Nucleic Acids Research

A microarray-based high throughput molecular marker genotyping method: the tagged microarray marker (TAM) approach
pp. e115-e115(1)
Authors: Andrew J. Flavell; Viacheslav N. Bolshakov; Allan Booth; Runchun Jing; Joanne Russell; T. H. Noel Ellis; Peter Isaac

A non-parametric model for transcription factor binding sites
pp. e116-e116(1)
Authors: Oliver D. King; Frederick P. Roth

Real-time closed tube single nucleotide polymorphism (SNP) quantification in pooled samples by quencher extension (QEXT)
pp. e117-e117(1)
Authors: Knut Rudi; Askild L. Holck

DNA display for in vitro selection of diverse peptide libraries
pp. e118-e118(1)
Authors: Masato Yonezawa; Nobuhide Doi; Yuko Kawahashi; Toru Higashinakagawa; Hiroshi Yanagawa

PNA microarrays for hybridisation of unlabelled DNA samples
pp. e119-e119(1)
Authors: Ole Brandt; Julia Feldner; Achim Stephan; Markus Schröder; Martina Schnölzer; Heinrich F. Arlinghaus; Jörg D. Hoheisel; Anette Jacob

Reconstitution of an efficient thymidine salvage pathway in Saccharomyces cerevisiae
pp. e120-e120(1)
Authors: Laurence Vernis; Jure Piskur; John F. X. Diffley

Structures of trinucleotide repeats in human transcripts and their functional implications
pp. 5463-5468(6)
Authors: Anna Jasinska; Gracjan Michlewski; Mateusz de Mezer; Krzysztof Sobczak; Piotr Kozlowski; Marek Napierala; Wlodzimierz J. Krzyzosiak

RNA structure of trinucleotide repeats associated with human neurological diseases
pp. 5469-5482(14)
Authors: Krzysztof Sobczak; Mateusz de Mezer; Gracjan Michlewski; Jacek Krol; Wlodzimierz J. Krzyzosiak

Requirements for selective recruitment of Ets proteins and activation of mb-1/Ig- gene transcription by Pax-5 (BSAP)
pp. 5483-5489(7)
Authors: Holly Maier; Rachel Ostraat; Sarah Parenti; Daniel Fitzsimmons; Lawrence J. Abraham; Colin W. Garvie; James Hagman

Using pyrene-labeled HIV-1 TAR to measure RNA–small molecule binding
pp. 5490-5500(11)
Authors: Kenneth F. Blount; Yitzhak Tor

Vanillins—a novel family of DNA-PK inhibitors
pp. 5501-5512(12)
Authors: Stephen Durant; Peter Karran

GLIS3, a novel member of the GLIS subfamily of Krüppel-like zinc finger proteins with repressor and activation functions
pp. 5513-5525(13)
Authors: Yong-Sik Kim; Gen Nakanishi; Mark Lewandoski; Anton M. Jetten

A requirement for PARP-1 for the assembly or stability of XRCC1 nuclear foci at sites of oxidative DNA damage
pp. 5526-5533(8)
Authors: Sherif F. El-Khamisy; Mitsuko Masutani; Hiroshi Suzuki; Keith W. Caldecott

Characterization of the RNA motif responsible for the specific interaction of potato spindle tuber viroid RNA (PSTVd) and the tomato protein Virp1
pp. 5534-5543(10)
Authors: Mariyana Gozmanova; Michela Alessandra Denti; Ivan Nikiforov Minkov; Mina Tsagris; Martin Tabler

Biochemical characterization of the kink-turn RNA motif
pp. 5544-5551(8)
Authors: Shigeyoshi Matsumura; Yoshiya Ikawa; Tan Inoue

Allosteric regulation of tRNA import: interactions between tRNA domains at the inner membrane of Leishmania mitochondria
pp. 5552-5559(8)
Authors: Srikanta Goswami; Saibal Chatterjee; Suvendra Nath Bhattacharyya; Sudarshana Basu; Samit Adhya

Characterization of AP lyase activities of Saccharomyces cerevisiae Ntg1p and Ntg2p: implications for biological function
pp. 5560-5567(8)
Authors: Kellen L. Meadows; Binwei Song; Paul W. Doetsch

The human checkpoint Rad protein Rad17 is chromatin-associated throughout the cell cycle, localizes to DNA replication sites, and interacts with DNA polymerase
pp. 5568-5575(8)
Authors: Sean M. Post; Alan E. Tomkinson; Eva Y.-H. P. Lee

Genome-scale design of PCR primers and long oligomers for DNA microarrays
pp. 5576-5581(6)
Authors: Stefan A. Haas; Marc Hild; Anthony P. H. Wright; Torsten Hain; Driss Talibi; Martin Vingron

EXCAVATOR: a computer program for efficiently mining gene expression data
pp. 5582-5589(8)
Authors: Dong Xu; Victor Olman; Li Wang; Ying Xu

Thermodynamics of the binding of Thermus aquaticus DNA polymerase to primed-template DNA
pp. 5590-5597(8)
Authors: Kausiki Datta; Vince J. LiCata

