| | Molecular Biology Twin gradients in APOBEC3 edited HIV-1 DNA reflect the dynamics of lentiviral replication Rodolphe Suspène, Christophe Rusniok, Jean-Pierre Vartanian, and Simon Wain-Hobson Nucleic Acids Res. 2006 October; 34(17): 4677–4684. Published online 2006 September 8. doi: 10.1093/nar/gkl555.PMCID: PMC1635257 CK2-mediated stimulation of Pol I transcription by stabilization of UBF–SL1 interaction Chih-Yin Lin, Sonia Navarro, Sita Reddy, and Lucio Comai Nucleic Acids Res. 2006 October; 34(17): 4752–4766. Published online 2006 September 13. doi: 10.1093/nar/gkl581.PMCID: PMC1635259 Identification of a plastid response element that acts as an enhancer within the Chlamydomonas HSP70A promoter Erika D. von Gromoff, Michael Schroda, Ulrike Oster, and Christoph F. Beck Nucleic Acids Res. 2006 October; 34(17): 4767–4779. Published online 2006 September 13. doi: 10.1093/nar/gkl602.PMCID: PMC1635268 Zfp206 regulates ES cell gene expression and differentiation Wen Zhang, Emily Walker, Owen J. Tamplin, Janet Rossant, William L. Stanford, and Timothy R. Hughes Nucleic Acids Res. 2006 October; 34(17): 4780–4790. Published online 2006 September 13. doi: 10.1093/nar/gkl631.PMCID: PMC1635278 Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells Daniela Schmitter, Jody Filkowski, Alain Sewer, Ramesh S. Pillai, Edward J. Oakeley, Mihaela Zavolan, Petr Svoboda, and Witold Filipowicz Nucleic Acids Res. 2006 October; 34(17): 4801–4815. Published online 2006 September 13. doi: 10.1093/nar/gkl646.PMCID: PMC1635286 A novel archaeal regulatory protein, Sta1, activates transcription from viral promoters Alexandra Kessler, Guennadi Sezonov, J. Iñaki Guijarro, Nicole Desnoues, Thierry Rose, Muriel Delepierre, Stephen D. Bell, and David Prangishvili Nucleic Acids Res. 2006 October; 34(17): 4837–4845. Published online 2006 August 14. doi: 10.1093/nar/gkl502.PMCID: PMC1635249 Isolation and characterization of the TIGA genes, whose transcripts are induced by growth arrest Norikazu Yabuta, Hiroaki Onda, Masafumi Watanabe, Naohisa Yoshioka, Ippei Nagamori, Tomoyuki Funatsu, Shingo Toji, Katsuyuki Tamai, and Hiroshi Nojima Nucleic Acids Res. 2006 October; 34(17): 4878–4892. Published online 2006 September 14. doi: 10.1093/nar/gkl651.PMCID: PMC1635288 Identification of a structural and functional domain in xNAP1 involved in protein–protein interactions Christine Friedeberg, Garry Scarlett, John McGeeghan, Anita Abu-daya, Matthew Guille, and Geoff Kneale Nucleic Acids Res. 2006 October; 34(17): 4893–4899. Published online 2006 September 18. doi: 10.1093/nar/gkl434.PMCID: PMC1635243 A peptide with alternating lysines can act as a highly specific Z-DNA binding domain Yang-Gyun Kim, Hyun-Ju Park, Kyeong Kyu Kim, Ky Lowenhaupt, and Alexander Rich Nucleic Acids Res. 2006 October; 34(17): 4937–4942. Published online 2006 September 18. doi: 10.1093/nar/gkl607.PMCID: PMC1635270 XE7: A novel splicing factor that interacts with ASF/SF2 and ZNF265 A. Helena Mangs, Helen J.L. Speirs, Christine Goy, David J. Adams, M. Andrea Markus, and Brian J. Morris Nucleic Acids Res. 2006 October; 34(17): 4976–4986. Published online 2006 September 18. doi: 10.1093/nar/gkl660.PMCID: PMC1635291 CTD kinase I is required for the integrity of the rDNA tandem array Sabrina Grenetier, Céline Bouchoux, and Valérie Goguel Nucleic Acids Res. 2006 October; 34(17): 4996–5006. Published online 2006 August 19. doi: 10.1093/nar/gkl493.PMCID: PMC1635248 RNA Exportin-5 orthologues are functionally divergent among species Satoshi Shibata, Mitsuho Sasaki, Takashi Miki, Akira Shimamoto, Yasuhiro Furuichi, Jun Katahira, and Yoshihiro Yoneda Nucleic Acids Res. 2006 October; 34(17): 4711–4721. Published online 2006 September 8. doi: 10.1093/nar/gkl663.PMCID: PMC1635293 Amino acid residues critical for RNA-binding in the N-terminal domain of the nucleocapsid protein are essential determinants for the infectivity of coronavirus in cultured cells Yong Wah Tan, Shouguo Fang, Hui Fan, Julien Lescar, and D.X. Liu Nucleic Acids