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Volume 34(20);  November 2006
Molecular Biology
Identification of insertion hot spots for non-LTR retrotransposons: computational and biochemical application to Entamoeba histolytica
Prabhat K. Mandal, Kamal Rawal, Ram Ramaswamy, Alok Bhattacharya, and Sudha Bhattacharya
Nucleic Acids Res. 2006 November; 34(20): 5752–5763. Published online 2006 October 13. doi: 10.1093/nar/gkl710.
PMCID: PMC1635306
The germ line limited M element of Tetrahymena is targeted for elimination from the somatic genome by a homology-dependent mechanism
Christina A. Kowalczyk, Alissa M. Anderson, Maria Arce-Larreta, and Douglas L. Chalker
Nucleic Acids Res. 2006 November; 34(20): 5778–5789. Published online 2006 November 19. doi: 10.1093/nar/gkl699.
PMCID: PMC1635302
Alterations to the expression level of mitochondrial transcription factor A, TFAM, modify the mode of mitochondrial DNA replication in cultured human cells
Jaakko L. O. Pohjoismäki, Sjoerd Wanrooij, Anne K. Hyvärinen, Steffi Goffart, Ian J. Holt, Johannes N. Spelbrink, and Howard T. Jacobs
Nucleic Acids Res. 2006 November; 34(20): 5815–5828. Published online 2006 November 24. doi: 10.1093/nar/gkl703.
PMCID: PMC1635303
Limiting amounts of budding yeast Rad53 S-phase checkpoint activity results in increased resistance to DNA alkylation damage
Violeta Cordón-Preciado, Sandra Ufano, and Avelino Bueno
Nucleic Acids Res. 2006 November; 34(20): 5852–5862. Published online 2006 November 12. doi: 10.1093/nar/gkl741.
PMCID: PMC1635317
MIR-206 regulates connexin43 expression during skeletal muscle development
Curtis Anderson, Heath Catoe, and Rudolf Werner
Nucleic Acids Res. 2006 November; 34(20): 5863–5871. Published online 2006 November 12. doi: 10.1093/nar/gkl743.
PMCID: PMC1635318
The budding yeast protein Chl1p is required to preserve genome integrity upon DNA damage in S-phase
Suparna Laha, Shankar Prasad Das, Sujata Hajra, Soumitra Sau, and Pratima Sinha
Nucleic Acids Res. 2006 November; 34(20): 5880–5891. Published online 2006 November 24. doi: 10.1093/nar/gkl749.
PMCID: PMC1635322
Functional interactions between Dlx2 and lymphoid enhancer factor regulate Msx2
Evan Diamond, Melanie Amen, Qiaoyan Hu, Herbert M. Espinoza, and Brad A. Amendt
Nucleic Acids Res. 2006 November; 34(20): 5951–5965. Published online 2006 November 26. doi: 10.1093/nar/gkl689.
PMCID: PMC1635299
The molecular basis of the interaction between the proline-rich SH3-binding motif of PNRC and estrogen receptor alpha
Dujin Zhou, Jing jing Ye, Yuping Li, Ki Lui, and Shiuan Chen
Nucleic Acids Res. 2006 November; 34(20): 5974–5986. Published online 2006 October 26. doi: 10.1093/nar/gkl764.
PMCID: PMC1635328
Non-canonical CRP sites control competence regulons in Escherichia coli and many other γ-proteobacteria
Andrew D. S. Cameron and Rosemary J. Redfield
Nucleic Acids Res. 2006 November; 34(20): 6001–6014. Published online 2006 October 26. doi: 10.1093/nar/gkl734.
PMCID: PMC1635313
Replication fork regression in repetitive DNAs
Nicole Fouché, Sezgin Özgür, Debasmita Roy, and Jack D. Griffith
Nucleic Acids Res. 2006 November; 34(20): 6044–6050. Published online 2006 October 28. doi: 10.1093/nar/gkl757.
PMCID: PMC1635326
RNA
Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides
Flore Joli, Nadia Bouchemal, Alain Laigle, Brigitte Hartmann, and Edith Hantz
Nucleic Acids Res. 2006 November; 34(20): 5740–5751. Published online 2006 November 13. doi: 10.1093/nar/gkl617.
PMCID: PMC1694020
Characterization of a nucleocapsid-like region and of two distinct primer tRNALys,2 binding sites in the endogenous retrovirus Gypsy
Caroline Gabus, Roland Ivanyi-Nagy, Julien Depollier, Alain Bucheton, Alain Pelisson, and Jean-Luc Darlix
Nucleic Acids Res. 2006 November; 34(20): 5764–5777. Published online 2006 November 13. doi: 10.1093/nar/gkl722.
