Volume 41; Issue 4

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Nucleic Acids Research
Volume 41; Issue 4

Nucleic Acids Research

Volume 41; Issue 4

1

Using defined finger-finger interfaces as units of assembly for constructing zinc-finger nucleases

Zhu, C., Gupta, A., Hall, V. L., Rayla, A. L., Christensen, R. G., Dake, B., Lakshmanan, A., Kuperwasser, C., Stormo, G. D., Wolfe, S. A.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.43 MB

english, 2013

2

Replication-independent nucleosome exchange is enhanced by local and specific acetylation of histone H4

Elliott, G. O., Murphy, K. J., Hayes, J. J., Thiriet, C.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 5.37 MB

english, 2013

3

Crystal structure of an intermediate of rotating dimers within the synaptic tetramer of the G-segment invertase

Ritacco, C. J., Kamtekar, S., Wang, J., Steitz, T. A.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 9.40 MB

english, 2013

4

A novel non-radioactive primase-pyrophosphatase activity assay and its application to the discovery of inhibitors of Mycobacterium tuberculosis primase DnaG

Biswas, T., Resto-Roldan, E., Sawyer, S. K., Artsimovitch, I., Tsodikov, O. V.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 5.03 MB

english, 2013

5

Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast

McIsaac, R. S., Oakes, B. L., Wang, X., Dummit, K. A., Botstein, D., Noyes, M. B.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 989 KB

english, 2013

6

Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs

Patra, A., Harp, J., Pallan, P. S., Zhao, L., Abramov, M., Herdewijn, P., Egli, M.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 5.71 MB

english, 2013

7

iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks

Rockel, S., Geertz, M., Hens, K., Deplancke, B., Maerkl, S. J.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.10 MB

english, 2013

8

Imprinting at the PLAGL1 domain is contained within a 70-kb CTCF/cohesin-mediated non-allelic chromatin loop

Iglesias-Platas, I., Court, F., Camprubi, C., Sparago, A., Guillaumet-Adkins, A., Martin-Trujillo, A., Riccio, A., Moore, G. E., Monk, D.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 6.19 MB

english, 2013

9

Mycobacterium fluoroquinolone resistance protein B, a novel small GTPase, is involved in the regulation of DNA gyrase and drug resistance

Tao, J., Han, J., Wu, H., Hu, X., Deng, J., Fleming, J., Maxwell, A., Bi, L., Mi, K.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 3.47 MB

english, 2013

10

Two-dimensional intact mitochondrial DNA agarose electrophoresis reveals the structural complexity of the mammalian mitochondrial genome

Kolesar, J. E., Wang, C. Y., Taguchi, Y. V., Chou, S.-H., Kaufman, B. A.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 5.33 MB

english, 2013

11

Functional characterization of motif sequences under purifying selection

Chen, D.-H., Chang, A. Y.-F., Liao, B.-Y., Yeang, C.-H.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 3.35 MB

english, 2013

12

Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale

Islam, B., Sgobba, M., Laughton, C., Orozco, M., Sponer, J., Neidle, S., Haider, S.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 11.26 MB

english, 2013

13

Coordinated induction of multi-gene pathways in Saccharomyces cerevisiae

Liang, J., Ning, J. C., Zhao, H.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 447 KB

english, 2013

14

GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data

Benoukraf, T., Wongphayak, S., Hadi, L. H. A., Wu, M., Soong, R.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 4.37 MB

english, 2013

15

Oxygen-dependent expression of cytochrome c oxidase subunit 4-2 gene expression is mediated by transcription factors RBPJ, CXXC5 and CHCHD2

Aras, S., Pak, O., Sommer, N., Finley, R., Huttemann, M., Weissmann, N., Grossman, L. I.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 4.77 MB

english, 2013

16

Engineering of interlocked DNA G-quadruplexes as a robust scaffold

Phan, A. T., Do, N. Q.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.72 MB

english, 2013

17

Spatial localization of co-regulated genes exceeds genomic gene clustering in the Saccharomyces cerevisiae genome

Ben-Elazar, S., Yakhini, Z., Yanai, I.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 11.53 MB

english, 2013

18

Circularized synthetic oligodeoxynucleotides serve as promoterless RNA polymerase III templates for small RNA generation in human cells

Seidl, C. I., Lama, L., Ryan, K.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 5.24 MB

english, 2013

19

The structural stabilization of the three-way junction by Mg(II) represents the first step in the folding of a group II intron

Donghi, D., Pechlaner, M., Finazzo, C., Knobloch, B., Sigel, R. K. O.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 10.61 MB

english, 2013

20

RNA-interacting proteins act as site-specific repressors of ADAR2-mediated RNA editing and fluctuate upon neuronal stimulation

