NMR structural analysis of DNA recognition by a novel Myb1 DNA-binding domain in the protozoan parasite Trichomonas vaginalis.

abstract：:VapD-like virulence-associated proteins have been found in many organisms, but little is known about this protein family including the 3D structure of these proteins. Recently, a relationship between the Cas2 family of ribonucleases associated with the CRISPR system of microbial immunity and VapD was suggested. Here, ...

journal_title：Nucleic acids research

authors： Kwon AR,Kim JH,Park SJ,Lee KY,Min YH,Im H,Lee I,Lee KY,Lee BJ

更新日期：2012-05-01 00:00:00

abstract：:Sequences from -3500 to +1365 of the chicken histone H5 gene have been analyzed for the presence of cis-acting elements in H5 expressing (transformed CFU-E) and non-expressing cells (fibroblasts). The region from -3500 to -115 had little effect on transcription. Proximal upstream sequences contain a negative element (...

journal_title：Nucleic acids research

authors： Rousseau S,Renaud J,Ruiz-Carrillo A

更新日期：1989-09-25 00:00:00

abstract：:The environmental carcinogen benzo[a]pyrene (BP) is metabolized to reactive diol epoxides that bind to cellular DNA by predominantly forming N2-guanine adducts (G*). Mutation hotspots for these adducts are frequently found in 5'- ... GG ... dinucleotide sequences, but their origins are poorly understood. Here we used ...

journal_title：Nucleic acids research

authors： Rodríguez FA,Cai Y,Lin C,Tang Y,Kolbanovskiy A,Amin S,Patel DJ,Broyde S,Geacintov NE

更新日期：2007-01-01 00:00:00

abstract：:Molecular models of six anthracycline antibiotics and their complexes with 32 distinct DNA octamer sequences were created and analyzed using HINT (Hydropathic INTeractions) to describe binding. The averaged binding scores were then used to calculate the free energies of binding for comparison with experimentally deter...

journal_title：Nucleic acids research

authors： Cashman DJ,Scarsdale JN,Kellogg GE

更新日期：2003-08-01 00:00:00

abstract：:A linear DNA plasmid, designated pLLE1, has been isolated from a mitochondrial fraction of a strain of Lentinus edodes. pLLE1(11.0 kbp) was sensitive to the 3'----5'-acting exonuclease III and resistant to the 5'----3'-acting lambda exonuclease. It showed no homology with mitochondrial and nuclear genomic DNAs of plas...

journal_title：Nucleic acids research

authors： Katayose Y,Kajiwara S,Shishido K

更新日期：1990-03-25 00:00:00

abstract：:Properties of a mutant bacteriophage T2 DNA [N:(6)-adenine] methyltransferase (T2 Dam MTase) have been investigated for its potential utilization in RecA-assisted restriction endonuclease (RARE) cleavage. Steady-state kinetic analyses with oligonucleotide duplexes revealed that, compared to wild-type T4 Dam, both wild...

journal_title：Nucleic acids research

authors： Minko I,Hattman S,Lloyd RS,Kossykh V

更新日期：2001-04-01 00:00:00

abstract：:Codon usage data has been compiled for 110 yeast genes. Cluster analysis on relative synonymous codon usage revealed two distinct groups of genes. One group corresponds to highly expressed genes, and has much more extreme synonymous codon preference. The pattern of codon usage observed is consistent with that expected...

journal_title：Nucleic acids research

authors： Sharp PM,Tuohy TM,Mosurski KR

更新日期：1986-07-11 00:00:00

abstract：:Neph et al. (2012) (Circuitry and dynamics of human transcription factor regulatory networks. Cell, 150: 1274-1286) reported the transcription factor (TF) regulatory networks of 41 human cell types using the DNaseI footprinting technique. This provides a valuable resource for uncovering regulation principles in differ...

journal_title：Nucleic acids research

authors： Zhang S,Tian D,Tran NH,Choi KP,Zhang L

更新日期：2014-11-10 00:00:00

abstract：:The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently offers prediction of secondary structure from a single sequence, prediction of the consensus secondary structure for a s...

journal_title：Nucleic acids research

authors： Hofacker IL

更新日期：2003-07-01 00:00:00

abstract：:Influenza viruses have a segmented viral RNA (vRNA) genome, which is replicated by the viral RNA-dependent RNA polymerase (RNAP). Replication initiates on the vRNA 3' terminus, producing a complementary RNA (cRNA) intermediate, which serves as a template for the synthesis of new vRNA. RNAP structures show the 3' termi...

journal_title：Nucleic acids research

authors： Robb NC,Te Velthuis AJ,Wieneke R,Tampé R,Cordes T,Fodor E,Kapanidis AN

更新日期：2016-12-01 00:00:00

abstract：:Sequence heterogeneity is a common characteristic of RNA viruses that is often referred to as sub-populations or quasispecies. Traditional techniques used for assembly of short sequence reads produced by deep sequencing, such as de-novo assemblers, ignore the underlying diversity. Here, we introduce a novel algorithm ...

