An ES cell system for rapid, spatial and temporal analysis of gene function in vitro and in vivo.

abstract：:Primer design is a fundamental technique that is widely used for polymerase chain reaction (PCR). Although many methods have been proposed for primer design, they require a great deal of manual effort to generate feasible and valid primers, including homology tests on off-target sequences using BLAST-like tools. That ...

journal_title：Nucleic acids research

authors： Kim H,Kang N,Chon KW,Kim S,Lee N,Koo J,Kim MS

更新日期：2015-11-16 00:00:00

abstract：:Previous work has demonstrated that the yeast SPT3 gene is required for transcription from delta sequences, the long terminal repeats that flank yeast Ty elements. In spt3 null mutants, transcription fails to initiate in delta sequences and instead initiates farther downstream. Null mutations in SPT3 cause other mutan...

journal_title：Nucleic acids research

authors： Winston F,Minehart PL

更新日期：1986-09-11 00:00:00

abstract：:Competition binding and UV melting studies of a DNA model system consisting of three, four or five mutually complementary oligonucleotides demonstrate that unpaired bases at the branch point stabilize three- and five-way junction loops but destabilize four-way junctions. The inclusion of unpaired nucleotides permits t...

journal_title：Nucleic acids research

authors： Kadrmas JL,Ravin AJ,Leontis NB

更新日期：1995-06-25 00:00:00

abstract：:The widely accepted model for the processing of tRNAs in Escherichia coli involves essential initial cleavages by RNase E within polycistronic transcripts to generate pre-tRNAs that subsequently become substrates for RNase P. However, recently we identified two polycistronic tRNA transcripts whose endonucleolytic proc...

journal_title：Nucleic acids research

authors： Mohanty BK,Kushner SR

更新日期：2008-02-01 00:00:00

abstract：:Mitochondrial transcription factor A (TFAM) stimulates transcription from mitochondrial DNA (mtDNA) promoters in vitro and in organello. To investigate whether changes of TFAM levels also modulate transcription and replication in situ, the protein was transiently overexpressed in cultured cells. Mitochondrial mRNAs we...

journal_title：Nucleic acids research

authors： Maniura-Weber K,Goffart S,Garstka HL,Montoya J,Wiesner RJ

更新日期：2004-11-16 00:00:00

abstract：:The nucleotide sequence of the 5S ribosomal RNA of Streptococcus cremoris has been determined. The sequence is 5' (sequence in text) 3'. Comparison of the S. cremoris 5S RNA sequence to an updated prokaryotic generalized 5S RNA structural model shows that this 5S RNA contains some unusual structural features. These fe...

journal_title：Nucleic acids research

authors： Neimark H,Andersen J,Delihas N

更新日期：1983-11-11 00:00:00

abstract：:Comparisons of proteins show that they evolve through the movement of domains. However, in many cases, the underlying mechanisms remain unclear. Here, we observed the movements of DNA recognition domains between non-orthologous proteins within a prokaryote genome. Restriction-modification (RM) systems, consisting of a...

journal_title：Nucleic acids research

authors： Furuta Y,Kobayashi I

更新日期：2012-10-01 00:00:00

abstract：:Publicly available database of co-expressed gene sets would be a valuable tool for a wide variety of experimental designs, including targeting of genes for functional identification or for regulatory investigation. Here, we report the construction of an Arabidopsis thaliana trans-factor and cis-element prediction data...

journal_title：Nucleic acids research

authors： Obayashi T,Kinoshita K,Nakai K,Shibaoka M,Hayashi S,Saeki M,Shibata D,Saito K,Ohta H

更新日期：2007-01-01 00:00:00

abstract：:Escherichia coli leucyl-tRNA synthetase (LeuRS) aminoacylates up to six different class II tRNA(leu) molecules. Each has a distinct anticodon and varied nucleotides in other regions of the tRNA. Attempts to construct a minihelix RNA that can be aminoacylated with leucine have been unsuccessful. Herein, we describe the...

journal_title：Nucleic acids research

authors： Larkin DC,Williams AM,Martinis SA,Fox GE

更新日期：2002-05-15 00:00:00

abstract：:Abasic substitutions in the non-template strand and promoter sequence changes were made to assess the roles of various promoter features in sigma70 holoenzyme interactions with fork junction probes. Removal of -10 element non-template single strand bases, leaving the phosphodiester backbone intact, did not interfere w...

