| | 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:m 5C methyltransferase catalysing intron-dependent m 5C formation in the first position of the anticodon of the 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. |