Tariq, A., Garncarz, W., Handl, C., Balik, A., Pusch, O., Jantsch, M. F.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 8.16 MB

english, 2013

21

Octamer-dependent transcription in T cells is mediated by NFAT and NF- B

Mueller, K., Quandt, J., Marienfeld, R. B., Weihrich, P., Fiedler, K., Claussnitzer, M., Laumen, H., Vaeth, M., Berberich-Siebelt, F., Serfling, E., Wirth, T., Brunner, C.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 7.87 MB

english, 2013

22

p300-mediated acetylation of TRF2 is required for maintaining functional telomeres

Her, Y. R., Chung, I. K.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 3.69 MB

english, 2013

23

A new structural framework for integrating replication protein A into DNA processing machinery

Brosey, C. A., Yan, C., Tsutakawa, S. E., Heller, W. T., Rambo, R. P., Tainer, J. A., Ivanov, I., Chazin, W. J.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 9.11 MB

english, 2013

24

Structural and functional evidence that Rad4 competes with Rad2 for binding to the Tfb1 subunit of TFIIH in NER

Lafrance-Vanasse, J., Arseneault, G., Cappadocia, L., Legault, P., Omichinski, J. G.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 5.05 MB

english, 2013

25

Gene-specific factors determine mitotic expression and bookmarking via alternate regulatory elements

Arampatzi, P., Gialitakis, M., Makatounakis, T., Papamatheakis, J.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 6.21 MB

english, 2013

26

Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity

Shabalina, S. A., Spiridonov, N. A., Kashina, A.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.45 MB

english, 2013

27

Space exploration by the promoter of a long human gene during one transcription cycle

Larkin, J. D., Papantonis, A., Cook, P. R., Marenduzzo, D.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 5.88 MB

english, 2013

28

Molecular determinants of HIV-1 NCp7 chaperone activity in maturation of the HIV-1 dimerization initiation site

Aduri, R., Briggs, K. T., Gorelick, R. J., Marino, J. P.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 21.61 MB

english, 2013

29

Transcription-independent role for human mitochondrial RNA polymerase in mitochondrial ribosome biogenesis

Surovtseva, Y. V., Shadel, G. S.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 5.89 MB

english, 2013

30

TrueSight: a new algorithm for splice junction detection using RNA-seq

Li, Y., Li-Byarlay, H., Burns, P., Borodovsky, M., Robinson, G. E., Ma, J.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 602 KB

english, 2013

31

Clostridium difficile TcdC protein binds four-stranded G-quadruplex structures

van Leeuwen, H. C., Bakker, D., Steindel, P., Kuijper, E. J., Corver, J.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.51 MB

english, 2013

32

Ribonucleotides and manganese ions improve non-homologous end joining by human Pol

Martin, M. J., Garcia-Ortiz, M. V., Esteban, V., Blanco, L.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 3.64 MB

english, 2013

33

Tight intramolecular regulation of the human Upf1 helicase by its N- and C-terminal domains

Fiorini, F., Boudvillain, M., Le Hir, H.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 1.67 MB

english, 2013

34

Unwinding of primer-templates by archaeal family-B DNA polymerases in response to template-strand uracil

Richardson, T. T., Wu, X., Keith, B. J., Heslop, P., Jones, A. C., Connolly, B. A.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 1.41 MB

english, 2013

35

Combinatorial mRNA binding by AUF1 and Argonaute 2 controls decay of selected target mRNAs

Wu, X., Chesoni, S., Rondeau, G., Tempesta, C., Patel, R., Charles, S., Daginawala, N., Zucconi, B. E., Kishor, A., Xu, G., Shi, Y., Li, M.-L., Irizarry-Barreto, P., Welsh, J., Wilson, G. M., Brewer,

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 965 KB

english, 2013

36

Cell cycle stage-specific roles of Rad18 in tolerance and repair of oxidative DNA damage

Yang, Y., Durando, M., Smith-Roe, S. L., Sproul, C., Greenwalt, A. M., Kaufmann, W., Oh, S., Hendrickson, E. A., Vaziri, C.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 5.82 MB

english, 2013

37

Evidence that a consensus element found in naturally intronless mRNAs promotes mRNA export

Lei, H., Zhai, B., Yin, S., Gygi, S., Reed, R.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 1.61 MB

english, 2013

38

Hepatitis C virus RNA: molecular switches mediated by long-range RNA-RNA interactions?

