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Previous 		Contents: Volume 36, Number 13, August 2008   [Index by Author] 

Down Editorial
Down Survey and Summary
Down Chemistry and Synthetic Biology
Down Computational Biology
Down Gene Regulation, Chromatin and Epigenetics
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Down Nucleic Acid Enzymes
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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.

Editorial Back

Editorial
Nucl. Acids Res. 2008 36: 4221; doi:10.1093/nar/gkn478 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Survey and Summary Back

Joost van Mameren, Erwin J. G. Peterman, and Gijs J. L. Wuite
See me, feel me: methods to concurrently visualize and manipulate single DNA molecules and associated proteins
Nucleic Acids Research Advance Access published on June 27, 2008
Nucl. Acids Res. 2008 36: 4381-4389; doi:10.1093/nar/gkn412 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chemistry and Synthetic Biology Back

Masayasu Kuwahara, Satoshi Obika, Jun-ichi Nagashima, Yuki Ohta, Yoshiyuki Suto, Hiroaki Ozaki, Hiroaki Sawai, and Takeshi Imanishi
Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2',4'-bridged nucleosides
Nucleic Acids Research Advance Access published on June 26, 2008
Nucl. Acids Res. 2008 36: 4257-4265; doi:10.1093/nar/gkn404 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology Back

S. Pitre, C. North, M. Alamgir, M. Jessulat, A. Chan, X. Luo, J. R. Green, M. Dumontier, F. Dehne, and A. Golshani
Global investigation of protein–protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences
Nucleic Acids Research Advance Access published on June 27, 2008
Nucl. Acids Res. 2008 36: 4286-4294; doi:10.1093/nar/gkn390 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jianfei Hu, Haiyan Hu, and Xiaoman Li
MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs
Nucleic Acids Research Advance Access published on July 7, 2008
Nucl. Acids Res. 2008 36: 4488-4497; doi:10.1093/nar/gkn407 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gene Regulation, Chromatin and Epigenetics Back

Carmen Spatuzza, Marco Schiavone, Emanuela Di Salle, Elzbieta Janda, Marco Sardiello, Giuseppe Fiume, Olga Fierro, Marco Simonetta, Notis Argiriou, Raffaella Faraonio, Rosanna Capparelli, Ileana Quinto, and Giuseppe Scala
Physical and functional characterization of the genetic locus of IBtk, an inhibitor of Bruton's tyrosine kinase: evidence for three protein isoforms of IBtk
Nucleic Acids Research Advance Access published on July 2, 2008
Nucl. Acids Res. 2008 36: 4402-4416; doi:10.1093/nar/gkn413 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Wen Hong Toh, Emmanuelle Logette, Laurent Corcos, and Kanaga Sabapathy
TAp73β and DNp73β activate the expression of the pro-survival caspase-2S
Nucleic Acids Research Advance Access published on July 8, 2008
Nucl. Acids Res. 2008 36: 4498-4509; doi:10.1093/nar/gkn414 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Sutapa Ray, Chang Lee, Tieying Hou, Istvan Boldogh, and Allan R. Brasier
Requirement of histone deacetylase1 (HDAC1) in signal transducer and activator of transcription 3 (STAT3) nucleocytoplasmic distribution
Nucleic Acids Research Advance Access published on July 8, 2008
Nucl. Acids Res. 2008 36: 4510-4520; doi:10.1093/nar/gkn419 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Genomics Back

David Benovoy, Tony Kwan, and Jacek Majewski
Effect of polymorphisms within probe–target sequences on olignonucleotide microarray experiments
Nucleic Acids Research Advance Access published on July 2, 2008
Nucl. Acids Res. 2008 36: 4417-4423; doi:10.1093/nar/gkn409 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology Back

