Nucleic Acids Research

Nucleic Acids Research
pp. i-i(1)

Nucleic Acids Research
pp. ii-ii(1)

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pp. iii-iii(1)

TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences
pp. e78-e78(1)
Authors: Han, Yujun; Burnette, James M.; Wessler, Susan R.

Text-based over-representation analysis of microarray gene lists with annotation bias
pp. e79-e79(1)
Authors: Leong, Hui Sun; Kipling, David

Sim4cc: a cross-species spliced alignment program
pp. e80-e80(1)
Authors: Zhou, Leming; Pertea, Mihaela; Delcher, Arthur L.; Florea, Liliana

Robust methods for purification of histones from cultured mammalian cells with the preservation of their native modifications
pp. e81-e81(1)
Authors: Rodriguez-Collazo, Pedro; Leuba, Sanford H.; Zlatanova, Jordanka

Tissue-specific regulatory network extractor (TS-REX): a database and software resource for the tissue and cell type-specific investigation of transcription factor-gene networks
pp. e82-e82(1)
Authors: Colecchia, Federico; Kottwitz, Denise; Wagner, Mandy; Pfenninger, Cosima V.; Thiel, Gerald; Tamm, Ingo; Peterson, Carsten; Nuber, Ulrike A.

MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming
pp. e83-e83(1)
Authors: Mukherjee, Srayanta; Zhang, Yang

Replication fork reversal and the maintenance of genome stability
pp. 3475-3492(18)
Authors: Atkinson, John; McGlynn, Peter

Nontarget DNA binding shapes the dynamic landscape for enzymatic recognition of DNA damage
pp. 3493-3500(8)
Authors: Friedman, Joshua I.; Majumdar, Ananya; Stivers, James T.

Poly(ADP-ribosyl)ation of heterogeneous nuclear ribonucleoproteins modulates splicing
pp. 3501-3513(13)
Authors: Ji, Yingbiao; Tulin, Alexei V.

The amino terminal domain from Mrt4 protein can functionally replace the RNA binding domain of the ribosomal P0 protein
pp. 3514-3521(8)
Authors: Rodríguez-Mateos, María; Abia, David; García-Gómez, Juan J.; Morreale, Antonio; de la Cruz, Jesús; Santos, Cruz; Remacha, Miguel; Ballesta, Juan P. G.

PROCAIN: protein profile comparison with assisting information
pp. 3522-3530(9)
Authors: Wang, Yong; Sadreyev, Ruslan I.; Grishin, Nick V.

Cleavage of a model DNA replication fork by a Type I restriction endonuclease
pp. 3531-3544(14)
Authors: Ishikawa, Ken; Handa, Naofumi; Kobayashi, Ichizo

A genotype-to-phenotype map of in vitro selected RNA-cleaving DNAzymes: implications for accessing the target phenotype
pp. 3545-3557(13)
Authors: Schlosser, Kenny; Lam, Jeffrey C. F.; Li, Yingfu

Non-specific interactions are sufficient to explain the position of heterochromatic chromocenters and nucleoli in interphase nuclei
pp. 3558-3568(11)
Authors: de Nooijer, S.; Wellink, J.; Mulder, B.; Bisseling, T.

Accurate prediction of NAGNAG alternative splicing
pp. 3569-3579(11)
Authors: Sinha, Rileen; Nikolajewa, Swetlana; Szafranski, Karol; Hiller, Michael; Jahn, Niels; Huse, Klaus; Platzer, Matthias; Backofen, Rolf

mwr Xer site-specific recombination is hypersensitive to DNA supercoiling
pp. 3580-3587(8)
Authors: Trigueros, Sonia; Tran, Tung; Sorto, Nohemy; Newmark, Jason; Colloms, Sean D.; Sherratt, David J.; Tolmasky, Marcelo E.

Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii
pp. 3588-3601(14)
Authors: Zhang, Jian; Li, Enhu; Olsen, Gary J.

Rapid Cdc13 turnover and telomere length homeostasis are controlled by Cdk1-mediated phosphorylation of Cdc13
pp. 3602-3611(10)
Authors: Tseng, Shun-Fu; Shen, Zih-Jie; Tsai, Hung-Ji; Lin, Yi-Hsuan; Teng, Shu-Chun

Alternative polyadenylation variants of the RNA binding protein, HuR: abundance, role of AU-rich elements and auto-Regulation
pp. 3612-3624(13)
Authors: Al-Ahmadi, Wijdan; Al-Ghamdi, Maha; Al-Haj, Latifa; Al-Saif, Maher; Khabar, Khalid S. A.

Dramatic effect of single-base mutation on the conformational dynamics of human telomeric G-quadruplex
pp. 3625-3634(10)
Authors: Lee, Ja Yil; Kim, D. S.

