Nucleic Acids Research

Obituary:

Gerhart Wagner, Wolfgang Nellen, Alfredo Berzal-Herranz, and Georg Sczakiel

OBITUARY
Nucl. Acids Res. 2005 33: 3083-3084; doi:10.1093/nar/gki620 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Articles:

Ujjini H. Manjunatha, Anthony Maxwell, and Valakunja Nagaraja

A monoclonal antibody that inhibits mycobacterial DNA gyrase by a novel mechanism
Nucl. Acids Res. 2005 33: 3085-3094; doi:10.1093/nar/gki622 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sigrid Cornelis, Sandrine A. Tinton, Bert Schepens, Yanik Bruynooghe, and Rudi Beyaert

UNR translation can be driven by an IRES element that is negatively regulated by polypyrimidine tract binding protein
Nucl. Acids Res. 2005 33: 3095-3108; doi:10.1093/nar/gki611 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Rong-bin Guo, Pascal Rigolet, Loussiné Zargarian, Serge Fermandjian, and Xu Guang Xi

Structural and functional characterizations reveal the importance of a zinc binding domain in Bloom's syndrome helicase
Nucl. Acids Res. 2005 33: 3109-3124; doi:10.1093/nar/gki619 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Emmanuelle Lerat and Howard Ochman

Recognizing the pseudogenes in bacterial genomes
Nucl. Acids Res. 2005 33: 3125-3132; doi:10.1093/nar/gki631 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Bruno Charpentier, Sébastien Muller, and Christiane Branlant

Reconstitution of archaeal H/ACA small ribonucleoprotein complexes active in pseudouridylation
Nucl. Acids Res. 2005 33: 3133-3144; doi:10.1093/nar/gki630 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Qin Zhao, Uma Nagaswamy, Hunjoong Lee, Youlin Xia, Hung-Chung Huang, Xiaolian Gao, and George E. Fox

NMR structure and Mg²⁺ binding of an RNA segment that underlies the L7/L12 stalk in the E.coli 50S ribosomal subunit
Nucl. Acids Res. 2005 33: 3145-3153; doi:10.1093/nar/gki621 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Shannan J. Ho Sui, James R. Mortimer, David J. Arenillas, Jochen Brumm, Christopher J. Walsh, Brian P. Kennedy, and Wyeth W. Wasserman

oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes
Nucl. Acids Res. 2005 33: 3154-3164; doi:10.1093/nar/gki624 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Aditi Kanhere and Manju Bansal

Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes
Nucl. Acids Res. 2005 33: 3165-3175; doi:10.1093/nar/gki627 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

J. David Ahle, Stephen Barr, A. Michael Chin, and Thomas R. Battersby

Sequence determination of nucleic acids containing 5-methylisocytosine and isoguanine: identification and insight into polymerase replication of the non-natural nucleobases
Nucl. Acids Res. 2005 33: 3176-3184; doi:10.1093/nar/gki628 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jianying Qi and Richard H. Shafer

Covalent ligation studies on the human telomere quadruplex
Nucl. Acids Res. 2005 33: 3185-3192; doi:10.1093/nar/gki632 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Huiling Chen and Huan-Xiang Zhou

Prediction of solvent accessibility and sites of deleterious mutations from protein sequence
Nucl. Acids Res. 2005 33: 3193-3199; doi:10.1093/nar/gki633 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Satoko Adachi and Ellen V. Rothenberg

Cell-type-specific epigenetic marking of the IL2 gene at a distal cis-regulatory region in competent, nontranscribing T-cells
Nucl. Acids Res. 2005 33: 3200-3210; doi:10.1093/nar/gki637 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Pierre-Olivier Estève, Debasis Patnaik, Hang Gyeong Chin, Jack Benner, Michael A. Teitell, and Sriharsa Pradhan

Functional analysis of the N- and C-terminus of mammalian G9a histone H3 methyltransferase
Nucl. Acids Res. 2005 33: 3211-3223; doi:10.1093/nar/gki635 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Morgan N. Price, Eric J. Alm, and Adam P. Arkin

Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication
Nucl. Acids Res. 2005 33: 3224-3234; doi:10.1093/nar/gki638 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Tsueu-Ju Su, Mark R. Tock, Stefan U. Egelhaaf, Wilson C. K. Poon, and David T. F. Dryden