journal_title：Nucleic acids research

authors： Fenton MS,Gralla JD

更新日期：2003-06-01 00:00:00

abstract：:A type II restriction endonuclease, DraI, isolated from Deinococcus radiophilus ATCC 27603 recognises the palindromic hexanucleotide sequence (formula; see text) and cleaves it, as indicated by the arrows, to produce blunt-ended fragments. The yield of enzyme is 100 to 1000 times that of the only other known type II r...

journal_title：Nucleic acids research

authors： Purvis IJ,Moseley BE

更新日期：1983-08-25 00:00:00

abstract：:In a pilot study on SAGE on Reed-Sternberg cells we have sequenced 1055 tags representing 701 genes. Screening of the GenBank database resulted in the identification of a corresponding gene or EST for 490 of them. For 211 of the tags no homology could be detected. A major problem of the serial analysis of gene express...

journal_title：Nucleic acids research

authors： van den Berg A,van der Leij J,Poppema S

更新日期：1999-09-01 00:00:00

abstract：:Using a combination of mathematical modelling, statistical simulation and large-scale data analysis we study the properties of linear regulatory chains (LRCs) within gene regulatory networks (GRNs). Our modelling indicates that downstream genes embedded within LRCs are highly insulated from the variation in expression...

journal_title：Nucleic acids research

authors： Liu D,Albergante L,Newman TJ

更新日期：2017-07-07 00:00:00

abstract：:Genomic Denaturing Gradient Gel Electrophoresis (gDGGE) provides an alternative to the standard method of restriction fragment length polymorphism (RFLP) analysis for identifying polymorphic sequence variation in genomic DNA. For gDGGE, genomic DNA is cleaved by restriction enzymes, separated in a polyacrylamide gel c...

journal_title：Nucleic acids research

authors： Burmeister M,diSibio G,Cox DR,Myers RM

更新日期：1991-04-11 00:00:00

abstract：:Proteins engage in highly selective interactions with their macromolecular partners. Sequence variants that alter protein binding affinity may cause significant perturbations or complete abolishment of function, potentially leading to diseases. There exists a persistent need to develop a mechanistic understanding of i...

journal_title：Nucleic acids research

authors： Li M,Simonetti FL,Goncearenco A,Panchenko AR

更新日期：2016-07-08 00:00:00

abstract：:Herpes simplex virus-1 US11 is a RNA-binding protein with a novel RNA-binding domain. US11 has been reported to exhibit sequence- and conformation-specific RNA-binding, but the sequences and conformations important for binding are not known. US11 has also been described as a double-stranded RNA (dsRNA)-binding protein...

journal_title：Nucleic acids research

authors： Bryant KF,Cox JC,Wang H,Hogle JM,Ellington AD,Coen DM

更新日期：2005-10-24 00:00:00

abstract：:In order to investigate the possible role of RNA secondary structure in determining the efficiency and specificity of mRNA splicing, the structures of sequences at three acceptor splice sites in adenovirus were studied. Transcripts spanning intron-exon junctions were synthesized using SP6 RNA polymerase and analyzed u...

journal_title：Nucleic acids research

authors： Munroe SH

更新日期：1984-11-26 00:00:00

abstract：:Ditercalinium, an antitumor bifunctional intercalator which forms a high affinity reversible complex with DNA, was found to be specifically cytotoxic for polA and lig7 E. coli strains. In the polA strain, the cytotoxic effect of ditercalinium was suppressed by the uvrA mutation. DNA single strand breaks accumulated in...

journal_title：Nucleic acids research

authors： Lambert B,Roques BP,Le Pecq JB

更新日期：1988-02-11 00:00:00

abstract：:The potency of the immune response has still to be harnessed effectively to combat human cancers. However, the discovery of T-cell targets in melanomas and other tumors has raised the possibility that cancer vaccines can be used to induce a therapeutically effective immune response against cancer. The targets, cancer-...

journal_title：Nucleic acids research

authors： Almeida LG,Sakabe NJ,deOliveira AR,Silva MC,Mundstein AS,Cohen T,Chen YT,Chua R,Gurung S,Gnjatic S,Jungbluth AA,Caballero OL,Bairoch A,Kiesler E,White SL,Simpson AJ,Old LJ,Camargo AA,Vasconcelos AT

更新日期：2009-01-01 00:00:00

abstract：:The contacts of phosphate groups in mRNAs with ribosomes were studied. Two mRNAs were used: one mRNA contained in the middle two defined codons to construct the pre- and the post-translocational states, the other was a sequence around the initiation site of the natural cro-mRNA. Phosphorothioate nucleotides were rando...

