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Volume 41; Issue 4
Main
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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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39
Nucleic Acids Research: VOLUME 41 ISSUE 4 2013
Journal:
Nucleic Acids Research
Year:
2013
File:
PDF, 520 KB
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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
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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
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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
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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
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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
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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
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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
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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
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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
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49
Subscriptions
Journal:
Nucleic Acids Research
Year:
2013
Language:
english
File:
PDF, 50 KB
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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