GBA server: EST-based digital gene expression profiling.

abstract：:Clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated Cas proteins comprise a prokaryotic RNA-guided adaptive immune system that interferes with mobile genetic elements, such as plasmids and phages. The type I-E CRISPR interference complex Cascade from Escherichia coli is composed of...

journal_title：Nucleic acids research

authors： Beloglazova N,Kuznedelov K,Flick R,Datsenko KA,Brown G,Popovic A,Lemak S,Semenova E,Severinov K,Yakunin AF

更新日期：2015-01-01 00:00:00

abstract：:'Linker scanning' has been used as an efficient method for systematically surveying a segment of DNA for functional elements by mutagenesis. A three-step PCR method was developed to simplify this process. In this method, a set of 'mutation primers' was made with 6 to 8 base substitutions in the center of the primers. ...

journal_title：Nucleic acids research

authors： Li XM,Shapiro LJ

更新日期：1993-08-11 00:00:00

abstract：:The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The s...

journal_title：Nucleic acids research

authors： Wacker A,Weigand JE,Akabayov SR,Altincekic N,Bains JK,Banijamali E,Binas O,Castillo-Martinez J,Cetiner E,Ceylan B,Chiu LY,Davila-Calderon J,Dhamotharan K,Duchardt-Ferner E,Ferner J,Frydman L,Fürtig B,Gallego J,Grün JT

更新日期：2020-12-16 00:00:00

abstract：:Nucleosomes, a basic structural unit of eukaryotic chromatin, play a significant role in regulating gene expression. We have developed a web tool based on DNA sequences known from empirical and theoretical studies to influence DNA bending and flexibility, and to exclude nucleosomes. NXSensor (available at http://www.s...

journal_title：Nucleic acids research

authors： Luykx P,Bajić IV,Khuri S

更新日期：2006-07-01 00:00:00

abstract：:Methionyl-tRNA synthetase belongs to the class I aminoacyl-tRNA synthetase family characterized both by a catalytic center built around a Rossmann Fold and by the presence of the two peptidic marker sequences HIGH and KMSKS. In this study, the role of the 21HLGH24 motif of Escherichia coli methionyl-tRNA synthetase wa...

journal_title：Nucleic acids research

authors： Schmitt E,Panvert M,Blanquet S,Mechulam Y

更新日期：1995-12-11 00:00:00

abstract：:From a library of nucleic acid molecules, which are randomized in parts of their sequence, unique sequence variants can be selected for specific properties. The planning of such an in vitro selection experiment requires some consideration regarding how much DNA template or RNA transcript should be used initially. The ...

journal_title：Nucleic acids research

authors： Tabler M,Benos P,Dörr M

更新日期：1996-09-01 00:00:00

abstract：:Chinese hamster genomic DNA sequences from the region downstream of the dihydrofolate reductase (DHFR) gene reported to contain a chromosomal origin of bidirectional DNA replication (OBR-1) were tested for their ability to support autonomous DNA replication in human cells. A 13.3 kilobase fragment containing OBR-1 and...

journal_title：Nucleic acids research

authors： Caddle MS,Calos MP

更新日期：1992-11-25 00:00:00

abstract：:This paper describes a computer program designed to look for similarities between pairs of nucleic or amino acid sequences. The program looks both for segments of perfect identity or for regions where, using a scoring matrix, a minimum value is exceeded. The results of comparisons are presented as a matrix which is di...

journal_title：Nucleic acids research

authors： Staden R

更新日期：1982-05-11 00:00:00

abstract：:The Membranome database was developed to assist analysis and computational modeling of single-pass (bitopic) transmembrane (TM) proteins and their complexes by providing structural information about these proteins on a genomic scale. The database currently collects data on >6000 bitopic proteins from Homo sapiens, Ara...

journal_title：Nucleic acids research

authors： Lomize AL,Lomize MA,Krolicki SR,Pogozheva ID

更新日期：2017-01-04 00:00:00

abstract：:Mitochondrial DNA maintenance and segregation are dependent on the actin cytoskeleton in budding yeast. We found two cytoskeletal proteins among six proteins tightly associated with rat liver mitochondrial DNA: non-muscle myosin heavy chain IIA and β-actin. In human cells, transient gene silencing of MYH9 (encoding no...

journal_title：Nucleic acids research

authors： Reyes A,He J,Mao CC,Bailey LJ,Di Re M,Sembongi H,Kazak L,Dzionek K,Holmes JB,Cluett TJ,Harbour ME,Fearnley IM,Crouch RJ,Conti MA,Adelstein RS,Walker JE,Holt IJ