Shetty, S., Stefanovic, S., Mihailescu, M. R.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 6.24 MB

english, 2013

39

Nucleic Acids Research: VOLUME 41 ISSUE 4 2013

Journal:

Nucleic Acids Research

Year:

2013

File:

PDF, 520 KB

2013

40

Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions

Hutchins, A. P., Diez, D., Takahashi, Y., Ahmad, S., Jauch, R., Tremblay, M. L., Miranda-Saavedra, D.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 4.15 MB

english, 2013

41

Rev3, the catalytic subunit of Pol , is required for maintaining fragile site stability in human cells

Bhat, A., Andersen, P. L., Qin, Z., Xiao, W.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 11.34 MB

english, 2013

42

Engineering of a target site-specific recombinase by a combined evolution- and structure-guided approach

Abi-Ghanem, J., Chusainow, J., Karimova, M., Spiegel, C., Hofmann-Sieber, H., Hauber, J., Buchholz, F., Pisabarro, M. T.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 5.81 MB

english, 2013

43

RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus

Ishimaru, D., Plant, E. P., Sims, A. C., Yount, B. L., Roth, B. M., Eldho, N. V., Perez-Alvarado, G. C., Armbruster, D. W., Baric, R. S., Dinman, J. D., Taylor, D. R., Hennig, M.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 3.44 MB

english, 2013

44

Mechanical unfolding of human telomere G-quadruplex DNA probed by integrated fluorescence and magnetic tweezers spectroscopy

Long, X., Parks, J. W., Bagshaw, C. R., Stone, M. D.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.58 MB

english, 2013

45

DNA target sequence identification mechanism for dimer-active protein complexes

Landry, M. P., Zou, X., Wang, L., Huang, W. M., Schulten, K., Chemla, Y. R.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 7.15 MB

english, 2013

46

ellipsoidFN: a tool for identifying a heterogeneous set of cancer biomarkers based on gene expressions

Ren, X., Wang, Y., Chen, L., Zhang, X.-S., Jin, Q.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 739 KB

english, 2013

47

Phosphorylation and ubiquitination-dependent degradation of CABIN1 releases p53 for transactivation upon genotoxic stress

Choi, S.-Y., Jang, H., Roe, J.-S., Kim, S.-T., Cho, E.-J., Youn, H.-D.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 7.36 MB

english, 2013

48

Rbm20 regulates titin alternative splicing as a splicing repressor

Li, S., Guo, W., Dewey, C. N., Greaser, M. L.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 16.49 MB

english, 2013

49

Subscriptions

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 50 KB

english, 2013

50

Patterns of methylation heritability in a genome-wide analysis of four brain regions

Quon, G., Lippert, C., Heckerman, D., Listgarten, J.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 1.06 MB

english, 2013

51

A Myc-microRNA network promotes exit from quiescence by suppressing the interferon response and cell-cycle arrest genes

Polioudakis, D., Bhinge, A. A., Killion, P. J., Lee, B.-K., Abell, N. S., Iyer, V. R.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 676 KB

english, 2013

52

A dual role for mycobacterial RecO in RecA-dependent homologous recombination and RecA-independent single-strand annealing

Gupta, R., Ryzhikov, M., Koroleva, O., Unciuleac, M., Shuman, S., Korolev, S., Glickman, M. S.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 8.48 MB

english, 2013

53

A dual-site simultaneous binding mode in the interaction between parallel-stranded G-quadruplex [d(TGGGGT)]4 and cyanine dye 2,2'-diethyl-9-methyl-selenacarbocyanine bromide

Gai, W., Yang, Q., Xiang, J., Jiang, W., Li, Q., Sun, H., Guan, A., Shang, Q., Zhang, H., Tang, Y.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 7.12 MB

english, 2013

54

RAG and HMGB1 create a large bend in the 23RSS in the V(D)J recombination synaptic complexes

Ciubotaru, M., Trexler, A. J., Spiridon, L. N., Surleac, M. D., Rhoades, E., Petrescu, A. J., Schatz, D. G.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 4.67 MB

english, 2013

55

Decoding system for the AUA codon by tRNAIle with the UAU anticodon in Mycoplasma mobile

Taniguchi, T., Miyauchi, K., Nakane, D., Miyata, M., Muto, A., Nishimura, S., Suzuki, T.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 2.79 MB

english, 2013

56

Dissecting the in vivo assembly of the 30S ribosomal subunit reveals the role of RimM and general features of the assembly process

Guo, Q., Goto, S., Chen, Y., Feng, B., Xu, Y., Muto, A., Himeno, H., Deng, H., Lei, J., Gao, N.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 10.49 MB

english, 2013

57

A large-scale in vivo analysis reveals that TALENs are significantly more mutagenic than ZFNs generated using context-dependent assembly

Chen, S., Oikonomou, G., Chiu, C. N., Niles, B. J., Liu, J., Lee, D. A., Antoshechkin, I., Prober, D. A.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 4.21 MB

english, 2013

58

The high kinetic stability of a G-quadruplex limits hnRNP F qRRM3 binding to G-tract RNA

Samatanga, B., Dominguez, C., Jelesarov, I., Allain, F. H.- T.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 3.16 MB

english, 2013

59

Thermodynamic properties distinguish human mitochondrial aspartyl-tRNA synthetase from bacterial homolog with same 3D architecture

Neuenfeldt, A., Lorber, B., Ennifar, E., Gaudry, A., Sauter, C., Sissler, M., Florentz, C.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 7.45 MB

english, 2013