Thermodynamic and kinetic stability of intermolecular triple helices containing different proportions of C⁺·GC and T·AT triplets
pp. 5598-5606(9)
Authors: Peter L. James; Tom Brown; Keith R. Fox

Global mapping of nucleic acid conformational space: dinucleoside monophosphate conformations and transition pathways among conformational classes
pp. 5607-5616(10)
Authors: Gregory E. Sims; Sung-Hou Kim

PANDORA: keyword-based analysis of protein sets by integration of annotation sources
pp. 5617-5626(10)
Authors: Noam Kaplan; Avishay Vaaknin; Michal Linial

hMSH2 expression is driven by AP1-dependent regulation through phorbol-ester exposure
pp. 5627-5634(8)
Authors: Odile Humbert; Ikbel Achour; Dominique Lautier; Guy Laurent; Bernard Salles

Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences
pp. 5635-5643(9)
Authors: Qiang Xu; Christopher Lee

RNAi-mediated depletion of the 15 KH domain protein, vigilin, induces death of dividing and non-dividing human cells but does not initially inhibit protein synthesis
pp. 5644-5653(10)
Authors: Kathryn M. Goolsby; David J. Shapiro

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
pp. 5654-5666(13)
Authors: Brian J. Haas; Arthur L. Delcher; Stephen M. Mount; Jennifer R. Wortman; Roger K. Smith Jr; Linda I. Hannick; Rama Maiti; Catherine M. Ronning; Douglas B. Rusch; Christopher D. Town; Steven L. Salzberg; Owen White

Advanced computational techniques for re-sequencing DNA with polymerase signaling assay arrays
pp. 5667-5675(9)
Authors: Itsik Pe’er; Naama Arbili; Yi Liu; Colby Enck; Craig A. Gelfand; Ron Shamir

Evaluation of gene expression measurements from commercial microarray platforms
pp. 5676-5684(9)
Authors: Paul K. Tan; Thomas J. Downey; Edward L. Spitznagel Jr; Pin Xu; Dadin Fu; Dimiter S. Dimitrov; Richard A. Lempicki; Bruce M. Raaka; Margaret C. Cam

3-Modified oligonucleotides by reverse DNA synthesis
pp. 5685-5691(7)
Authors: Christopher D. Claeboe; Rong Gao; Sidney M. Hecht

Long-distance radical cation reactions in DNA three-way junctions: inter-arm interaction and migration through the junction
pp. 5692-5699(8)
Authors: U. Santhosh; Gary B. Schuster

In vitro selection of molecular beacons
pp. 5700-5713(14)
Authors: Manjula Rajendran; Andrew D. Ellington

Modulation of drug sensitivity in yeast cells by the ATP-binding domain of human DNA topoisomerase II
pp. 5714-5722(9)
Authors: Nathalie Vilain; Monika Tsai-Pflugfelder; Audrey Benoit; Susan M. Gasser; Didier Leroy

Enhanced gene activation by Notch and BMP signaling cross-talk
pp. 5723-5731(9)
Authors: Takumi Takizawa; Wataru Ochiai; Kinichi Nakashima; Tetsuya Taga

The DNA and RNA specificity of eilatin Ru(II) complexes as compared to eilatin and ethidium bromide
pp. 5732-5740(9)
Authors: Nathan W. Luedtke; Judy S. Hwang; Eileen Nava; Dalia Gut; Moshe Kol; Yitzhak Tor

dsRBM1 and a proline-rich domain of RNA helicase A can form a composite binder to recognize a specific dsDNA
pp. 5741-5753(13)
Authors: Ming-Lung Hung; Ping Chao; Kung-Yao Chang

G-quartets direct assembly of HIV-1 nucleocapsid protein along single-stranded DNA
pp. 5754-5763(10)
Authors: Sébastien Lyonnais; Robert J. Gorelick; Jean-Louis Mergny; Eric Le Cam; Gilles Mirambeau

Structure–function relationships of the initiation complex of HIV-1 reverse transcription: the case of mutant viruses using tRNA^His as primer
pp. 5764-5775(12)
Authors: Mickaël Rigourd; Valérie Goldschmidt; Fabienne Brulé; Casey D. Morrow; Bernard Ehresmann; Chantal Ehresmann; Roland Marquet

Selective inhibitory DNA aptamers of the human RNase H1
pp. 5776-5788(13)
Authors: Frédéric Pileur; Marie-Line Andreola; Eric Dausse; Justine Michel; Serge Moreau; Hirofumi Yamada; Sergei A. Gaidamakov; Robert J. Crouch; Jean-Jacques Toulmé; Christian Cazenave

Integrated transcriptome analysis of the cellular mechanisms associated with Ha-ras-dependent malignant transformation of the human breast epithelial MCF7 cell line
pp. 5789-5804(16)
Authors: Franck Gadal; Christophe Bozic; Céline Pillot-Brochet; Sophie Malinge; Sarah Wagner; Aurélie Le Cam; Laurent Buffat; Michel Crepin; François Iris