SIDDBASE: a database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes.

abstract：:The structural simplicity and ability to capture serial correlations make Markov models a popular modeling choice in several genomic analyses, such as identification of motifs, genes and regulatory elements. A critical, yet relatively unexplored, issue is the determination of the order of the Markov model. Most biolog...

journal_title：Nucleic acids research

authors： Narlikar L,Mehta N,Galande S,Arjunwadkar M

更新日期：2013-02-01 00:00:00

abstract：:Cellular senescence, an integral component of aging and cancer, arises in response to diverse triggers, including telomere attrition, macromolecular damage and signaling from activated oncogenes. At present, senescent cells are identified by the combined presence of multiple traits, such as senescence-associated prote...

journal_title：Nucleic acids research

authors： Casella G,Munk R,Kim KM,Piao Y,De S,Abdelmohsen K,Gorospe M

更新日期：2019-08-22 00:00:00

abstract：:A small library of 49 peptide-oligonucleotide conjugates were synthesized to explore the influence of various peptide side chains on the hybridization properties of the DNA. An invariant 8mer oligonucleotide was coupled to a peptide portion that contained a five residue variable region composed of the cationic amino a...

journal_title：Nucleic acids research

authors： Harrison JG,Balasubramanian S

更新日期：1998-07-01 00:00:00

abstract：:UMSBP is a CCHC-type zinc finger protein, which functions during replication initiation of kinetoplast DNA minicircles and the segregation of kinetoplast DNA networks. Interactions of UMSBP with origin sequences, as well as the protein oligomerization, are affected by its redox state. Reduction yields UMSBP monomers a...

journal_title：Nucleic acids research

authors： Sela D,Shlomai J

更新日期：2009-01-01 00:00:00

abstract：:Puromycin, an analog of the 3' end of aminoacyl-tRNA, causes premature termination of translation by being linked non-specifically to growing polypeptide chains. Here we report the interesting phenomenon that puromycin acting as a non-inhibitor at very low concentration (e.g. 0.04 microM) can bond only to full-length ...

journal_title：Nucleic acids research

authors： Miyamoto-Sato E,Nemoto N,Kobayashi K,Yanagawa H

更新日期：2000-03-01 00:00:00

abstract：:The FSSP database presents a continuously updated classification of 3-D protein folds based on an all-against-all comparison of structures currently in the Protein Data Bank (PDB) [Bernstein et al. (1977) J. Mol. Biol., 112, 535- 542]. The database currently contains an extended structural family for each of 600 repre...

journal_title：Nucleic acids research

authors： Holm L,Sander C

更新日期：1996-01-01 00:00:00

abstract：:The proposition that the 2-amino group of guanine plays a critical role in determining how antibiotics recognise their binding sites in DNA has been tested by relocating it, using tyrT DNA derivative molecules substituted with inosine plus 2,6-diaminopurine (DAP). Irrespective of their mode of interaction with DNA, su...

journal_title：Nucleic acids research

authors： Bailly C,Waring MJ

更新日期：1995-03-25 00:00:00

abstract：:A physical mapping strategy has been developed to verify and accelerate the assembly and gap closure phase of a microbial genome shotgun-sequencing project. The protocol was worked out during the ongoing Pseudomonas putida KT2440 genome project. A macro-restriction map was constructed by linking probe hybridisation of...

journal_title：Nucleic acids research

authors： Weinel C,Tümmler B,Hilbert H,Nelson KE,Kiewitz C

更新日期：2001-11-15 00:00:00

abstract：:In non-malignant RWPE-1 prostate epithelial cells signaling by the nuclear receptor Vitamin D Receptor (VDR, NR1I1) induces cell cycle arrest through targets including CDKN1A (encodes p21((waf1/cip1))). VDR dynamically induced individual histone modification patterns at three VDR binding sites (R1, 2, 3) on the CDKN1A...

journal_title：Nucleic acids research

authors： Thorne JL,Maguire O,Doig CL,Battaglia S,Fehr L,Sucheston LE,Heinaniemi M,O'Neill LP,McCabe CJ,Turner BM,Carlberg C,Campbell MJ

更新日期：2011-03-01 00:00:00

abstract：:Phylogenetic analysis and examination of protein domains allow accurate genome annotation and are invaluable to study proteins and protein complex evolution. However, two sequences can be homologous without sharing statistically significant amino acid or nucleotide identity, presenting a challenging bioinformatics pro...

journal_title：Nucleic acids research

authors： Alako BT,Rainey D,Nijveen H,Leunissen JA

更新日期：2006-07-01 00:00:00

abstract：:Frequencies for each of the 61 amino acid codons have been determined in every published mRNA sequence of 50 or more codons. The frequencies are shown for each kind of genome and for each individual gene. A surprising consistency of choices exists among genes of the same or similar genomes. Thus each genome, or kind o...