DNA bending by M.EcoKI methyltransferase is coupled to nucleotide flipping
Nucl. Acids Res. 2005 33: 3235-3244; doi:10.1093/nar/gki618 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zong-Qiang Cui, Zhi-Ping Zhang, Xian-En Zhang, Ji-Kai Wen, Ya-Feng Zhou, and Wei-Hong Xie

Visualizing the dynamic behavior of poliovirus plus-strand RNA in living host cells
Nucl. Acids Res. 2005 33: 3245-3252; doi:10.1093/nar/gki629 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Martin T. Edwards, Stuart C. G. Rison, Neil G. Stoker, and Lorenz Wernisch

A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context
Nucl. Acids Res. 2005 33: 3253-3262; doi:10.1093/nar/gki634 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Pål Sætrom, Ragnhild Sneve, Knut I. Kristiansen, Ola Snøve, Jr, Thomas Grünfeld, Torbjørn Rognes, and Erling Seeberg

Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming
Nucl. Acids Res. 2005 33: 3263-3270; doi:10.1093/nar/gki644 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jingping Hu, Syed Z. Imam, Kazunari Hashiguchi, Nadja C. de Souza-Pinto, and Vilhelm A. Bohr

Phosphorylation of human oxoguanine DNA glycosylase (-OGG1) modulates its function
Nucl. Acids Res. 2005 33: 3271-3282; doi:10.1093/nar/gki636 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Peter H. Clingen, Inusha U. De Silva, Peter J. McHugh, Farid J Ghadessy, Michael J. Tilby, David E. Thurston, and John A. Hartley

The XPF-ERCC1 endonuclease and homologous recombination contribute to the repair of minor groove DNA interstrand crosslinks in mammalian cells produced by the pyrrolo[2,1-c][1,4]benzodiazepine dimer SJG-136
Nucl. Acids Res. 2005 33: 3283-3291; doi:10.1093/nar/gki639 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Dejan Ristic, Mauro Modesti, Thijn van der Heijden, John van Noort, Cees Dekker, Roland Kanaar, and Claire Wyman

Human Rad51 filaments on double- and single-stranded DNA: correlating regular and irregular forms with recombination function
Nucl. Acids Res. 2005 33: 3292-3302; doi:10.1093/nar/gki640 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Elias B. Jackson, Corey A. Theriot, Ranajoy Chattopadhyay, Sankar Mitra, and Tadahide Izumi

Analysis of nuclear transport signals in the human apurinic/apyrimidinic endonuclease (APE1/Ref1)
Nucl. Acids Res. 2005 33: 3303-3312; doi:10.1093/nar/gki641 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Euan W. Baxter, W. Jason Cummings, and R. E. K. Fournier

Formation of a large, complex domain of histone hyperacetylation at human 14q32.1 requires the serpin locus control region
Nucl. Acids Res. 2005 33: 3313-3322; doi:10.1093/nar/gki645 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jill E. Clodfelter, Michael B. Gentry, and Karin Drotschmann

MSH2 missense mutations alter cisplatin cytotoxicity and promote cisplatin-induced genome instability
Nucl. Acids Res. 2005 33: 3323-3330; doi:10.1093/nar/gki646 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Carissa J. Wiederholt, Jennifer N. Patro, Yu Lin Jiang, Kazuhiro Haraguchi, and Marc M. Greenberg

Excision of formamidopyrimidine lesions by endonucleases III and VIII is not a major DNA repair pathway in Escherichia coli
Nucl. Acids Res. 2005 33: 3331-3338; doi:10.1093/nar/gki655 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Giovanni Chillemi, Paola Fiorani, Silvia Castelli, Alessandro Bruselles, Piero Benedetti, and Alessandro Desideri

Effect on DNA relaxation of the single Thr718Ala mutation in human topoisomerase I: a functional and molecular dynamics study
Nucl. Acids Res. 2005 33: 3339-3350; doi:10.1093/nar/gki642 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jun Yao, Jin Zhong, and Alan M. Lambowitz

Gene targeting using randomly inserted group II introns (targetrons) recovered from an Escherichia coli gene disruption library
Nucl. Acids Res. 2005 33: 3351-3362; doi:10.1093/nar/gki649 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Melissa S. Rohrer, Matthew P. Lazio, and H. Steven Seifert

A real-time semi-quantitative RT–PCR assay demonstrates that the pilE sequence dictates the frequency and characteristics of pilin antigenic variation in Neisseria gonorrhoeae
Nucl. Acids Res. 2005 33: 3363-3371; doi:10.1093/nar/gki650 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Shinya Murakami, Katrin Kuehnle, and David B. Stern

