OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs.

abstract：:An improved and simplified protocol for DNA immobilization was developed to enhance DNA-DNA hybridization on microwell plates. Target DNA was immobilized by simple dry-adsorption. Efficiencies of DNA immobilization and retention were enhanced 1.4-6.5 times and 4.2-19.6 times, respectively, compared with a conventional...

journal_title：Nucleic acids research

authors： Hirayama H,Tamaoka J,Horikoshi K

更新日期：1996-10-15 00:00:00

abstract：:The macronuclear genome of Euplotes crassus contains two different genes, EFA1 and EFA2, encoding EF-1alpha proteins. They are derived from micronuclear precursors in the course of a sexual process termed conjugation. We have found that two apparent micronuclear precursors exist for EFA1. They differ in their potentia...

journal_title：Nucleic acids research

authors： Florian V,Klein A

更新日期：1996-08-15 00:00:00

abstract：:Holliday junctions (four-way DNA junctions), formed during homologous recombination, are bound and resolved by junction-specific endonucleases to yield recombinant duplex DNA products. The junction-resolving enzymes are a structurally diverse class of proteins that nevertheless have many properties in common; in parti...

journal_title：Nucleic acids research

authors： White MF,Lilley DM

更新日期：1998-12-15 00:00:00

abstract：:Here we analyze the effect of DNA folding on the performance of short primers and describe a simple technique for assessing hitherto uncertain values of thermodynamic parameters that determine the folding of single-stranded DNA into secondary structure. An 8mer with two degenerate positions is extended simultaneously ...

journal_title：Nucleic acids research

authors： Lvovsky L,Ioshikhes I,Raja MC,Zevin-Sonkin D,Sobolev IA,Liberzon A,Shwartzburd J,Ulanovsky LE

更新日期：1998-12-01 00:00:00

abstract：:To prevent progressive telomere shortening as a result of conventional DNA replication, new telomeric DNA must be added onto the chromosome end. The de novo DNA synthesis involves elongation of the G-rich strand of the telomere by telomerase. In human cells, the CST complex (CTC1-STN1-TEN1) also functions in telomere ...

journal_title：Nucleic acids research

authors： Feng X,Hsu SJ,Kasbek C,Chaiken M,Price CM

更新日期：2017-05-05 00:00:00

abstract：:Gene finding is complicated in organisms that exhibit insertional RNA editing. Here, we demonstrate how our new algorithm Predictor of Insertional Editing (PIE) can be used to locate genes whose mRNAs are subjected to multiple frameshifting events, and extend the algorithm to include probabilistic predictions for site...

journal_title：Nucleic acids research

authors： Gott JM,Parimi N,Bundschuh R

更新日期：2005-09-07 00:00:00

abstract：:In Saccharomyces cerevisiae, RNA polymerase II assembly is probably initiated by the formation of the RPB3-RPB11 heterodimer. RPB3 is encoded by a single copy gene in the yeast, mouse and human genomes. The RPB11 gene is also unique in yeast and mouse, but in humans a gene family has been identified that potentially e...

journal_title：Nucleic acids research

authors： Benga WJ,Grandemange S,Shpakovski GV,Shematorova EK,Kedinger C,Vigneron M

更新日期：2005-06-24 00:00:00

abstract：:Characterization of the ability of human interferons (IFNs) to rapidly induce genes led to the identification of the first two members of the STAT (signal transducers and activators of transcription) family, Stat1 and Stat2. To study the unique role of this transcription factor in IFN signaling under more physiologica...

journal_title：Nucleic acids research

authors： Park C,Lecomte MJ,Schindler C

更新日期：1999-11-01 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 homing endonuclease PI-SceI from Saccharo myces cerevisiae consists of two domains. The protein splicing domain I catalyzes the excision of the mature endonuclease (intein) from a precursor protein and the religation of the flanking amino acid sequences (exteins) to a functional protein. Furthermore, domain I is i...

journal_title：Nucleic acids research

authors： Werner E,Wende W,Pingoud A,Heinemann U

更新日期：2002-09-15 00:00:00

abstract：:Activation of the transcription factor NF-kappaB is critical for the tumor necrosis factor-alpha (TNF-alpha)-induced inflammatory response. Here we report the complete gene expression profile from activated microvascular endothelial cells emphasizing the direct contribution of the NF-kappaB pathway. Human microvascula...