journal_title：Nucleic acids research

authors： Grantham R,Gautier C,Gouy M,Mercier R,Pavé A

更新日期：1980-01-11 00:00:00

abstract：:We describe a new, broadly applicable methodology for screening in parallel interactions of RNA-binding proteins (RBPs) with large numbers of microRNA (miRNA) precursors and for determining their affinities in native form in the presence of cellular factors. The assays aim at identifying pre-miRNAs that are potentiall...

journal_title：Nucleic acids research

authors： Towbin H,Wenter P,Guennewig B,Imig J,Zagalak JA,Gerber AP,Hall J

更新日期：2013-02-01 00:00:00

abstract：:A sensitive gel retention assay has been utilized to detect proteins from uninfected Hela nuclei which interact with the adenovirus type 2 enhancer. This assay has been employed to monitor fractionation of nuclear extracts. Three enhancer binding factors were resolved by chromatography on DEAE-Sepharose and one of the...

journal_title：Nucleic acids research

authors： Barrett P,Clark L,Hay RT

更新日期：1987-03-25 00:00:00

abstract：:The FREP database (http://facts.gsc.riken.go.jp/FREP/) contains 31 396 RepeatMasker-identified non-redundant variant repeat sequences derived from 16,527 mouse cDNAs with protein-coding potential. The repeats were computationally associated with potential effects on transcriptional variation, translation, protein func...

journal_title：Nucleic acids research

authors： Nagashima T,Matsuda H,Silva DG,Petrovsky N,Konagaya A,Schönbach C,Kasukawa T,Arakawa T,Carninci P,Kawai J,Hayashizaki Y,RIKEN GER Group.,Genome Science Laoratory Members.

更新日期：2004-01-01 00:00:00

abstract：:Eukaryotic elongation factor 1 A (eEF1A, formerly elongation factor-1 alpha) is an important component of the protein synthesis apparatus. Here we report the isolation and characterization of the cDNA sequence encoding rabbit eEF1A-2, an isoform of eEF1A, as well as a structural and functional comparison of the two ra...

journal_title：Nucleic acids research

authors： Kahns S,Lund A,Kristensen P,Knudsen CR,Clark BF,Cavallius J,Merrick WC

更新日期：1998-04-15 00:00:00

abstract：:Gene trap vectors developed for genome-wide mutagenesis can be used to study factors governing the expression of exons inserted throughout the genome. For example, entrapment vectors consisting of a partial 3'-terminal exon [i.e. a neomycin resistance gene (Neo), a poly(A) site, but no 3' splice site] were typically e...

journal_title：Nucleic acids research

authors： Osipovich AB,White-Grindley EK,Hicks GG,Roshon MJ,Shaffer C,Moore JH,Ruley HE

更新日期：2004-05-20 00:00:00

abstract：:PIWI-interacting RNAs (piRNAs) engage PIWI proteins to silence transposons and promote germ cell development in animals. In diverse species, piRNA biogenesis occurs near the mitochondrial surface, and involves mitochondrial membrane-anchored factors. In mice, two cytoplasmic PIWI proteins, MIWI and MILI, receive proce...

journal_title：Nucleic acids research

authors： Ding D,Liu J,Dong K,Melnick AF,Latham KE,Chen C

更新日期：2019-03-18 00:00:00

abstract：:The synthetic DNA fragment (formula, see text) (corresponding to nucleotides 4299-4314 of the phi X DNA sequence) was cloned into either the AmpR gene or the KmR gene of plasmid pACYC 177. The DNA sequence of the KmR gene around the insertion site was determined by nucleotide sequence analysis of the pACYC 177 FnudII ...

journal_title：Nucleic acids research

authors： Heidekamp F,Baas PD,van Boom JH,Veeneman GH,Zipursky SL,Jansz HS

更新日期：1981-07-24 00:00:00

abstract：:Reactive oxygen species produced by endogenous metabolic activity and exposure to a multitude of exogenous agents impact cells in a variety of ways. The DNA base damage 8-oxodeoxyguanosine (8-oxodG) is a prominent indicator of oxidative stress and has been well-characterized as a premutagenic lesion in mammalian cells...

journal_title：Nucleic acids research

authors： Ghosh R,Mitchell DL

更新日期：1999-08-01 00:00:00

abstract：:Adaptation of the P1 phage-derived Cre /loxP site- specific recombination system to the gene targeting technique allows for the conditional deletion of genes in mice. To selectively modify genes in B lymphocytes, we have generated mice (designated CD19-Cre) which express cre under the transcriptional control of the B ...

