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Previous Next 		Contents: Volume 34, Number 2, 2006   [Index by Author] 

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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

Bauke Ylstra, Paul van den IJssel, Beatriz Carvalho, Ruud H. Brakenhoff, and Gerrit A. Meijer
BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH)
Nucl. Acids Res. 2006 34: 445-450; doi:10.1093/nar/gkj456 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alexander Hüttenhofer and Jörg Vogel
Experimental approaches to identify non-coding RNAs
Nucl. Acids Res. 2006 34: 635-646; doi:10.1093/nar/gkj469 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Murray P. Deutscher
Degradation of RNA in bacteria: comparison of mRNA and stable RNA
Nucl. Acids Res. 2006 34: 659-666; doi:10.1093/nar/gkj472 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Mark Helm
Post-transcriptional nucleotide modification and alternative folding of RNA
Nucl. Acids Res. 2006 34: 721-733; doi:10.1093/nar/gkj471 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online Back

Bettina Harr and Christian Schlötterer
Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons
Nucl. Acids Res. 2006 34: e8; doi:10.1093/nar/gnj010 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Fuchou Tang, Petra Hajkova, Sheila C. Barton, Kaiqin Lao, and M. Azim Surani
MicroRNA expression profiling of single whole embryonic stem cells
Nucl. Acids Res. 2006 34: e9; doi:10.1093/nar/gnj009 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Naoki Kanayama, Kagefumi Todo, Satoko Takahashi, Masaki Magari, and Hitoshi Ohmori
Genetic manipulation of an exogenous non-immunoglobulin protein by gene conversion machinery in a chicken B cell line
Nucl. Acids Res. 2006 34: e10; doi:10.1093/nar/gnj013 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kyotaro Hirashima, Tomoko Iwaki, Kaoru Takegawa, Yuko Giga-Hama, and Hideki Tohda
A simple and effective chromosome modification method for large-scale deletion of genome sequences and identification of essential genes in fission yeast
Nucl. Acids Res. 2006 34: e11; doi:10.1093/nar/gnj011 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ji-Dung Luo, Err-Cheng Chan, Chun-Liang Shih, Tai-Long Chen, Ying Liang, Tsann-Long Hwang, and Chiuan-Chian Chiou
Detection of rare mutant K-ras DNA in a single-tube reaction using peptide nucleic acid as both PCR clamp and sensor probe
Nucl. Acids Res. 2006 34: e12; doi:10.1093/nar/gnj008 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Weilin Wu, Emily Hodges, and Christer Höög
Thorough validation of siRNA-induced cell death phenotypes defines new anti-apoptotic protein
Nucl. Acids Res. 2006 34: e13; doi:10.1093/nar/gnj015 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Xiaochun Shi and Jonathan B. Chaires
Sequence- and structural-selective nucleic acid binding revealed by the melting of mixtures
Nucl. Acids Res. 2006 34: e14; doi:10.1093/nar/gnj012 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Derek N. Fuller, Gregory J. Gemmen, John Peter Rickgauer, Aurelie Dupont, Rachel Millin, Pierre Recouvreux, and Douglas E. Smith
A general method for manipulating DNA sequences from any organism with optical tweezers
Nucl. Acids Res. 2006 34: e15; doi:10.1093/nar/gnj016 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nils Link, Corinne Aubel, Jens M. Kelm, René R. Marty, David Greber, Valentin Djonov, Jean Bourhis, Wilfried Weber, and Martin Fussenegger
Therapeutic protein transduction of mammalian cells and mice by nucleic acid-free lentiviral nanoparticles
Nucl. Acids Res. 2006 34: e16; doi:10.1093/nar/gnj014 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Articles Back

Marc Brackertz, Zihua Gong, Jörg Leers, and Rainer Renkawitz
p66{alpha} and p66ß of the Mi-2/NuRD complex mediate MBD2 and histone interaction
Nucl. Acids Res. 2006 34: 397-406; doi:10.1093/nar/gkj437 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Cui-Ping Yang, Yong-Bin Chen, Fei-Long Meng, and Jin-Qiu Zhou
Saccharomyces cerevisiae Est3p dimerizes in vitro and dimerization contributes to efficient telomere replication in vivo
Nucl. Acids Res. 2006 34: 407-416; doi:10.1093/nar/gkj445 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Bo Zhao, Jillian Wang, Nicholas E. Geacintov, and Zhigang Wang
Pol{eta}, Pol{zeta} and Rev1 together are required for G to T transversion mutations induced by the (+)- and (–)-trans-anti-BPDE-N2-dG DNA adducts in yeast cells
Nucl. Acids Res. 2006 34: 417-425; doi:10.1093/nar/gkj446 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sarah L. Williams and Joel F. Schildbach
Examination of an inverted repeat within the F factor origin of transfer: context dependence of F TraI relaxase DNA specificity
Nucl. Acids Res. 2006 34: 426-435; doi:10.1093/nar/gkj444 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jacinthe Azevedo, Florence Courtois, and Silva Lerbs-Mache
Sub-plastidial localization of two different phage-type RNA polymerases in spinach chloroplasts
Nucl. Acids Res. 2006 34: 436-444; doi:10.1093/nar/gkj451 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