Emilie Horvilleur, Matthieu Bauer, David Goldschneider, Xénia Mergui, Alix de La Motte, Jean Bénard, Sétha Douc-Rasy, and David Cappellen
p73{alpha} isoforms drive opposite transcriptional and post-transcriptional regulation of MYCN expression in neuroblastoma cells
Nucleic Acids Research Advance Access published on June 25, 2008
Nucl. Acids Res. 2008 36: 4222-4232; doi:10.1093/nar/gkn394 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Eva Jacinto-Loeza, Serafín Vivanco-Domínguez, Gabriel Guarneros, and Javier Hernández-Sánchez
Minigene-like inhibition of protein synthesis mediated by hungry codons near the start codon
Nucleic Acids Research Advance Access published on June 25, 2008
Nucl. Acids Res. 2008 36: 4233-4241; doi:10.1093/nar/gkn395 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Isao Sakane, Chiaki Kamataki, Yoshimasa Takizawa, Marina Nakashima, Seiichi Toki, Hiroaki Ichikawa, Shukuko Ikawa, Takehiko Shibata, and Hitoshi Kurumizaka
Filament formation and robust strand exchange activities of the rice DMC1A and DMC1B proteins
Nucleic Acids Research Advance Access published on June 26, 2008
Nucl. Acids Res. 2008 36: 4266-4276; doi:10.1093/nar/gkn405 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Dong-Liang Huang, Dong-Jie Tang, Qing Liao, Heng-Cong Li, Qi Chen, Yong-Qiang He, Jia-Xun Feng, Bo-Le Jiang, Guang-Tao Lu, Baoshan Chen, and Ji-Liang Tang
The Zur of Xanthomonas campestris functions as a repressor and an activator of putative zinc homeostasis genes via recognizing two distinct sequences within its target promoters
Nucleic Acids Research Advance Access published on June 27, 2008
Nucl. Acids Res. 2008 36: 4295-4309; doi:10.1093/nar/gkn328 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Sugopa Sengupta and Valakunja Nagaraja
YacG from Escherichia coli is a specific endogenous inhibitor of DNA gyrase
Nucleic Acids Research Advance Access published on June 27, 2008
Nucl. Acids Res. 2008 36: 4310-4316; doi:10.1093/nar/gkn355 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Laura M. McLane, Kanika F. Pulliam, Scott E. Devine, and Anita H. Corbett
The Ty1 integrase protein can exploit the classical nuclear protein import machinery for entry into the nucleus
Nucleic Acids Research Advance Access published on June 27, 2008
Nucl. Acids Res. 2008 36: 4317-4326; doi:10.1093/nar/gkn383 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kozue Ando, Satoshi Hirao, Yasuaki Kabe, Yuji Ogura, Iwao Sato, Yuki Yamaguchi, Tadashi Wada, and Hiroshi Handa
A new APE1/Ref-1-dependent pathway leading to reduction of NF-{kappa}B and AP-1, and activation of their DNA-binding activity
Nucleic Acids Research Advance Access published on June 27, 2008
Nucl. Acids Res. 2008 36: 4327-4336; doi:10.1093/nar/gkn416 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Liang-Yi Hung, Joseph T. Tseng, Yi-Chao Lee, Weiya Xia, Ying-Nai Wang, Min-Li Wu, Yu-Hsuan Chuang, Chein-Hsien Lai, and Wen-Chang Chang
Nuclear epidermal growth factor receptor (EGFR) interacts with signal transducer and activator of transcription 5 (STAT5) in activating Aurora-A gene expression
Nucleic Acids Research Advance Access published on June 27, 2008
Nucl. Acids Res. 2008 36: 4337-4351; doi:10.1093/nar/gkn417 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Takehiko Shiraishi, Ramin Hamzavi, and Peter E. Nielsen
Subnanomolar antisense activity of phosphonate-peptide nucleic acid (PNA) conjugates delivered by cationic lipids to HeLa cells
Nucleic Acids Research Advance Access published on July 2, 2008
Nucl. Acids Res. 2008 36: 4424-4432; doi:10.1093/nar/gkn401 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Luchezar Karagyozov, Rinesh Godfrey, Sylvia-Annette Böhmer, Astrid Petermann, Sebastian Hölters, Arne Östman, and Frank-D. Böhmer
The structure of the 5'-end of the protein-tyrosine phosphatase PTPRJ mRNA reveals a novel mechanism for translation attenuation
Nucleic Acids Research Advance Access published on July 4, 2008
Nucl. Acids Res. 2008 36: 4443-4453; doi:10.1093/nar/gkn391 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Camille Godon, Fabrice P. Cordelières, Denis Biard, Nicole Giocanti, Frédérique Mégnin-Chanet, Janet Hall, and Vincent Favaudon
PARP inhibition versus PARP-1 silencing: different outcomes in terms of single-strand break repair and radiation susceptibility
Nucleic Acids Research Advance Access published on July 4, 2008
Nucl. Acids Res. 2008 36: 4454-4464; doi:10.1093/nar/gkn403 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nucleic Acid Enzymes Back

Gregory Sowd, Ming Lei, and Patricia L. Opresko
Mechanism and substrate specificity of telomeric protein POT1 stimulation of the Werner syndrome helicase
Nucleic Acids Research Advance Access published on June 25, 2008
Nucl. Acids Res. 2008 36: 4242-4256; doi:10.1093/nar/gkn385 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Moritz Niemann, Michael Brecht, Elke Schlüter, Kerstin Weitzel, Martin Zacharias, and H. Ulrich Göringer
TbMP42 is a structure-sensitive ribonuclease that likely follows a metal ion catalysis mechanism
Nucleic Acids Research Advance Access published on July 4, 2008
Nucl. Acids Res. 2008 36: 4465-4473; doi:10.1093/nar/gkn410 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

