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Previous Next 		Contents: Volume 36, Number 16, September 2008   [Index by Author] 

Down Survey and Summary
Down Computational Biology
Down Gene regulation, Chromatin and Epigenetics
Down Genome integrity, repair and replication
Down Genomics
Down Molecular Biology
Down Nucleic Acid Enzymes
Down RNA
Down Structural Biology
Down Corrigendum
Down Methods Online


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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.

Survey and Summary Back

Maria Duca, Pierre Vekhoff, Kahina Oussedik, Ludovic Halby, and Paola B. Arimondo
The triple helix: 50 years later, the outcome
Nucleic Acids Research Advance Access published on August 1, 2008
Nucl. Acids Res. 2008 36: 5123-5138; doi:10.1093/nar/gkn493 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Computational Biology Back

Raja Jothi, Suresh Cuddapah, Artem Barski, Kairong Cui, and Keji Zhao
Genome-wide identification of in vivo protein–DNA binding sites from ChIP-Seq data
Nucleic Acids Research Advance Access published on August 6, 2008
Nucl. Acids Res. 2008 36: 5221-5231; doi:10.1093/nar/gkn488 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jiajian Liu, Xing Xu, and Gary D. Stormo
The cis-regulatory map of Shewanella genomes
Nucleic Acids Research Advance Access published on August 13, 2008
Nucl. Acids Res. 2008 36: 5376-5390; doi:10.1093/nar/gkn515 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gene regulation, Chromatin and Epigenetics Back

Sailen Barik
An intronic microRNA silences genes that are functionally antagonistic to its host gene
Nucleic Acids Research Advance Access published on August 6, 2008
Nucl. Acids Res. 2008 36: 5232-5241; doi:10.1093/nar/gkn513 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Catherine Teyssier, Stéphanie Bianco, Olivia Lanvin, and Jean-Marc Vanacker
The orphan receptor ERR{alpha} interferes with steroid signaling
Nucleic Acids Research Advance Access published on August 12, 2008
Nucl. Acids Res. 2008 36: 5350-5361; doi:10.1093/nar/gkn520 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Genome integrity, repair and replication Back

Nives Selak, Csanád Z. Bachrati, Igor Shevelev, Tobias Dietschy, Barbara van Loon, Anette Jacob, Ulrich Hübscher, Joerg D. Hoheisel, Ian D. Hickson, and Igor Stagljar
The Bloom's syndrome helicase (BLM) interacts physically and functionally with p12, the smallest subunit of human DNA polymerase {delta}
Nucleic Acids Research Advance Access published on August 5, 2008
Nucl. Acids Res. 2008 36: 5166-5179; doi:10.1093/nar/gkn498 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Anja Restle, Martin Färber, Cindy Baumann, Michael Böhringer, Karl Heinz Scheidtmann, Carsten Müller-Tidow, and Lisa Wiesmüller
Dissecting the role of p53 phosphorylation in homologous recombination provides new clues for gain-of-function mutants
Nucleic Acids Research Advance Access published on August 12, 2008
Nucl. Acids Res. 2008 36: 5362-5375; doi:10.1093/nar/gkn503 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics Back

Chaysavanh Manichanh, Charles E. Chapple, Lionel Frangeul, Karine Gloux, Roderic Guigo, and Joel Dore
A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library
Nucleic Acids Research Advance Access published on August 5, 2008
Nucl. Acids Res. 2008 36: 5180-5188; doi:10.1093/nar/gkn496 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology Back