更新日期：2011-07-01 00:00:00

abstract：:Most small nucleolar RNAs (snoRNAs) guide rRNA nucleotide modifications, some participate in pre-rRNA cleavages, and a few have both functions. These activities involve direct base-pairing of the snoRNA with pre-rRNA using different domains. It is not known if the modification and processing functions occur independen...

journal_title：Nucleic acids research

authors： Liang XH,Liu Q,Liu Q,King TH,Fournier MJ

更新日期：2010-06-01 00:00:00

abstract：:From a sarkosyl-insoluble outer membrane fraction prepared from the Helicobacter pylori strain ATCC 43504, 19 proteins could be sequenced N-terminally by Edman degradation. Oligonucleotides were deduced and used for screening of a genomic library. From the isolated genes, five code for different members of a H.pylori ...

journal_title：Nucleic acids research

authors： Peck B,Ortkamp M,Diehl KD,Hundt E,Knapp B

更新日期：1999-08-15 00:00:00

abstract：:Based on parameters governing promoter activity and using regulatory elements of the lac, ara and tet operon transcription control sequences were composed which permit the regulation in Escherichia coli of several gene activities independently and quantitatively. The novel promoter PLtetO-1 allows the regulation of ge...

journal_title：Nucleic acids research

authors： Lutz R,Bujard H

更新日期：1997-03-15 00:00:00

abstract：:Plasmids p749, p106, and p150 contain cDNA inserts complementary to rat skeletal muscle actin mRNA. Nucleotide sequence analysis indicates the following sequence relationships: p749 specifies codons 171 to 360; p150 specifies codons 357 to 374 together with 120 nucleotides of the 3'-non-translated region; p106 specifi...

journal_title：Nucleic acids research

authors： Shani M,Nudel U,Zevin-Sonkin D,Zakut R,Givol D,Katcoff D,Carmon Y,Reiter J,Frischauf AM,Yaffe D

更新日期：1981-02-11 00:00:00

abstract：:Rotaviruses are a major cause of acute, often fatal, gastroenteritis in infants and young children world-wide. Virions contain an 11 segment double-stranded RNA genome. Little is known about the cis-acting sequences and structural elements of the viral RNAs. Using a database of 1621 full-length sequences of mammalian ...

journal_title：Nucleic acids research

authors： Li W,Manktelow E,von Kirchbach JC,Gog JR,Desselberger U,Lever AM

更新日期：2010-11-01 00:00:00

abstract：:A highly sensitive method to detect traces of aldehyde-containing apurinic/apyrimidinic (AP) sites in nucleic acids has been developed. Based on this method, a novel approach to detect DNA base mismatches recognized by the mismatch repair glycosylase MutY is demonstrated. Open chain aldehydes generated in nucleic acid...

journal_title：Nucleic acids research

authors： Maulik G,Botchway S,Chakrabarti S,Tetradis S,Price B,Makrigiorgos GM

更新日期：1999-03-01 00:00:00

abstract：:PUF proteins, named for Drosophila Pumilio (PUM) and Caenorhabditis elegans fem-3-binding factor (FBF), recognize specific sequences in the mRNAs they bind and control. RNA binding by classical PUF proteins is mediated by a characteristic PUM homology domain (PUM-HD). The Puf1 and Puf2 proteins possess a distinct arch...

journal_title：Nucleic acids research

authors： Qiu C,Dutcher RC,Porter DF,Arava Y,Wickens M,Hall TMT

更新日期：2019-09-19 00:00:00

abstract：:With the development of High-Throughput Sequencing (HTS) thousands of human genomes have now been sequenced. Whenever different studies analyze the same genome they usually agree on the amount of single-nucleotide polymorphisms, but differ dramatically on the number of insertion and deletion variants (indels). Further...

journal_title：Nucleic acids research

authors： Jiang Y,Turinsky AL,Brudno M

更新日期：2015-09-03 00:00:00

abstract：:A series of unusual folding regions (UFR) immediately 3' to the cleavage site of the outer membrane protein (OMP) and transmembrane protein (TMP) were detected in the envelope gene RNA of the human immunodeficiency virus (HIV-1, HIV-2) and simian immunodeficiency virus (SIV) by an extensive Monte Carlo simulation. The...

journal_title：Nucleic acids research

authors： Le SY,Malim MH,Cullen BR,Maizel JV

更新日期：1990-03-25 00:00:00

abstract：:Transcription factors are important gene regulators with distinctive roles in development, cell signaling and cell cycling, and they have been associated with many diseases. The ConTra v3 web server allows easy visualization and exploration of predicted transcription factor binding sites (TFBSs) in any genomic region ...