A. Kalota, L. Karabon, C. R. Swider, E. Viazovkina, M. Elzagheid, M. J. Damha, and A. M. Gewirtz
2'-Deoxy-2'-fluoro-ß-D-arabinonucleic acid (2'F-ANA) modified oligonucleotides (ON) effect highly efficient, and persistent, gene silencing
Nucl. Acids Res. 2006 34: 451-461; doi:10.1093/nar/gkj455 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Rashid Akbergenov, Azeddine Si-Ammour, Todd Blevins, Imran Amin, Claudia Kutter, Herve Vanderschuren, Peng Zhang, Wilhelm Gruissem, Frederick Meins, Jr, Thomas Hohn, and Mikhail M. Pooggin
Molecular characterization of geminivirus-derived small RNAs in different plant species
Nucl. Acids Res. 2006 34: 462-471; doi:10.1093/nar/gkj447 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Robert J. Fisher, Matthew J. Fivash, Andrew G. Stephen, Nathan A. Hagan, Shilpa R. Shenoy, Maxine V. Medaglia, Lindsey R. Smith, Karen M. Worthy, John T. Simpson, Robert Shoemaker, Karen L. McNitt, Donald G. Johnson, Catherine V. Hixson, Robert J. Gorelick, Daniele Fabris, Louis E. Henderson, and Alan Rein
Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides
Nucl. Acids Res. 2006 34: 472-484; doi:10.1093/nar/gkj442 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Erratum]  

Yadong Zhang, Deepak Bhatia, Hongfeng Xia, Vince Castranova, Xianglin Shi, and Fei Chen
Nucleolin links to arsenic-induced stabilization of GADD45{alpha} mRNA
Nucl. Acids Res. 2006 34: 485-495; doi:10.1093/nar/gkj459 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Alexey V. Lobanov, Cesar Delgado, Stefan Rahlfs, Sergey V. Novoselov, Gregory V. Kryukov, Stephan Gromer, Dolph L. Hatfield, Katja Becker, and Vadim N. Gladyshev
The Plasmodium selenoproteome
Nucl. Acids Res. 2006 34: 496-505; doi:10.1093/nar/gkj450 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Mahrukh Azam, Julia Y. Lee, Veena Abraham, Rebecca Chanoux, Kimberly A. Schoenly, and F. Brad Johnson
Evidence that the S.cerevisiae Sgs1 protein facilitates recombinational repair of telomeres during senescence
Nucl. Acids Res. 2006 34: 506-516; doi:10.1093/nar/gkj452 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Li Kai Wang, Beate Schwer, Markus Englert, Hildburg Beier, and Stewart Shuman
Structure–function analysis of the kinase-CPD domain of yeast tRNA ligase (Trl1) and requirements for complementation of tRNA splicing by a plant Trl1 homolog
Nucl. Acids Res. 2006 34: 517-527; doi:10.1093/nar/gkj441 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Axel Schumacher, Philipp Kapranov, Zachary Kaminsky, James Flanagan, Abbas Assadzadeh, Patrick Yau, Carl Virtanen, Neil Winegarden, Jill Cheng, Thomas Gingeras, and Arturas Petronis
Microarray-based DNA methylation profiling: technology and applications
Nucl. Acids Res. 2006 34: 528-542; doi:10.1093/nar/gkj461 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Anna Saramäki, Claire M. Banwell, Moray J. Campbell, and Carsten Carlberg
Regulation of the human p21(waf1/cip1) gene promoter via multiple binding sites for p53 and the vitamin D3 receptor
Nucl. Acids Res. 2006 34: 543-554; doi:10.1093/nar/gkj460 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Zhiqing Huang, Yaqing Wen, Ruby Shandilya, Jeffrey R. Marks, Andrew Berchuck, and Susan K. Murphy
High throughput detection of M6P/IGF2R intronic hypermethylation and LOH in ovarian cancer
Nucl. Acids Res. 2006 34: 555-563; doi:10.1093/nar/gkj468 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Peter Yakovchuk, Ekaterina Protozanova, and Maxim D. Frank-Kamenetskii
Base-stacking and base-pairing contributions into thermal stability of the DNA double helix
Nucl. Acids Res. 2006 34: 564-574; doi:10.1093/nar/gkj454 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Erratum]  

