Good
Paired termini stabilize antisense RNAs and enhance conditional gene silencing in Escherichia coli
Nucleic Acids Research Advance Access published on October 24, 2006
Nucl. Acids Res. 2006 34: e138; doi:10.1093/nar/gkl697 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Qing Lin, Sarah L. Donahue, Tracy Moore-Jarrett, Shang Cao, Anna B. Osipovich, and H. Earl Ruley
Mutagenesis of diploid mammalian genes by gene entrapment
Nucleic Acids Research Advance Access published on October 24, 2006
Nucl. Acids Res. 2006 34: e139; doi:10.1093/nar/gkl728 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Manish Biyani, Yuzuru Husimi, and Naoto Nemoto
Solid-phase translation and RNA–protein fusion: a novel approach for folding quality control and direct immobilization of proteins using anchored mRNA
Nucleic Acids Research Advance Access published on October 24, 2006
Nucl. Acids Res. 2006 34: e140; doi:10.1093/nar/gkl771 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Besik I. Kankia
A real-time assay for monitoring nucleic acid cleavage by quadruplex formation
Nucleic Acids Research Advance Access published on October 28, 2006
Nucl. Acids Res. 2006 34: e141; doi:10.1093/nar/gkl594 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Joshua D. Levin, Dean Fiala, Meinrado F. Samala, Jason D. Kahn, and Raymond J. Peterson
Position-dependent effects of locked nucleic acid (LNA) on DNA sequencing and PCR primers
Nucleic Acids Research Advance Access published on October 28, 2006
Nucl. Acids Res. 2006 34: e142; doi:10.1093/nar/gkl756 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Corrigendum Back

Corrigendum
Nucl. Acids Res. 2006 34: 6064; doi:10.1093/nar/gkl918 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

To see an article, click its [Full Text] or [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.