Targeted correction of a thalassemia-associated β-globin mutation induced by pseudo-complementary peptide nucleic acids
pp. 3635-3644(10)
Authors: Lonkar, Pallavi; Kim, Ki-Hyun; Kuan, Jean Y.; Chin, Joanna Y.; Rogers, Faye A.; Knauert, Melissa P.; Kole, Ryszard; Nielsen, Peter E.; Glazer, Peter M.

Coupled termination/reinitiation for translation of the downstream open reading frame B of the prototypic hypovirus CHV1-EP713
pp. 3645-3659(15)
Authors: Guo, Li-hua; Sun, Liying; Chiba, Sotaro; Araki, Hiroyuki; Suzuki, Nobuhiro

Mutational analysis of the HIV-1 auxiliary protein Vif identifies independent domains important for the physical and functional interaction with HIV-1 reverse transcriptase
pp. 3660-3669(10)
Authors: Kataropoulou, Alexandra; Bovolenta, Chiara; Belfiore, Amalia; Trabatti, Sonia; Garbelli, Anna; Porcellini, Simona; Lupo, Rossella; Maga, Giovanni

Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition
pp. 3670-3679(10)
Authors: Frank, Aaron T.; Stelzer, Andrew C.; Al-Hashimi, Hashim M.; Andricioaei, Ioan

Transcriptional regulation shapes the organization of genes on bacterial chromosomes
pp. 3680-3688(9)
Authors: Janga, Sarath Chandra; Salgado, Heladia; Martínez-Antonio, Agustino

The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors
pp. 3689-3698(10)
Authors: Reece-Hoyes, John S.; Deplancke, Bart; Barrasa, M. Inmaculada; Hatzold, Julia; Smit, Ryan B.; Arda, H. Efsun; Pope, Patricia A.; Gaudet, Jeb; Conradt, Barbara; Walhout, Albertha J. M.

Histone deacetylase Rpd3 antagonizes Sir2-dependent silent chromatin propagation
pp. 3699-3713(15)
Authors: Zhou, Jing; Zhou, Bo O.; Lenzmeier, Brian A.; Zhou, Jin-Qiu

Nucleotide analogs and molecular modeling studies reveal key interactions involved in substrate recognition by the yeast RNA triphosphatase
pp. 3714-3722(9)
Authors: Issur, Moheshwarnath; Despins, Simon; Bougie, Isabelle; Bisaillon, Martin

Molecular mechanism of poly(ADP-ribosyl)ation by PARP1 and identification of lysine residues as ADP-ribose acceptor sites
pp. 3723-3738(16)
Authors: Altmeyer, Matthias; Messner, Simon; Hassa, Paul O.; Fey, Monika; Hottiger, Michael O.

Silencing of a plant gene by transcriptional interference
pp. 3739-3746(8)
Authors: Hedtke, Boris; Grimm, Bernhard

Low modularity of aminoacyl-tRNA substrates in polymerization by the ribosome
pp. 3747-3755(9)
Author: Forster, Anthony C.

Kinetics and thermodynamics of DNA hybridization on gold nanoparticles
pp. 3756-3765(10)
Authors: Chen, Chunlai; Wang, Wenjuan; Ge, Jing; Zhao, Xin Sheng

Local and global effects of strong DNA bending induced during molecular dynamics simulations
pp. 3766-3773(8)
Authors: Curuksu, Jeremy; Zacharias, Martin; Lavery, Richard; Zakrzewska, Krystyna

Low-fidelity DNA synthesis by the L979F mutator derivative of Saccharomyces cerevisiae DNA polymerase ζ
pp. 3774-3787(14)
Authors: Stone, Jana E.; Kissling, Grace E.; Lujan, Scott A.; Rogozin, Igor B.; Stith, Carrie M.; Burgers, Peter M. J.; Kunkel, Thomas A.

Molecular genetics and comparative genomics reveal RNAi is not functional in malaria parasites
pp. 3788-3798(11)
Authors: Baum, Jake; Papenfuss, Anthony T.; Mair, Gunnar R.; Janse, Chris J.; Vlachou, Dina; Waters, Andrew P.; Cowman, Alan F.; Crabb, Brendan S.; de Koning-Ward, Tania F.

Crystal structure of the ββα-Me type II restriction endonuclease Hpy99I with target DNA
pp. 3799-3810(12)
Authors: Sokolowska, Monika; Czapinska, Honorata; Bochtler, Matthias

Transcriptionally active TFIIH of the early-diverged eukaryote Trypanosoma brucei harbors two novel core subunits but not a cyclin-activating kinase complex
pp. 3811-3820(10)
Authors: Lee, Ju Huck; Jung, Hyun Suk; Günzl, Arthur

MicroRNA-338-3p and microRNA-451 contribute to the formation of basolateral polarity in epithelial cells
pp. 3821-3827(7)
Authors: Tsuchiya, Soken; Oku, Masahito; Imanaka, Yukako; Kunimoto, Ryo; Okuno, Yasushi; Terasawa, Kazuya; Sato, Fumiaki; Tsujimoto, Gozoh; Shimizu, Kazuharu