journal_title：Nucleic acids research

authors： Karagiannis K,Simonyan V,Chumakov K,Mazumder R

更新日期：2017-11-02 00:00:00

abstract：:PSF (a.k.a. SFPQ) is a ubiquitously expressed, essential nuclear protein with important roles in DNA damage repair and RNA biogenesis. In stimulated T cells, PSF binds to and suppresses the inclusion of CD45 exon 4 in the final mRNA; however, in resting cells, TRAP150 binds PSF and prevents access to the CD45 RNA, tho...

journal_title：Nucleic acids research

authors： Yarosh CA,Tapescu I,Thompson MG,Qiu J,Mallory MJ,Fu XD,Lynch KW

更新日期：2015-10-15 00:00:00

abstract：:The HIV-1 nucleocapsid (NC) protein is a small, basic protein containing two retroviral zinc fingers. It is a highly active nucleic acid chaperone; because of this activity, it plays a crucial role in virus replication as a cofactor during reverse transcription, and is probably important in other steps of the replicat...

journal_title：Nucleic acids research

authors： Fisher RJ,Fivash MJ,Stephen AG,Hagan NA,Shenoy SR,Medaglia MV,Smith LR,Worthy KM,Simpson JT,Shoemaker R,McNitt KL,Johnson DG,Hixson CV,Gorelick RJ,Fabris D,Henderson LE,Rein A

更新日期：2006-01-24 00:00:00

abstract：:About 40% of the genes in the nematode Caenorhabditis elegans have homologs in humans. Based on the history of this model system, it is clear that the application of genetic methods to the study of this set of genes would provide important clues to their function in humans. To facilitate such genetic studies, we are e...

journal_title：Nucleic acids research

authors： Edgley M,D'Souza A,Moulder G,McKay S,Shen B,Gilchrist E,Moerman D,Barstead R

更新日期：2002-06-15 00:00:00

abstract：:The nucleotide sequence of the celD gene, encoding the previously crystallized endoglucanase D of Clostridium thermocellum, is reported. The enzyme shares a conserved, reiterated domain with the COOH-terminal end of endoglucanases A and B from the same organism. The overexpression in Escherichia coli of celD subcloned...

journal_title：Nucleic acids research

authors： Joliff G,Béguin P,Aubert JP

更新日期：1986-11-11 00:00:00

abstract：:The B-subunits associated with the replicative DNA polymerases are conserved from Archaea to humans, whereas the corresponding catalytic subunits are not related. The latter belong to the B and D DNA polymerase families in eukaryotes and archaea, respectively. Sequence analysis places the B-subunits within the calcine...

journal_title：Nucleic acids research

authors： Jokela M,Eskelinen A,Pospiech H,Rouvinen J,Syväoja JE

更新日期：2004-04-30 00:00:00

abstract：:We report, herein, a new class of RNAi trigger molecules based on the unconventional parallel hybridization of two oligonucleotide chains. We have prepared and studied several parallel stranded (ps) duplexes, in which the parallel orientation is achieved through incorporation of isoguanine and isocytosine to form reve...

journal_title：Nucleic acids research

authors： Habibian M,Yahyaee-Anzahaee M,Lucic M,Moroz E,Martín-Pintado N,Di Giovanni LD,Leroux JC,Hall J,González C,Damha MJ

更新日期：2018-02-28 00:00:00

abstract：:eIF4E-binding proteins (4E-BPs) regulate translation of mRNAs in eukaryotes. However the extent to which specific mRNA targets are regulated by 4E-BPs remains unknown. We performed translational profiling by microarray analysis of polysome and monosome associated mRNAs in wild-type and mutant cells to identify mRNAs i...

journal_title：Nucleic acids research

authors： Cridge AG,Castelli LM,Smirnova JB,Selley JN,Rowe W,Hubbard SJ,McCarthy JE,Ashe MP,Grant CM,Pavitt GD

更新日期：2010-12-01 00:00:00

abstract：:Soil salinity is a significant threat to sustainable agricultural production worldwide. Plants must adjust their developmental and physiological processes to cope with salt stress. Although the capacity for adaptation ultimately depends on the genome, the exceptional versatility in gene regulation provided by the spli...

journal_title：Nucleic acids research

authors： Gu J,Xia Z,Luo Y,Jiang X,Qian B,Xie H,Zhu JK,Xiong L,Zhu J,Wang ZY

更新日期：2018-02-28 00:00:00

abstract：:Non-homologous DNA end joining (NHEJ) is considered the major pathway of double-strand break (DSB) repair in mammalian cells and depends, among other things, on the DNA end-binding Ku70/80 hetero-dimer. To investigate the function of Ku in NHEJ we have compared the ability of cell-free extracts from wild-type CHO-K1 c...