Res. 2006 October; 34(17): 4816–4825. Published online 2006 September 13. doi: 10.1093/nar/gkl650.PMCID: PMC1635287 Controlling activation of the RNA-dependent protein kinase by siRNAs using site-specific chemical modification Sujiet Puthenveetil, Landon Whitby, Jin Ren, Kevin Kelnar, Joseph F. Krebs, and Peter A. Beal Nucleic Acids Res. 2006 October; 34(17): 4900–4911. Published online 2006 September 18. doi: 10.1093/nar/gkl464.PMCID: PMC1635244 A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation Zhi John Lu, Douglas H. Turner, and David H. Mathews Nucleic Acids Res. 2006 October; 34(17): 4912–4924. Published online 2006 August 18. doi: 10.1093/nar/gkl472.PMCID: PMC1635246 Examination of the structural and functional versatility of glmS ribozymes by using in vitro selection Kristian H. Link, Lixia Guo, and Ronald R. Breaker Nucleic Acids Res. 2006 October; 34(17): 4968–4975. Published online 2006 September 18. doi: 10.1093/nar/gkl643.PMCID: PMC1635283 Binding of human SLBP on the 3′-UTR of histone precursor H4-12 mRNA induces structural rearrangements that enable U7 snRNA anchoring Sophie Jaeger, Franck Martin, Joëlle Rudinger-Thirion, Richard Giegé, and Gilbert Eriani Nucleic Acids Res. 2006 October; 34(17): 4987–4995. Published online 2006 September 18. doi: 10.1093/nar/gkl666.PMCID: PMC1635294 Structural Biology Site-directed spin labeling measurements of nanometer distances in nucleic acids using a sequence-independent nitroxide probe Qi Cai, Ana Karin Kusnetzow, Wayne L. Hubbell, Ian S. Haworth, Gian Paola C. Gacho, Ned Van Eps, Kálmán Hideg, Eric J. Chambers, and Peter Z. Qin Nucleic Acids Res. 2006 October; 34(17): 4722–4730. Published online 2006 August 10. doi: 10.1093/nar/gkl546.PMCID: PMC1635252 DNA bending by bHLH charge variants Robert J. McDonald, Jason D. Kahn, and L. James Maher, III Nucleic Acids Res. 2006 October; 34(17): 4846–4856. Published online 2006 September 14. doi: 10.1093/nar/gkl552.PMCID: PMC1635255 Survey and Summary Spatial organization of transcription by RNA polymerase III Rebecca A. Haeusler and David R. Engelke Nucleic Acids Res. 2006 October; 34(17): 4826–4836. Published online 2006 October. doi: 10.1093/nar/gkl656.PMCID: PMC1635290 Sequence-specific binding of single-stranded RNA: is there a code for recognition? Sigrid D. Auweter, Florian C. Oberstrass, and Frédéric H.-T. Allain Nucleic Acids Res. 2006 October; 34(17): 4943–4959. Published online 2006 September 18. doi: 10.1093/nar/gkl620.PMCID: PMC1635273 Genomics Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae Cathryn Rehmeyer, Weixi Li, Motoaki Kusaba, Yun-Sik Kim, Doug Brown, Chuck Staben, Ralph Dean, and Mark Farman Nucleic Acids Res. 2006 October; 34(17): 4685–4701. Published online 2006 September 8. doi: 10.1093/nar/gkl588.PMCID: PMC1635262 Transcriptome response to heavy metal stress in Drosophila reveals a new zinc transporter that confers resistance to zinc Hasmik Yepiskoposyan, Dieter Egli, Tim Fergestad, Anand Selvaraj, Carina Treiber, Gerd Multhaup, Oleg Georgiev, and Walter Schaffner Nucleic Acids Res. 2006 October; 34(17): 4866–4877. Published online 2006 September 14. doi: 10.1093/nar/gkl606.PMCID: PMC1635269 Chemistry Dynamic assembly of primers on nucleic acid templates Nicole A. Leal, Makoto Sukeda, and Steven A. Benner Nucleic Acids Res. 2006 October; 34(17): 4702–4710. Published online 2006 September 8. doi: 10.1093/nar/gkl625.PMCID: PMC1635275 Methods Online Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection Dylan Chivian and David Baker Nucleic Acids Res. 2006 October; 34(17): e112. Published online 2006 August 13. doi: 10.1093/nar/gkl480.PMCID: PMC1635247 A simple DNA stretching method for fluorescence imaging of single DNA molecules Ting-Fung Chan, Connie Ha, Angie Phong, Dongmei Cai, Eunice Wan, Lucinda Leung, Pui-Yan Kwok, and Ming Xiao Nucleic Acids Res. 2006 October; 34(17): e113. Published online 2006 September 13. doi: 10.1093/nar/gkl593.PMCID: PMC1635263 A spreadable, non-integrative and high copy number