journal_title：Nucleic acids research

authors： Alexeeva EV,Shpanchenko OV,Dontsova OA,Bogdanov AA,Nierhaus KH

更新日期：1996-06-15 00:00:00

abstract：:The nucleotide sequence of the control region of the divergent argECBH operon has been established in the wild type and in mutants affecting expression of these genes. The argE and argCBH promoters face each other and overlap with an operator region containing two domains which may act as distinct repressor binding si...

journal_title：Nucleic acids research

authors： Piette J,Cunin R,Boyen A,Charlier D,Crabeel M,Van Vliet F,Glansdorff N,Squires C,Squires CL

更新日期：1982-12-20 00:00:00

abstract：:We show that using low denaturation temperatures (80-88 degrees C) during ligation mediated PCR (LM PCR) of bacterial DNA leads to the amplification of limited sets of the less stable DNA fragments. A set of electrophoretic patterns of such fragments obtained at different denaturation temperatures forms the PCR meltin...

journal_title：Nucleic acids research

authors： Masny A,Płucienniczak A

更新日期：2003-09-15 00:00:00

abstract：:The σ subunit of bacterial RNA polymerase (RNAP) has been implicated in all steps of transcription initiation, including promoter recognition and opening, priming of RNA synthesis, abortive initiation and promoter escape. The post-promoter-recognition σ functions were proposed to depend on its conserved region σ3.2 th...

journal_title：Nucleic acids research

authors： Pupov D,Kuzin I,Bass I,Kulbachinskiy A

更新日期：2014-04-01 00:00:00

abstract：:Identification of common sub-sequences for a group of functionally related DNA sequences can shed light on the role of such elements in cell-specific gene expression. In the megakaryocytic lineage, no one single unique transcription factor was described as linage specific, raising the possibility that a cluster of gen...

journal_title：Nucleic acids research

authors： Hazony Y,Lu J,St Hilaire C,Ravid K

更新日期：2006-01-01 00:00:00

abstract：:MLL, the trithorax ortholog, is a well-characterized histone 3 lysine 4 methyltransferase that is crucial for proper regulation of the Hox genes during embryonic development. Chromosomal translocations, disrupting the Mll gene, lead to aggressive leukemia with poor prognosis. However, the functions of MLL in cellular ...

journal_title：Nucleic acids research

authors： Ali A,Veeranki SN,Tyagi S

更新日期：2014-07-01 00:00:00

abstract：:The adenovirus late region 1 (L1) represents an example of an alternatively spliced gene where one 5' splice site is spliced to two alternative 3' splice sites, to produce two mRNAs; the 52,55K and IIIa mRNAs, respectively. Accumulation of the L1 mRNAs is temporally regulated during the infectious cycle. Thus, the pro...

journal_title：Nucleic acids research

authors： Kreivi JP,Akusjärvi G

更新日期：1994-02-11 00:00:00

abstract：:Cellular liquid-liquid phase separation (LLPS) results in the formation of dynamic granules that play an important role in many biological processes. On a molecular level, the clustering of proteins into a confined space results from an indefinite network of intermolecular interactions. Here, we introduce and exploit ...

journal_title：Nucleic acids research

authors： Schütz S,Nöldeke ER,Sprangers R

更新日期：2017-06-20 00:00:00

abstract：:The presence of a homing endonuclease gene (HEG) within a microbial intron or intein empowers the entire element with the ability to invade genomic targets. The persistence of a homing endonuclease lineage depends in part on conservation of its DNA target site. One such rDNA sequence has been invaded both in archaea a...

journal_title：Nucleic acids research

authors： Nomura N,Nomura Y,Sussman D,Klein D,Stoddard BL

更新日期：2008-12-01 00:00:00

abstract：:Mammalian mRNAs are generated by complex and coordinated biogenesis pathways and acquire 5'-end m(7)G caps that play fundamental roles in processing and translation. Here we show that several selenoprotein mRNAs are not recognized efficiently by translation initiation factor eIF4E because they bear a hypermethylated c...

journal_title：Nucleic acids research

authors： Wurth L,Gribling-Burrer AS,Verheggen C,Leichter M,Takeuchi A,Baudrey S,Martin F,Krol A,Bertrand E,Allmang C

更新日期：2014-07-01 00:00:00

abstract：:Knowledge of subcellular localizations (SCLs) of plant proteins relates to their functions and aids in understanding the regulation of biological processes at the cellular level. We present PlantLoc, a highly accurate and fast webserver for predicting the multi-label SCLs of plant proteins. The PlantLoc server has two...

journal_title：Nucleic acids research

authors： Tang S,Li T,Cong P,Xiong W,Wang Z,Sun J

更新日期：2013-07-01 00:00:00