RNA Back

Nan Li, Alex S. Flynt, H. Rosemary Kim, Lilianna Solnica-Krezel, and James G. Patton
Dispatched Homolog 2 is targeted by miR-214 through a combination of three weak microRNA recognition sites
Nucleic Acids Research Advance Access published on June 26, 2008
Nucl. Acids Res. 2008 36: 4277-4285; doi:10.1093/nar/gkn388 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Martine M. Vrolijk, Marcel Ooms, Alex Harwig, Atze T. Das, and Ben Berkhout
Destabilization of the TAR hairpin affects the structure and function of the HIV-1 leader RNA
Nucleic Acids Research Advance Access published on June 27, 2008
Nucl. Acids Res. 2008 36: 4352-4363; doi:10.1093/nar/gkn364 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Åsa Segerstolpe, Pär Lundkvist, Yvonne N. Osheim, Ann L. Beyer, and Lars Wieslander
Mrd1p binds to pre-rRNA early during transcription independent of U3 snoRNA and is required for compaction of the pre-rRNA into small subunit processomes
Nucleic Acids Research Advance Access published on June 27, 2008
Nucl. Acids Res. 2008 36: 4364-4380; doi:10.1093/nar/gkn384 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kirsi Paukku, Nisse Kalkkinen, Olli Silvennoinen, Kimmo K. Kontula, and Jukka Y. A. Lehtonen
p100 increases AT1R expression through interaction with AT1R 3'-UTR
Nucleic Acids Research Advance Access published on July 4, 2008
Nucl. Acids Res. 2008 36: 4474-4487; doi:10.1093/nar/gkn411 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Structural Biology Back

Marcus Resch, Harald Striegl, Eva Maria Henssler, Madhumati Sevvana, Claudia Egerer-Sieber, Emile Schiltz, Wolfgang Hillen, and Yves A. Muller
A protein functional leap: how a single mutation reverses the function of the transcription regulator TetR
Nucleic Acids Research Advance Access published on June 28, 2008
Nucl. Acids Res. 2008 36: 4390-4401; doi:10.1093/nar/gkn400 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Niti Kumar, Bankanidhi Sahoo, K. A. S. Varun, Sudipta Maiti, and Souvik Maiti
Effect of loop length variation on quadruplex-Watson Crick duplex competition
Nucleic Acids Research Advance Access published on July 3, 2008
Nucl. Acids Res. 2008 36: 4433-4442; doi:10.1093/nar/gkn402 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online Back

Amy J. Baldwin, Kathy Busse, Alan M. Simm, and D. Dafydd Jones
Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx)
Nucleic Acids Research Advance Access published on June 17, 2008
Nucl. Acids Res. 2008 36: e77; doi:10.1093/nar/gkn358 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Wayne R. Edwards, Kathy Busse, Rudolf K. Allemann, and D. Dafydd Jones
Linking the functions of unrelated proteins using a novel directed evolution domain insertion method
Nucleic Acids Research Advance Access published on June 17, 2008
Nucl. Acids Res. 2008 36: e78; doi:10.1093/nar/gkn363 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Ying Li, Hyun-Jin Kim, Chunyang Zheng, Wing Huen A. Chow, Jeonghwa Lim, Brendan Keenan, Xiaojing Pan, Bertrand Lemieux, and Huimin Kong
Primase-based whole genome amplification
Nucleic Acids Research Advance Access published on June 17, 2008
Nucl. Acids Res. 2008 36: e79; doi:10.1093/nar/gkn377 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

T. J. Pugh, A. D. Delaney, N. Farnoud, S. Flibotte, M. Griffith, H. I. Li, H. Qian, P. Farinha, R. D. Gascoyne, and M. A. Marra
Impact of whole genome amplification on analysis of copy number variants
Nucleic Acids Research Advance Access published on June 17, 2008
Nucl. Acids Res. 2008 36: e80; doi:10.1093/nar/gkn378 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Junichi Ryu and Edward Rowsell
Quick identification of Type I restriction enzyme isoschizomers using newly developed pTypeI and reference plasmids
Nucleic Acids Research Advance Access published on June 18, 2008
Nucl. Acids Res. 2008 36: e81; doi:10.1093/nar/gkn056 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Daniel J. Turner, Chris Tyler-Smith, and Matthew E. Hurles
Long-range, high-throughput haplotype determination via haplotype-fusion PCR and ligation haplotyping
Nucleic Acids Research Advance Access published on June 18, 2008
Nucl. Acids Res. 2008 36: e82; doi:10.1093/nar/gkn373 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Dagmar Pich, Sibille Humme, Mark-Peter Spindler, Aloys Schepers, and Wolfgang Hammerschmidt
Conditional gene vectors regulated in cis
Nucleic Acids Research Advance Access published on June 19, 2008
Nucl. Acids Res. 2008 36: e83; doi:10.1093/nar/gkn273 [Abstract] [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.