Yong-Hua Yang, Hongjian Li, Tianhong Zhou, Kihoon Kim, and Fenyong Liu
Engineered external guide sequences are highly effective in inducing RNase P for inhibition of gene expression and replication of human cytomegalovirus
Nucl. Acids Res. 2006 34: 575-583; doi:10.1093/nar/gkj431 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Atef Nehdi and Jean-Pierre Perreault
Unbiased in vitro selection reveals the unique character of the self-cleaving antigenomic HDV RNA sequence
Nucl. Acids Res. 2006 34: 584-592; doi:10.1093/nar/gkj463 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Margareta Cruceanu, Maria A. Urbaneja, Catherine V. Hixson, Donald G. Johnson, Siddhartha A. Datta, Matthew J. Fivash, Andrew G. Stephen, Robert J. Fisher, Robert J. Gorelick, Jose R. Casas-Finet, Alan Rein, Ioulia Rouzina, and Mark C. Williams
Nucleic acid binding and chaperone properties of HIV-1 Gag and nucleocapsid proteins
Nucl. Acids Res. 2006 34: 593-605; doi:10.1093/nar/gkj458 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Stefan Oehler, Siegfried Alberti, and Benno Müller-Hill
Induction of the lac promoter in the absence of DNA loops and the stoichiometry of induction
Nucl. Acids Res. 2006 34: 606-612; doi:10.1093/nar/gkj453 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yunling Wang and David Morse
Rampant polyuridylylation of plastid gene transcripts in the dinoflagellate Lingulodinium
Nucl. Acids Res. 2006 34: 613-619; doi:10.1093/nar/gkj438 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

J. S. Yakisich and G. M. Kapler
Deletion of the Tetrahymena thermophila rDNA replication fork barrier region disrupts macronuclear rDNA excision and creates a fragile site in the micronuclear genome
Nucl. Acids Res. 2006 34: 620-634; doi:10.1093/nar/gkj466 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ikuo Uchiyama
Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes
Nucl. Acids Res. 2006 34: 647-658; doi:10.1093/nar/gkj448 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Zhiyong Yang, Yon W. Ebright, Bin Yu, and Xuemei Chen
HEN1 recognizes 21–24 nt small RNA duplexes and deposits a methyl group onto the 2' OH of the 3' terminal nucleotide
Nucl. Acids Res. 2006 34: 667-675; doi:10.1093/nar/gkj474 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jiro Kondo, Alexandre Urzhumtsev, and Eric Westhof
Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site
Nucl. Acids Res. 2006 34: 676-685; doi:10.1093/nar/gkj467 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Yuhua Cheng, Nikolay Korolev, and Lars Nordenskiöld
Similarities and differences in interaction of K+ and Na+ with condensed ordered DNA. A molecular dynamics computer simulation study
Nucl. Acids Res. 2006 34: 686-696; doi:10.1093/nar/gkj434 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Nad'a Spacková and Jirí Sponer
Molecular dynamics simulations of sarcin–ricin rRNA motif
Nucl. Acids Res. 2006 34: 697-708; doi:10.1093/nar/gkj470 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Katarzyna Ziolkowska, Philippe Derreumaux, Marc Folichon, Olivier Pellegrini, Philippe Régnier, Irina V. Boni, and Eliane Hajnsdorf
Hfq variant with altered RNA binding functions
Nucl. Acids Res. 2006 34: 709-720; doi:10.1093/nar/gkj464 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Sara Napoli, Umberto Negri, Federico Arcamone, Massimo L. Capobianco, Giuseppina M. Carbone, and Carlo V. Catapano
Growth inhibition and apoptosis induced by daunomycin-conjugated triplex-forming oligonucleotides targeting the c-myc gene in prostate cancer cells
Nucl. Acids Res. 2006 34: 734-744; doi:10.1093/nar/gkj473 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jeanine A. Harrigan, David M. Wilson, III, Rajendra Prasad, Patricia L. Opresko, Gad Beck, Alfred May, Samuel H. Wilson, and Vilhelm A. Bohr
The Werner syndrome protein operates in base excision repair and cooperates with DNA polymerase ß
Nucl. Acids Res. 2006 34: 745-754; doi:10.1093/nar/gkj475 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Srinivasa Rao Meneni, Rhijuta D'Mello, Gregory Norigian, Gregory Baker, Lan Gao, M. Paul Chiarelli, and Bongsup P. Cho
Sequence effects of aminofluorene-modified DNA duplexes: thermodynamic and circular dichroism properties
Nucl. Acids Res. 2006 34: 755-763; doi:10.1093/nar/gkj480 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Erratum Back

Annette MacLeod, Alison Tweedie, Sarah McLellan, Sonya Taylor, Neil Hall, Matthew Berriman, Najib M. El-Sayed, Michelle Hope, C. Michael R. Turner, and Andy Tait
The genetic map and comparative analysis with the physical map of Trypanosoma brucei
Nucl. Acids Res. 2006 34: 764; doi:10.1093/nar/gkj476 [Extract] [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.