journal_title：Nucleic acids research

authors： Kempe S,Kestler H,Lasar A,Wirth T

更新日期：2005-09-21 00:00:00

abstract：:Genotoxic stress induces alternative splicing of the oncogene MDM2 generating MDM2-ALT1, an isoform attributed with tumorigenic properties. However, the mechanisms underlying this event remain unclear. Here we explore MDM2 splicing regulation by utilizing a novel minigene that mimics endogenous MDM2 splicing in respon...

journal_title：Nucleic acids research

authors： Comiskey DF Jr,Jacob AG,Singh RK,Tapia-Santos AS,Chandler DS

更新日期：2015-04-30 00:00:00

abstract：:Transcription factors (TFs) and miRNAs are the most important dynamic regulators in the control of gene expression in multicellular organisms. These regulatory elements play crucial roles in development, cell cycling and cell signaling, and they have also been associated with many diseases. The Regulatory Network Anal...

journal_title：Nucleic acids research

authors： Bleda M,Medina I,Alonso R,De Maria A,Salavert F,Dopazo J

更新日期：2012-07-01 00:00:00

abstract：:DNA non-homologous end joining, the major mechanism for the repair of DNA double-strands breaks (DSB) in mammalian cells requires the DNA-dependent protein kinase (DNA-PK), a complex composed of a large catalytic subunit of 460 kDa (DNA-PKcs) and the heterodimer Ku70-Ku80 that binds to double-stranded DNA ends. Mutati...

journal_title：Nucleic acids research

authors： Marangoni E,Foray N,O'Driscoll M,Douc-Rasy S,Bernier J,Bourhis J,Jeggo P

更新日期：2000-12-01 00:00:00

abstract：:Decay of (125)I produces a shower of low energy electrons (Auger electrons) that cause strand breaks in DNA in a distance-dependent manner with 90% of the breaks located within 10 bp from the decay site. We studied strand breaks in RNA molecules produced by decay of (125)I incorporated into complementary DNA oligonucl...

journal_title：Nucleic acids research

authors： Gaidamakova EK,Neumann RD,Panyutin IG

更新日期：2002-11-15 00:00:00

abstract：:We have reported on the differences in site-specific cleavage between DNA and DNA-RNA hybrids by various prototypic DNA cleavers (accompanying paper). In the case of bleomycin (BLM), degradation at 5'-GC-3'sites was suppressed relative to the same sequence in double-stranded DNA, while 5'-GT-3' damage remained constan...

journal_title：Nucleic acids research

authors： Bansal M,Stubbe J,Kozarich JW

更新日期：1997-05-01 00:00:00

abstract：:To confirm the activity of an initial small molecule 'hit compound' from an activity screening, one needs to probe the structure-activity relationships by testing close analogs. The multi-fingerprint browser presented here (http://dcb-reymond23.unibe.ch:8080/MCSS/) enables one to rapidly identify such close analogs am...

journal_title：Nucleic acids research

authors： Awale M,Reymond JL

更新日期：2014-07-01 00:00:00

abstract：:Alternative first exons diversify the transcriptomes of eukaryotes by producing variants of the 5' Untranslated Regions (5'UTRs) and N-terminal coding sequences. Accurate transcriptome-wide detection of alternative first exons typically requires specialized experimental approaches that are designed to identify the 5' ...

journal_title：Nucleic acids research

authors： Qin Z,Stoilov P,Zhang X,Xing Y

更新日期：2018-05-04 00:00:00

abstract：:We have compared the properties of the poly(rA).oligo(dT) complex with those of the poly(rU).oligo(dA)n complex. Three main differences were found. First, poly(rA) and oligo(dT)n do not form a complex in concentrations of CsCl exceeding 2 M because the poly(rA) is insoluble in high salt. If the complex is made in low ...

journal_title：Nucleic acids research

authors： Mol JN,Borst P

更新日期：1976-04-01 00:00:00

abstract：:Synthetic deoxyoligonucleotides have been 5'-aminoalkylated at the end of step-wise synthesis on the polymer support. This was achieved through the activation of the 5'-hydroxyl group as its 5'-imidazolyl derivative using carbonyldiimidazole, which was subsequently displaced with hexamethylene diamine to yield the tit...

journal_title：Nucleic acids research

authors： Wachter L,Jablonski JA,Ramachandran KL

更新日期：1986-10-24 00:00:00

abstract：:High-throughput experimental technologies gradually shift the paradigm of biological research from hypothesis-validation toward hypothesis-generation science. Translating diverse types of large-scale experimental data into testable hypotheses, however, remains a daunting task. We previously demonstrated that heterogen...