shuttle vector for Sulfolobus solfataricus based on the genetic element pSSVx from Sulfolobus islandicus Tiziana Aucelli, Patrizia Contursi, Michele Girfoglio, Mosè Rossi, and Raffaele Cannio Nucleic Acids Res. 2006 October; 34(17): e114. Published online 2006 September 13. doi: 10.1093/nar/gkl615.PMCID: PMC1635272 Mouse microRNA profiles determined with a new and sensitive cloning method Shuji Takada, Eugene Berezikov, Yoshihiro Yamashita, Mariana Lagos-Quintana, Wigard P. Kloosterman, Munehiro Enomoto, Hisashi Hatanaka, Shin-ichiro Fujiwara, Hideki Watanabe, Manabu Soda, Young Lim Choi, Ronald H. A. Plasterk, Edwin Cuppen, and Hiroyuki Mano Nucleic Acids Res. 2006 October; 34(17): e115. Published online 2006 October. doi: 10.1093/nar/gkl653.PMCID: PMC1635289 AccuTyping: new algorithms for automated analysis of data from high-throughput genotyping with oligonucleotide microarrays Guohong Hu, Hui-Yun Wang, Danielle M. Greenawalt, Marco A. Azaro, Minjie Luo, Irina V. Tereshchenko, Xiangfeng Cui, Qifeng Yang, Richeng Gao, Li Shen, and Honghua Li Nucleic Acids Res. 2006 October; 34(17): e116. Published online 2006 September 18. doi: 10.1093/nar/gkl601.PMCID: PMC1635267 Using RNA secondary structures to guide sequence motif finding towards single-stranded regions Michael Hiller, Rainer Pudimat, Anke Busch, and Rolf Backofen Nucleic Acids Res. 2006 October; 34(17): e117. Published online 2006 August 20. doi: 10.1093/nar/gkl544.PMCID: PMC1903381 Computational Biology PLPD: reliable protein localization prediction from imbalanced and overlapped datasets KiYoung Lee, Dae-Won Kim, DoKyun Na, Kwang H. Lee, and Doheon Lee Nucleic Acids Res. 2006 October; 34(17): 4655–4666. Published online 2006 September 11. doi: 10.1093/nar/gkl638.PMCID: PMC1636404 Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues Xueping Yu, Jimmy Lin, Donald J. Zack, and Jiang Qian Nucleic Acids Res. 2006 October; 34(17): 4925–4936. Published online 2006 September 18. doi: 10.1093/nar/gkl595.PMCID: PMC1635265 Genetic regulation of fluxes: iron homeostasis of Escherichia coli Szabolcs Semsey, Anna M. C. Andersson, Sandeep Krishna, Mogens Høgh Jensen, Eric Massé, and Kim Sneppen Nucleic Acids Res. 2006 October; 34(17): 4960–4967. Published online 2006 September 18. doi: 10.1093/nar/gkl627.PMCID: PMC1635276 Nucleic Acid Enzymes A strand-passage conformation of DNA gyrase is required to allow the bacterial toxin, CcdB, to access its binding site Andrew B. Smith and Anthony Maxwell Nucleic Acids Res. 2006 October; 34(17): 4667–4676. Published online 2006 September 8. doi: 10.1093/nar/gkl636.PMCID: PMC1635281 The fidelity of DNA synthesis by yeast DNA polymerase zeta alone and with accessory proteins Xuejun Zhong, Parie Garg, Carrie M. Stith, Stephanie A. Nick McElhinny, Grace E. Kissling, Peter M. J. Burgers, and Thomas A. Kunkel Nucleic Acids Res. 2006 October; 34(17): 4731–4742. Published online 2006 September 13. doi: 10.1093/nar/gkl465.PMCID: PMC1635245 Biochemical analysis of the substrate specificity and sequence preference of endonuclease IV from bacteriophage T4, a dC-specific endonuclease implicated in restriction of dC-substituted T4 DNA synthesis Nobutaka Hirano, Hiroyuki Ohshima, and Hideo Takahashi Nucleic Acids Res. 2006 October; 34(17): 4743–4751. Published online 2006 September 13. doi: 10.1093/nar/gkl553.PMCID: PMC1635256 Homing endonuclease I-CreI derivatives with novel DNA target specificities Laura E. Rosen, Holly A. Morrison, Selma Masri, Michael J. Brown, Brendan Springstubb, Django Sussman, Barry L. Stoddard, and Lenny M. Seligman Nucleic Acids Res. 2006 October; 34(17): 4791–4800. Published online 2006 September 13. doi: 10.1093/nar/gkl645.PMCID: PMC1635285 Human replication protein A unfolds telomeric G-quadruplexes Tonatiuh Romero Salas, Irina Petruseva, Olga Lavrik, Anne Bourdoncle, Jean-Louis Mergny, Alain Favre, and Carole Saintomé Nucleic Acids Res. 2006 October; 34(17): 4857–4865. Published online 2006 September 14. doi: 10.1093/nar/gkl564.PMCID: PMC1635258 |