journal_title：Nucleic acids research

authors： Rickert RC,Roes J,Rajewsky K

更新日期：1997-03-15 00:00:00

abstract：:The nucleotide sequence for human argininosuccinate synthetase cDNA was determined by analysis of six clones isolated from a single experiment. The sequence covered 1623 nucleotides including 76 bases of poly(A) and contained a 1236 nucleotide open reading frame encoding a protein of 46,434 daltons. In one cDNA isolat...

journal_title：Nucleic acids research

authors： Bock HG,Su TS,O'Brien WE,Beaudet AL

更新日期：1983-09-24 00:00:00

abstract：:Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, her...

journal_title：Nucleic acids research

authors： Yan Y,Zhang D,Zhou P,Li B,Huang SY

更新日期：2017-07-03 00:00:00

abstract：:RNA G-quadruplexes (G4s) are secondary structures proposed to function as regulators of post-transcriptional mRNA localisation and translation. G4s within some neuronal mRNAs are known to control distal localisation and local translation, contributing to distinct local proteomes that facilitate the synaptic remodellin...

journal_title：Nucleic acids research

authors： Maltby CJ,Schofield JPR,Houghton SD,O'Kelly I,Vargas-Caballero M,Deinhardt K,Coldwell MJ

更新日期：2020-09-25 00:00:00

abstract：:Direct labeling of RNA is an expedient method for labeling large quantities (e.g. micrograms) of target RNA for microarray analysis. We have developed an efficient labeling system that uses T4 RNA ligase to attach a 3'-biotinylated donor molecule to target RNA. Microarray analyses indicate that directly labeled RNA is...

journal_title：Nucleic acids research

authors： Cole K,Truong V,Barone D,McGall G

更新日期：2004-06-17 00:00:00

abstract：:In human cells DNA damage caused by UV light is mainly repaired by the nucleotide excision repair pathway. This mechanism involves dual incisions on both sides of the damage catalyzed by two nucleases. In mammalian cells XPG cleaves 3' of the DNA lesion while the ERCC1-XPF complex makes the 5' incision. The amino acid...

journal_title：Nucleic acids research

authors： Rödel C,Jupitz T,Schmidt H

更新日期：1997-07-15 00:00:00

abstract：:Non-structural protein 3 (NS3) of hepatitis C virus (HCV) has two distinct activities, protease and helicase, which are essential for HCV proliferation. In previous work, we obtained RNA aptamers (G9-I, II and III) which specifically bound the NS3 protease domain (DeltaNS3), efficiently inhibiting protease activity in...

journal_title：Nucleic acids research

authors： Nishikawa F,Kakiuchi N,Funaji K,Fukuda K,Sekiya S,Nishikawa S

更新日期：2003-04-01 00:00:00

abstract：:We have determined the three-dimensional structure of a non-selfcomplementary nonanucleotide duplex which contains an abasic (apyrimidinic) site in the centre, i.e. a deoxyribose residue opposite an adenosine. The majority of the base and sugar proton resonances were assigned by NOESY, COSY and 2DQF spectra in D2O and...

journal_title：Nucleic acids research

authors： Cuniasse P,Sowers LC,Eritja R,Kaplan B,Goodman MF,Cognet JA,LeBret M,Guschlbauer W,Fazakerley GV

更新日期：1987-10-12 00:00:00

abstract：:The deoxyoctanucleotide 5'd (AAGGAGGT) which is complementary to the 3' terminus of 16S RNA has been used as a probe to measure the potential of this rRNA region to engage in intermolecular basepairing. The site specific binding of the octanucleotide is shown by labeling 16S RNA in situ at its 3' end with [32P]pCp and...

journal_title：Nucleic acids research

authors： Backendorf C,Ravensbergen CJ,Van der Plas J,van Boom JH,Veeneman G,Van Duin J

更新日期：1981-03-25 00:00:00

abstract：:Diethyl pyrocarbonate reacts with the single-stranded loops of cruciform structures with great selectivity. Adenine bases are carbethoxylated, as a result of which the backbone may be cleaved with piperidine, and the level of chemical modification at each base may be determined. We have studied the ColE1 and (A-T)34 c...

journal_title：Nucleic acids research

authors： Furlong JC,Lilley DM

更新日期：1986-05-27 00:00:00

abstract：:The repetitive zinc finger domain of transcription factor IIIA binds 5S DNA and 5S RNA with similar affinity. Site directed mutagenesis of the Xenopus borealis somatic 5S RNA gene has been used to produce a series of derivatives of 5S RNA containing local sequence substitutions or sequence deletions. Gel mobility shif...

journal_title：Nucleic acids research

authors： Bogenhagen DF,Sands MS

更新日期：1992-06-11 00:00:00