A spontaneous tRNA suppressor of a mutation in the Chlamydomonas reinhardtii nuclear MCD1 gene required for stability of the chloroplast petD mRNA
Nucl. Acids Res. 2005 33: 3372-3380; doi:10.1093/nar/gki651 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sylvain Lemeille, Amel Latifi, and Johannes Geiselmann

Inferring the connectivity of a regulatory network from mRNA quantification in Synechocystis PCC6803
Nucl. Acids Res. 2005 33: 3381-3389; doi:10.1093/nar/gki654 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Luciano Brocchieri and Samuel Karlin

Protein length in eukaryotic and prokaryotic proteomes
Nucl. Acids Res. 2005 33: 3390-3400; doi:10.1093/nar/gki615 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Pranee Somboonthum, Hiroshi Ohta, Shuichi Yamada, Masayoshi Onishi, Akiko Ike, Yoshitake Nishimune, and Masami Nozaki

cAMP-responsive element in TATA-less core promoter is essential for haploid-specific gene expression in mouse testis
Nucl. Acids Res. 2005 33: 3401-3411; doi:10.1093/nar/gki652 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Toshihiko Akiba, Noriyuki Ishii, Naeem Rashid, Masaaki Morikawa, Tadayuki Imanaka, and Kazuaki Harata

Structure of RadB recombinase from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1: an implication for the formation of a near-7-fold helical assembly
Nucl. Acids Res. 2005 33: 3412-3423; doi:10.1093/nar/gki662 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yasuo Tsunaka, Naoko Kajimura, Shin-ichi Tate, and Kosuke Morikawa

Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle
Nucl. Acids Res. 2005 33: 3424-3434; doi:10.1093/nar/gki663 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Vlad Cojocaru, Reinhard Klement, and Thomas M. Jovin

Loss of G–A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif
Nucl. Acids Res. 2005 33: 3435-3446; doi:10.1093/nar/gki664 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Methods Online:

Genevieve Pont-Kingdon and Elaine Lyon

Direct molecular haplotyping by melting curve analysis of hybridization probes: beta 2-adrenergic receptor haplotypes as an example
Nucl. Acids Res. 2005 33: e89; doi:10.1093/nar/gni090 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Soon Jin Oh, Jimin Ju, Byung Chul Kim, Eunsil Ko, Bong Jin Hong, Jae-Gahb Park, Joon Won Park, and Kwan Yong Choi

DNA microarrays on a dendron-modified surface improve significantly the detection of single nucleotide variations in the p53 gene
Nucl. Acids Res. 2005 33: e90; doi:10.1093/nar/gni087 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zhengwen Jiang, Xingqi Zhang, Ranjan Deka, and Li Jin

Genome amplification of single sperm using multiple displacement amplification
Nucl. Acids Res. 2005 33: e91; doi:10.1093/nar/gni089 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Andrew V. Oleinikov, Jun Zhao, and Matthew D. Gray

RNA interference by mixtures of siRNAs prepared using custom oligonucleotide arrays
Nucl. Acids Res. 2005 33: e92; doi:10.1093/nar/gni091 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Anatoliy A. Melnikov, Ronald B. Gartenhaus, Anait S. Levenson, Natalia A. Motchoulskaia, and Victor V. Levenson (Chernokhvostov)

MSRE-PCR for analysis of gene-specific DNA methylation
Nucl. Acids Res. 2005 33: e93; doi:10.1093/nar/gni092 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Juana Maria Gonzalez-Santos, Huibi Cao, Anan Wang, David R. Koehler, Bernard Martin, Roya Navab, and Jim Hu

A complementation method for functional analysis of mammalian genes
Nucl. Acids Res. 2005 33: e94; doi:10.1093/nar/gni093 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Zachary A. Kaminsky, Abbas Assadzadeh, James Flanagan, and Arturas Petronis

Single nucleotide extension technology for quantitative site-specific evaluation of ^metC/C in GC-rich regions
Nucl. Acids Res. 2005 33: e95; doi:10.1093/nar/gni094 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Robert H. H. van den Heuvel, Sara Gato, Cees Versluis, Pascal Gerbaux, Colin Kleanthous, and Albert J. R. Heck

Real-time monitoring of enzymatic DNA hydrolysis by electrospray ionization mass spectrometry
Nucl. Acids Res. 2005 33: e96; doi:10.1093/nar/gni099 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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