journal_title：Nucleic acids research

authors： Cho A,Shin J,Hwang S,Kim C,Shim H,Kim H,Kim H,Lee I

更新日期：2014-07-01 00:00:00

abstract：:The active form of Escherichia coli DNA polymerase V responsible for damage-induced mutagenesis is a multiprotein complex (UmuD'(2)C-RecA-ATP), called pol V Mut. Optimal activity of pol V Mut in vitro is observed on an SSB-coated single-stranded circular DNA template in the presence of the β/γ complex and a transactiv...

journal_title：Nucleic acids research

authors： Vaisman A,Kuban W,McDonald JP,Karata K,Yang W,Goodman MF,Woodgate R

更新日期：2012-07-01 00:00:00

abstract：:Eukaryotic gene expression is regulated by enhancer-promoter interactions but the molecular mechanisms that govern specificity have remained elusive. Genome-wide studies utilizing STARR-seq identified two enhancer classes in Drosophila that interact with different core promoters: housekeeping enhancers (hkCP) and deve...

journal_title：Nucleic acids research

authors： Cubeñas-Potts C,Rowley MJ,Lyu X,Li G,Lei EP,Corces VG

更新日期：2017-02-28 00:00:00

abstract：:The Cre-lox system is an important tool for genetic manipulation. To promote integrative reactions, two strategies using mutant lox sites have been developed. One is the left element/right element (LE/RE)-mutant strategy and the other is the cassette exchange strategy using heterospecific lox sites such as lox511 or l...

journal_title：Nucleic acids research

authors： Araki K,Araki M,Yamamura K

更新日期：2002-10-01 00:00:00

abstract：:With discovery of diverse roles for RNA, its centrality in cellular functions has become increasingly apparent. A number of algorithms have been developed to predict RNA secondary structure. Their performance has been benchmarked by comparing structure predictions to reference secondary structures. Generally, algorith...

journal_title：Nucleic acids research

authors： Xu Z,Almudevar A,Mathews DH

更新日期：2012-02-01 00:00:00

abstract：:Spirochetes of the genus Borrelia possess unusual genomes that consist in a linear chromosome and multiple linear and circular plasmids. The linear replicons are terminated by covalently closed hairpin ends, referred to as hairpin telomeres. The hairpin telomeres represent a simple solution to the end-replication prob...

journal_title：Nucleic acids research

authors： Huang SH,Kobryn K

更新日期：2016-06-20 00:00:00

abstract：:The Yeast Protein Localization database (YPL.db) contains information about the localization patterns of yeast proteins resulting from microscopic analyses. The data and parameters of the experiments to obtain the localization information, together with images from confocal or video microscopy, are stored in a relatio...

journal_title：Nucleic acids research

authors： Habeler G,Natter K,Thallinger GG,Crawford ME,Kohlwein SD,Trajanoski Z

更新日期：2002-01-01 00:00:00

abstract：:Cells deficient in the Werner syndrome protein (WRN) or BRCA1 are hypersensitive to DNA interstrand cross-links (ICLs), whose repair requires nucleotide excision repair (NER) and homologous recombination (HR). However, the roles of WRN and BRCA1 in the repair of DNA ICLs are not understood and the molecular mechanisms...

journal_title：Nucleic acids research

authors： Cheng WH,Kusumoto R,Opresko PL,Sui X,Huang S,Nicolette ML,Paull TT,Campisi J,Seidman M,Bohr VA

更新日期：2006-05-19 00:00:00

abstract：:Three clones containing both the human G gamma and A gamma globlin genes have been isolated and characterized from a library of DNA fragments generated by partial Eco RI digestion of cellular DNA using charon 4A phage as vector. Two of the clones (NY 2 and 3) are identical and have an insert of 14.0 kb. The third clon...

journal_title：Nucleic acids research

authors： Ramirez F,Burns AL,Mears JG,Spence S,Starkman D,Bank A

更新日期：1979-11-10 00:00:00

abstract：:A method is described which allows selection of sequences which can substitute for the normal AATAAA hexanucleotide involved in polyadenylation of SV40 late mRNAs. Plaques were generated from viral DNA lacking the motif, forcing acquisition of substitute sequences. Four variants were characterized. All displayed wild-...

journal_title：Nucleic acids research

authors： Swimmer C,Shenk T

更新日期：1985-11-25 00:00:00