journal_title：Nucleic acids research

authors： Feldmann E,Schmiemann V,Goedecke W,Reichenberger S,Pfeiffer P

更新日期：2000-07-01 00:00:00

abstract：:Equilibrative nucleoside transporters (ENTs) are a recently characterized and poorly understood group of membrane proteins that are important in the uptake of endogenous nucleosides required for nucleic acid and nucleoside triphosphate synthesis. Despite their central importance in cellular metabolism and nucleoside a...

journal_title：Nucleic acids research

authors： Sankar N,Machado J,Abdulla P,Hilliker AJ,Coe IR

更新日期：2002-10-15 00:00:00

abstract：:The Medaka Expression Pattern Database (MEPD) stores and integrates information of gene expression during embryonic development of the small freshwater fish Medaka (Oryzias latipes). Expression patterns of genes identified by ESTs are documented by images and by descriptions through parameters such as staining intensi...

journal_title：Nucleic acids research

authors： Henrich T,Ramialison M,Quiring R,Wittbrodt B,Furutani-Seiki M,Wittbrodt J,Kondoh H,Medaka Expression Pattern Database.

更新日期：2003-01-01 00:00:00

abstract：:Unmodified tRNA molecules are useful for many purposes in cell-free protein biosynthesis, but there is little information about how the lack of tRNA post-transcriptional modifications affects the coding specificity for synonymous codons. In the present study, we prepared an unmodified form of Escherichia coli tRNA1Ser...

journal_title：Nucleic acids research

authors： Takai K,Takaku H,Yokoyama S

更新日期：1996-08-01 00:00:00

abstract：:Tetramers of the arginine-rich histones H3 and H4 associate with supercoiled SV40 DNA either singly, giving tetrameric nucleoprotein complexes or in pairs giving octameric complexes, both of which are visualized as beads in the electron microscope. The relative amounts of the two complexes may be revealed by complete ...

journal_title：Nucleic acids research

authors： Thomas JO,Oudet P

更新日期：1979-10-10 00:00:00

abstract：:Ovarian poly (A) + RNA from Xenopus laevis and Xenopus borealis was used to construct two cDNA libraries which were screened for histone sequences. cDNA clones to H4 mRNA were obtained from both species and an H3 cDNA clone from Xenopus laevis. The complete DNA sequences of these clones have been determined and are pr...

journal_title：Nucleic acids research

authors： Turner PC,Woodland HR

更新日期：1982-06-25 00:00:00

abstract：:Simian cells have been transformed with SV40 origin-defective recombinant plasmids containing the tsA209 T-antigen gene. These plasmids contain deletions of either 5 or 52 nucleotides that include the BglI site at the SV40 ori, are defective for replication in COS-1 cells but retain a functional SV40 early promoter. T...

journal_title：Nucleic acids research

authors： Portela A,de la Luna S,Melero JA,Vara J,Jiménez A,Ortín J

更新日期：1985-11-25 00:00:00

abstract：:Nucleotide excision repair (NER) is a major DNA repair pathway for a variety of DNA lesions. XPB plays a key role in DNA opening at damage sites and coordinating damage incision by nucleases. XPB is conserved from archaea to human. In archaea, XPB is associated with a nuclease Bax1. Here we report crystal structures o...

journal_title：Nucleic acids research

authors： DuPrez K,He F,Chen Z,Hilario E,Fan L

更新日期：2020-06-19 00:00:00

abstract：:Transcription of transfer RNA genes by RNA polymerase III (Pol III) is controlled by general factors, TFIIIB and TFIIIC, and a negative regulator, Maf1. Here we report the interplay between TFIIIC and Maf1 in controlling Pol III activity upon the physiological switch of yeast from fermentation to respiration. TFIIIC d...

journal_title：Nucleic acids research

authors： Ciesla M,Skowronek E,Boguta M

更新日期：2018-10-12 00:00:00

abstract：:We have measured the amount of 5S-ribosomal DNA in the genomes of Xenopus laevis, Triturus cristatus carnifex and Ambystoma mexicanum, three species of Amphibians which have widely different C-values. Our best estimate is that these organisms have about 24,000, 32,000 and 61,000 5S-genes per haploid genome respectivel...

journal_title：Nucleic acids research

authors： Hilder VA,Dawson GA,Vlad MT

更新日期：1983-04-25 00:00:00

abstract：:A number of novel phosphate triester derivatives of the anti-cancer nucleoside analogue araC have been prepared by a rapid 2-step procedure, not necessitating prior sugar protection. Spectroscopic and lipophilicity data have been collected on these compounds. An in vitro assay indicated inhibition of thymidine incorpo...

journal_title：Nucleic acids research

authors： Jones BC,McGuigan C,Riley PA

更新日期：1989-09-25 00:00:00