journal_title：Nucleic acids research

authors： Kreft L,Soete A,Hulpiau P,Botzki A,Saeys Y,De Bleser P

更新日期：2017-07-03 00:00:00

abstract：:Analysis of processing, assembly, and function of higher eukaryotic ribosomal RNA (rRNA) has been hindered by the lack of an expression system that enables rRNA to be modified and then examined functionally. Given the potential usefulness of such a system, we have developed one for mammalian 18S rRNA. We inserted a se...

journal_title：Nucleic acids research

authors： Burman LG,Mauro VP

更新日期：2012-09-01 00:00:00

abstract：:We have studied the role of the C-terminal domain of the alpha subunit (alphaCTD) of Escherichia coli RNA polymerase during transcription initiation at promoters lacking an UP-element. The temperature requirement for open complex formation was used as an indication of the kinetics of this process. We have previously s...

journal_title：Nucleic acids research

authors： Burns HD,Ishihama A,Minchin SD

更新日期：1999-05-01 00:00:00

abstract：:The discovery of hydroxymethyl-, formyl- and carboxylcytosine, generated through oxidation of methylcytosine by TET dioxygenases, raised the question how these modifications contribute to epigenetic regulation. As they are subjected to complex regulation in vivo, we dissected links to gene expression with in vitro mod...

journal_title：Nucleic acids research

authors： Müller U,Bauer C,Siegl M,Rottach A,Leonhardt H

更新日期：2014-07-01 00:00:00

abstract：:Despite the large number of noncoding RNAs in human genome and their roles in many diseases include cancer, we know very little about them due to lack of structural clues. The centerpiece of the structural clues is the full RNA base-pairing structure of secondary and tertiary contacts that can be precisely obtained on...

journal_title：Nucleic acids research

authors： Zhang Z,Xiong P,Zhang T,Wang J,Zhan J,Zhou Y

更新日期：2020-02-20 00:00:00

abstract：:Compounds that are covalent analogues of nucleic acid base pairs of normal, long, and short C1' to C1' dimensions [B. Devadas and N.J. Leonard (1990) J. Am. Chem. Soc., 112, 3125-3135.] have been added to the oligodeoxyribonucleotide d(A)6 with bacteriophage T4 RNA ligase as a prelude to placing them at defined loci w...

journal_title：Nucleic acids research

authors： Petric A,Bhat B,Leonard NJ,Gumport RI

更新日期：1991-02-11 00:00:00

abstract：:Three Rat1/Xrn2 homologues exist in Arabidopsis thaliana: nuclear AtXRN2 and AtXRN3, and cytoplasmic AtXRN4. The latter has a role in degrading 3' products of miRNA-mediated mRNA cleavage, whereas all three proteins act as endogenous post-transcriptional gene silencing suppressors. Here we show that, similar to yeast ...

journal_title：Nucleic acids research

authors： Zakrzewska-Placzek M,Souret FF,Sobczyk GJ,Green PJ,Kufel J

更新日期：2010-07-01 00:00:00

abstract：:Directed molecular evolution and combinatorial methodologies are playing an increasingly important role in the field of protein engineering. The general approach of generating a library of partially randomized genes, expressing the gene library to generate the proteins the library encodes and then screening the protei...

journal_title：Nucleic acids research

authors： Neylon C

更新日期：2004-02-27 00:00:00

abstract：:Abasic sites (AP-sites) are frequent DNA lesions, arising by spontaneous base hydrolysis or as intermediates of base excision repair (BER). The hemiacetal at the anomeric centre renders them chemically reactive, which presents a challenge to biochemical and structural investigation. Chemically more stable AP-site anal...

journal_title：Nucleic acids research

authors： Schuermann D,Scheidegger SP,Weber AR,Bjørås M,Leumann CJ,Schär P

更新日期：2016-03-18 00:00:00

abstract：:With the rapid accumulation of our knowledge on diseases, disease-related genes and drug targets, network-based analysis plays an increasingly important role in systems biology, systems pharmacology and translational science. The new release of VisANT aims to provide new functions to facilitate the convenient network ...

journal_title：Nucleic acids research

authors： Hu Z,Chang YC,Wang Y,Huang CL,Liu Y,Tian F,Granger B,Delisi C

更新日期：2013-07-01 00:00:00

abstract：:Treatment of cells with DNA damaging agents leads to induction of a variety of genes involved in different cellular processes. We have applied a lacZ-based gene trap strategy to search for new mammalian genes induced by genotoxic stress. A population of 32 x 10(3) neo r clones stably transfected with a gene trap vecto...

journal_title：Nucleic acids research

authors： Menichini P,Viaggi S,Gallerani E,Fronza G,Ottaggio L,Comes A,Ellwart JW,Abbondandolo A

更新日期：1997-12-01 00:00:00