PMCID: PMC1635307
Stability of the ‘L12 stalk’ in ribosomes from mesophilic and (hyper)thermophilic Archaea and Bacteria
D. Shcherbakov, M. Dontsova, M. Tribus, M. Garber, and W. Piendl
Nucleic Acids Res. 2006 November; 34(20): 5800–5814. Published online 2006 October 19. doi: 10.1093/nar/gkl751.
PMCID: PMC1635324
Further insights into the tRNA modification process controlled by proteins MnmE and GidA of Escherichia coli
Lucía Yim, Ismaïl Moukadiri, Glenn R. Björk, and M.-Eugenia Armengod
Nucleic Acids Res. 2006 November; 34(20): 5892–5905. Published online 2006 October 24. doi: 10.1093/nar/gkl752.
PMCID: PMC1635325
Competitive inhibition of natural antisense Sok-RNA interactions activates Hok-mediated cell killing in Escherichia coli
Omid R. Faridani, Abbas Nikravesh, Deo Prakash Pandey, Kenn Gerdes, and Liam Good
Nucleic Acids Res. 2006 November; 34(20): 5915–5922. Published online 2006 October 25. doi: 10.1093/nar/gkl750.
PMCID: PMC1635323
RNA polyadenylation and degradation in different Archaea; roles of the exosome and RNase R
Victoria Portnoy and Gadi Schuster
Nucleic Acids Res. 2006 November; 34(20): 5923–5931. Published online 2006 October 25. doi: 10.1093/nar/gkl763.
PMCID: PMC1635327
Structural Biology
Structural diversity of target-specific homopyrimidine peptide nucleic acid–dsDNA complexes
Thomas Bentin, Georg I. Hansen, and Peter E. Nielsen
Nucleic Acids Res. 2006 November; 34(20): 5790–5799. Published online 2006 November 19. doi: 10.1093/nar/gkl736.
PMCID: PMC1635314
Structural basis of the Methanothermobacter thermautotrophicus MCM helicase activity
Alessandro Costa, Tillmann Pape, Marin van Heel, Peter Brick, Ardan Patwardhan, and Silvia Onesti
Nucleic Acids Res. 2006 November; 34(20): 5829–5838. Published online 2006 October 24. doi: 10.1093/nar/gkl708.
PMCID: PMC1635305
Mimicking damaged DNA with a small molecule inhibitor of human UNG2
Daniel J. Krosky, Mario A. Bianchet, Lauren Seiple, Suhman Chung, L. Mario Amzel, and James T. Stivers
Nucleic Acids Res. 2006 November; 34(20): 5872–5879. Published online 2006 October 24. doi: 10.1093/nar/gkl747.
PMCID: PMC1635321
Genomics
Differential annotation of tRNA genes with anticodon CAT in bacterial genomes
Francisco J. Silva, Eugeni Belda, and Santiago E. Talens
Nucleic Acids Res. 2006 November; 34(20): 6015–6022. Published online 2006 October 27. doi: 10.1093/nar/gkl739.
PMCID: PMC1635315
Chemistry
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
Xiaohua Peng, Hong Li, and Frank Seela
Nucleic Acids Res. 2006 November; 34(20): 5987–6000. Published online 2006 October 27. doi: 10.1093/nar/gkl719.
PMCID: PMC1694028
Methods Online
MMASS: an optimized array-based method for assessing CpG island methylation
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
Nucleic Acids Res. 2006 November; 34(20): e136. Published online 2006 November 13. doi: 10.1093/nar/gkl551.
PMCID: PMC1635254
Fluorescent T7 display phages obtained by translational frameshift
Erik J. Slootweg, Hans J.H.G. Keller, Mark A. Hink, Jan Willem Borst, Jaap Bakker, and Arjen Schots
Nucleic Acids Res. 2006 November; 34(20): e137. Published online 2006 November 13. doi: 10.1093/nar/gkl600.
PMCID: PMC1635266
Paired termini stabilize antisense RNAs and enhance conditional gene silencing in Escherichia coli
Nobutaka Nakashima, Tomohiro Tamura, and Liam Good
Nucleic Acids Res. 2006 November; 34(20): e138. Published online 2006 November 24. doi: 10.1093/nar/gkl697.
PMCID: PMC1635301
Mutagenesis of diploid mammalian genes by gene entrapment
Qing Lin, Sarah L. Donahue, Tracy Moore-Jarrett, Shang Cao, Anna B. Osipovich, and H. Earl Ruley
Nucleic Acids Res. 2006 November; 34(20): e139. Published online 2006 October 24. doi: 10.1093/nar/gkl728.