Seema Patel, Roger George, Flavia Autore, Franca Fraternali, John E. Ladbury, and Penka V. Nikolova
Molecular interactions of ASPP1 and ASPP2 with the p53 protein family and the apoptotic promoters PUMA and Bax
Nucleic Acids Research Advance Access published on August 2, 2008
Nucl. Acids Res. 2008 36: 5139-5151; doi:10.1093/nar/gkn490 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jana Prikryl, Kenneth P. Watkins, Giulia Friso, Klaas J. van Wijk, and Alice Barkan
A member of the Whirly family is a multifunctional RNA- and DNA-binding protein that is essential for chloroplast biogenesis
Nucleic Acids Research Advance Access published on August 2, 2008
Nucl. Acids Res. 2008 36: 5152-5165; doi:10.1093/nar/gkn492 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Yanfei Zou and Xin Bi
Positive roles of SAS2 in DNA replication and transcriptional silencing in yeast
Nucleic Acids Research Advance Access published on August 5, 2008
Nucl. Acids Res. 2008 36: 5189-5200; doi:10.1093/nar/gkn465 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Abrahem Abrahem and Martin Pelchat
Formation of an RNA polymerase II preinitiation complex on an RNA promoter derived from the hepatitis delta virus RNA genome
Nucleic Acids Research Advance Access published on August 5, 2008
Nucl. Acids Res. 2008 36: 5201-5211; doi:10.1093/nar/gkn501 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Cristina Cañas, Begoña Carrasco, Silvia Ayora, and Juan C. Alonso
The RecU Holliday junction resolvase acts at early stages of homologous recombination
Nucleic Acids Research Advance Access published on August 6, 2008
Nucl. Acids Res. 2008 36: 5242-5249; doi:10.1093/nar/gkn500 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Junko Kimura, Su Tien Nguyen, Hanshao Liu, Naoe Taira, Yoshio Miki, and Kiyotsugu Yoshida
A functional genome-wide RNAi screen identifies TAF1 as a regulator for apoptosis in response to genotoxic stress
Nucleic Acids Research Advance Access published on August 6, 2008
Nucl. Acids Res. 2008 36: 5250-5259; doi:10.1093/nar/gkn506 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Munehiko Asayama and Sousuke Imamura
Stringent promoter recognition and autoregulation by the group 3 {sigma}-factor SigF in the cyanobacterium Synechocystis sp. strain PCC 6803
Nucleic Acids Research Advance Access published on August 8, 2008
Nucl. Acids Res. 2008 36: 5297-5305; doi:10.1093/nar/gkn453 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tariq Perwez, Danyal Hami, Valerie F. Maples, Zhao Min, Bi-Cheng Wang, and Sidney R. Kushner
Intragenic suppressors of temperature-sensitive rne mutations lead to the dissociation of RNase E activity on mRNA and tRNA substrates in Escherichia coli
Nucleic Acids Research Advance Access published on August 8, 2008
Nucl. Acids Res. 2008 36: 5306-5318; doi:10.1093/nar/gkn476 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Na Liu, Lifeng Wang, Xia Li, Qi Yang, Xinping Liu, Jing Zhang, Jian Zhang, Yousheng Wu, Shaoping Ji, Yingqi Zhang, Angang Yang, Hua Han, and Libo Yao
N-Myc downstream-regulated gene 2 is involved in p53-mediated apoptosis
Nucleic Acids Research Advance Access published on August 9, 2008
Nucl. Acids Res. 2008 36: 5335-5349; doi:10.1093/nar/gkn504 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes Back

Andrea Just, Falk Butter, Michelle Trenkmann, Tony Heitkam, Mario Mörl, and Heike Betat
A comparative analysis of two conserved motifs in bacterial poly(A) polymerase and CCA-adding enzyme
Nucleic Acids Research Advance Access published on August 5, 2008
Nucl. Acids Res. 2008 36: 5212-5220; doi:10.1093/nar/gkn494 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Marilynn A. Larson, Rafael Bressani, Khalid Sayood, Jacob E. Corn, James M. Berger, Mark A. Griep, and Steven H. Hinrichs
Hyperthermophilic Aquifex aeolicus initiates primer synthesis on a limited set of trinucleotides comprised of cytosines and guanines
Nucleic Acids Research Advance Access published on August 6, 2008
Nucl. Acids Res. 2008 36: 5260-5269; doi:10.1093/nar/gkn461 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kevin V. Kepple, Namita Patel, Peter Salamon, and Anca M. Segall
Interactions between branched DNAs and peptide inhibitors of DNA repair
Nucleic Acids Research Advance Access published on August 8, 2008
Nucl. Acids Res. 2008 36: 5319-5334; doi:10.1093/nar/gkn512 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Michael A. Carpenter and Ashok S. Bhagwat
DNA base flipping by both members of the PspGI restriction–modification system
Nucleic Acids Research Advance Access published on August 20, 2008
Nucl. Acids Res. 2008 36: 5417-5425; doi:10.1093/nar/gkn528 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA Back

Yukio Kawahara, Molly Megraw, Edward Kreider, Hisashi Iizasa, Louis Valente, Artemis G. Hatzigeorgiou, and Kazuko Nishikura
Frequency and fate of microRNA editing in human brain
Nucleic Acids Research Advance Access published on August 6, 2008
Nucl. Acids Res. 2008 36: 5270-5280; doi:10.1093/nar/gkn479 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