PMCID: PMC1635309
Solid-phase translation and RNA–protein fusion: a novel approach for folding quality control and direct immobilization of proteins using anchored mRNA
Manish Biyani, Yuzuru Husimi, and Naoto Nemoto
Nucleic Acids Res. 2006 November; 34(20): e140. Published online 2006 October 12. doi: 10.1093/nar/gkl771.
PMCID: PMC1635333
A real-time assay for monitoring nucleic acid cleavage by quadruplex formation
Besik I. Kankia
Nucleic Acids Res. 2006 November; 34(20): e141. Published online 2006 November 28. doi: 10.1093/nar/gkl594.
PMCID: PMC1635264
Position-dependent effects of locked nucleic acid (LNA) on DNA sequencing and PCR primers
Joshua D. Levin, Dean Fiala, Meinrado F. Samala, Jason D. Kahn, and Raymond J. Peterson
Nucleic Acids Res. 2006 November; 34(20): e142. Published online 2006 November 24. doi: 10.1093/nar/gkl756.
PMCID: PMC1694044
Computational Biology
A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites
Brian T. Naughton, Eugene Fratkin, Serafim Batzoglou, and Douglas L. Brutlag
Nucleic Acids Res. 2006 November; 34(20): 5730–5739. Published online 2006 November 13. doi: 10.1093/nar/gkl585.
PMCID: PMC1635261
Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences
Derrick E. Fouts
Nucleic Acids Res. 2006 November; 34(20): 5839–5851. Published online 2006 October 24. doi: 10.1093/nar/gkl732.
PMCID: PMC1635311
‘Genome design’ model and multicellular complexity: golden middle
Alexander E. Vinogradov
Nucleic Acids Res. 2006 November; 34(20): 5906–5914. Published online 2006 November 12. doi: 10.1093/nar/gkl773.
PMCID: PMC1635334
Multiple alignment of protein sequences with repeats and rearrangements
Tu Minh Phuong, Chuong B. Do, Robert C. Edgar, and Serafim Batzoglou
Nucleic Acids Res. 2006 November; 34(20): 5932–5942. Published online 2006 November 26. doi: 10.1093/nar/gkl511.
PMCID: PMC1635250
Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction
Uwe Ohler
Nucleic Acids Res. 2006 November; 34(20): 5943–5950. Published online 2006 November 26. doi: 10.1093/nar/gkl608.
PMCID: PMC1635271
Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches
Yi-Kuo Yu, E. Michael Gertz, Richa Agarwala, Alejandro A. Schäffer, and Stephen F. Altschul
Nucleic Acids Res. 2006 November; 34(20): 5966–5973. Published online 2006 October 26. doi: 10.1093/nar/gkl731.
PMCID: PMC1635310
Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications
Ivaylo Ivanov, Brian R. Chapados, J. Andrew McCammon, and John A. Tainer
Nucleic Acids Res. 2006 November; 34(20): 6023–6033. Published online 2006 October 12. doi: 10.1093/nar/gkl744.
PMCID: PMC1635319
Nucleic Acid Enzymes
ATM mediates oxidative stress-induced dephosphorylation of DNA ligase IIIα
Zhiwan Dong and Alan E. Tomkinson
Nucleic Acids Res. 2006 November; 34(20): 5721–5279. Published online 2006 November 12. doi: 10.1093/nar/gkl705.
PMCID: PMC1694025
Identification of human tRNA:m5C methyltransferase catalysing intron-dependent m5C formation in the first position of the anticodon of the equation M1
Bartosz Brzezicha, Marcin Schmidt, Izabela Makałowska, Artur Jarmołowski, Joanna Pieńkowska, and Zofia Szweykowska-Kulińska
Nucleic Acids Res. 2006 November; 34(20): 6034–6043. Published online 2006 October 27. doi: 10.1093/nar/gkl765.
PMCID: PMC1635329
Functional characterization of highly processive protein-primed DNA polymerases from phages Nf and GA-1, endowed with a potent strand displacement capacity
Elisa Longás, Miguel de Vega, José M. Lázaro, and Margarita Salas
Nucleic Acids Res. 2006 November; 34(20): 6051–6063. Published online 2006 October 28. doi: 10.1093/nar/gkl769.
PMCID: PMC1635332
Corrigendum
Nucleic Acids Res. 2006 November; 34(20): 6064. doi: 10.1093/nar/gkl918.
PMCID: PMC1770951
Corrects: Jimin Pei, et al. MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Res. 2006 September; 34(16): 4364–4374.
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