P. Patrick Dotson, II, Ashley K. Johnson, and Stephen M. Testa
Tetrahymena thermophila and Candida albicans Group I intron-derived ribozymes can catalyze the trans-excision-splicing reaction
Nucleic Acids Research Advance Access published on August 6, 2008
Nucl. Acids Res. 2008 36: 5281-5289; doi:10.1093/nar/gkn507 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

María Flor García-Mayoral, Irene Díaz-Moreno, David Hollingworth, and Andres Ramos
The sequence selectivity of KSRP explains its flexibility in the recognition of the RNA targets
Nucleic Acids Research Advance Access published on August 6, 2008
Nucl. Acids Res. 2008 36: 5290-5296; doi:10.1093/nar/gkn509 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Qin Liu, Hanjiang Fu, Fang Sun, Haoming Zhang, Yi Tie, Jie Zhu, Ruiyun Xing, Zhixian Sun, and Xiaofei Zheng
miR-16 family induces cell cycle arrest by regulating multiple cell cycle genes
Nucleic Acids Research Advance Access published on August 13, 2008
Nucl. Acids Res. 2008 36: 5391-5404; doi:10.1093/nar/gkn522 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology Back

Pete W. Dunten, Elizabeth J. Little, Mark T. Gregory, Veena M. Manohar, Michael Dalton, David Hough, Jurate Bitinaite, and Nancy C. Horton
The structure of SgrAI bound to DNA; recognition of an 8 base pair target
Nucleic Acids Research Advance Access published on August 13, 2008
Nucl. Acids Res. 2008 36: 5405-5416; doi:10.1093/nar/gkn510 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Corrigendum Back

Takuma Gondai, Kazuya Yamaguchi, Naoko Miyano-Kurosaki, Yuichirou Habu, and Hiroshi Takaku
Short-hairpin RNAs synthesized by T7 phage polymerase do not induce interferon
Nucl. Acids Res. 2008 36: 5426; doi:10.1093/nar/gkn547 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online Back

Omid R. Faridani, Gerald M. McInerney, Katarina Gradin, and Liam Good
Specific ligation to double-stranded RNA for analysis of cellular RNA::RNA interactions
Nucleic Acids Research Advance Access published on July 15, 2008
Nucl. Acids Res. 2008 36: e99; doi:10.1093/nar/gkn445 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Kate E. Coldwell, Suzanne M. Cutts, Ted J. Ognibene, Paul T. Henderson, and Don R. Phillips
Detection of Adriamycin–DNA adducts by accelerator mass spectrometry at clinically relevant Adriamycin concentrations
Nucleic Acids Research Advance Access published on July 16, 2008
Nucl. Acids Res. 2008 36: e100; doi:10.1093/nar/gkn439 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

David Greber, Marie Daoud El-Baba, and Martin Fussenegger
Intronically encoded siRNAs improve dynamic range of mammalian gene regulation systems and toggle switch
Nucleic Acids Research Advance Access published on July 16, 2008
Nucl. Acids Res. 2008 36: e101; doi:10.1093/nar/gkn443 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ju Young Lee, Bong Hyun Sung, Byung Jo Yu, Jun Hyoung Lee, Sang Hee Lee, Mi Sun Kim, Michael D. Koob, and Sun Chang Kim
Phenotypic engineering by reprogramming gene transcription using novel artificial transcription factors in Escherichia coli
Nucleic Acids Research Advance Access published on July 18, 2008
Nucl. Acids Res. 2008 36: e102; doi:10.1093/nar/gkn449 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Chae-Ok Yun, Hyun-Chul Shin, Tae-Dong Kim, Wan-Hee Yoon, Yoon-A Kang, Heung-Sun Kwon, Seong Keun Kim, and Jin-Soo Kim
Transduction of artificial transcriptional regulatory proteins into human cells
Nucleic Acids Research Advance Access published on July 21, 2008
Nucl. Acids Res. 2008 36: e103; doi:10.1093/nar/gkn398 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

M. van den Hout, S. Hage, C. Dekker, and N. H. Dekker
End-joining long nucleic acid polymers
Nucleic Acids Research Advance Access published on July 25, 2008
Nucl. Acids Res. 2008 36: e104; doi:10.1093/nar/gkn442 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Juliane C. Dohm, Claudio Lottaz, Tatiana Borodina, and Heinz Himmelbauer
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
Nucleic Acids Research Advance Access published on July 26, 2008
Nucl. Acids Res. 2008 36: e105; doi:10.1093/nar/gkn425 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

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.