Human nucleotide excision repair in vitro: repair of pyrimidine dimers, psoralen and cisplatin adducts by HeLa cell-free extract.

abstract：:Cisplatin analogues were synthesised that consisted of platinum(II) diamine complexes tethered via a polymethylene chain ( n = 3, 5, 8 and 10) to a phenanthridinium cation. Both chloro and iodo leaving groups were examined. DNA adduct formation was quantitatively analysed using a linear amplification system with the p...

journal_title：Nucleic acids research

authors： Whittaker J,McFadyen WD,Wickham G,Wakelin LP,Murray V

更新日期：1998-09-01 00:00:00

abstract：:Deregulation of mini-chromosome maintenance (MCM) proteins is associated with genomic instability and cancer. MCM complexes are recruited to replication origins for genome duplication. Paradoxically, MCM proteins are in excess than the number of origins and are associated with chromatin regions away from the origins d...

journal_title：Nucleic acids research

authors： Slaymaker IM,Fu Y,Toso DB,Ranatunga N,Brewster A,Forsburg SL,Zhou ZH,Chen XS

更新日期：2013-03-01 00:00:00

abstract：:We have previously shown that the pyrimidine oligonucleotide 5'CTTCCTCCTCT (Y11) recognizes the double-helical stem of hairpin 5'GAAGGAGGAGA-T4-TCTCCTCCTTC (h26) by triple-helix formation (1). In this paper, we report the effect on triplex formation of substituting the cytosine residues of Y11 with 5-methylcytosines (...

journal_title：Nucleic acids research

authors： Xodo LE,Manzini G,Quadrifoglio F,van der Marel GA,van Boom JH

更新日期：1991-10-25 00:00:00

abstract：:We have analyzed the ATPase activity exhibited by the UvrABC DNA repair complex. The UvrA protein is an ATPase whose lack of DNA dependence may be related to the ATP induced monomer-dimer transitions. ATP induced dimerization may be responsible for the enhanced DNA binding activity observed in the presence of ATP. Alt...

journal_title：Nucleic acids research

authors： Oh EY,Claassen L,Thiagalingam S,Mazur S,Grossman L

更新日期：1989-06-12 00:00:00

abstract：:The mRNA encoding repressor cI of phage lambda is the only known E. coli message which starts directly with the initiation AUG codon. The ability of in vitro synthesized cI mRNA fragments (150 or 400 nts) to form ternary initiation complexes has been studied using the toeprint method. In the presence of tRNA(Met)f, th...

journal_title：Nucleic acids research

authors： Balakin AG,Skripkin EA,Shatsky IN,Bogdanov AA

更新日期：1992-02-11 00:00:00

abstract：:Bacteria occupy a diverse set of environmental niches with differing oxygen availability. Anaerobic environments such as mammalian digestive tracts and industrial reactors harbor an abundance of both obligate and facultative anaerobes, many of which play significant roles in human health and biomanufacturing. Studying...

journal_title：Nucleic acids research

authors： Wang XC,Wilson SC,Hammond MC

更新日期：2016-09-30 00:00:00

abstract：:Invariance of temporal order of genome replication in eukaryotic cells and its correlation with gene activity has been well-documented. However, recent data suggest a relax control of replication timing. To evaluate replication schedule accuracy, we detailed the replicational organization of the developmentally regula...

journal_title：Nucleic acids research

authors： Bénard M,Maric C,Pierron G

更新日期：2007-01-01 00:00:00

abstract：:For high-throughput in vitro protein selection using genotype (mRNA)-phenotype (protein) fusion formation and C-terminal protein labeling as a post-selection analysis, it is important to improve the stability and efficiency of mRNA templates for both technologies. Here we describe an efficient single-strand ligation (...

journal_title：Nucleic acids research

authors： Miyamoto-Sato E,Takashima H,Fuse S,Sue K,Ishizaka M,Tateyama S,Horisawa K,Sawasaki T,Endo Y,Yanagawa H

更新日期：2003-08-01 00:00:00

abstract：:The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing infor...

journal_title：Nucleic acids research

authors： Picardi E,Regina TM,Brennicke A,Quagliariello C

更新日期：2007-01-01 00:00:00

abstract：:The SIGnaling Network Open Resource 2.0 (SIGNOR 2.0) is a public repository that stores signaling information as binary causal relationships between biological entities. The captured information is represented graphically as a signed directed graph. Each signaling relationship is associated to an effect (up/down-regul...

journal_title：Nucleic acids research

authors： Licata L,Lo Surdo P,Iannuccelli M,Palma A,Micarelli E,Perfetto L,Peluso D,Calderone A,Castagnoli L,Cesareni G

更新日期：2020-01-08 00:00:00

abstract：:Most human genes generate multiple transcript isoforms. The differential expression of these isoforms can help specify cell types. Diverse transcript isoforms arise from the use of alternative transcription start sites, polyadenylation sites and splice sites; however, the relative contribution of these processes to is...

journal_title：Nucleic acids research

authors： Reyes A,Huber W

更新日期：2018-01-25 00:00:00

abstract：:We report the use of MonoQ FPLC (Fast Protein Liquid Chromatography) for the rapid purification of a novel Type II restriction endonuclease PmaCI, from Pseudomonas maltophila, which recognises the sequence 5'-CAC decreases GTG-3'. The resulting enzyme is free of other nucleases to a level suitable for its characterisa...

journal_title：Nucleic acids research

authors： Walker JN,Dean PD,Saunders JR

更新日期：1986-02-11 00:00:00

abstract：:In small oocytes of Xenopus species, two sets of 5S RNA genes, oocyte-type and somatic-type, are fully activated. The 5S RNA transcripts are temporarily stored, half in association with TFIIIA to form a 7S particle, the other half in association with tRNA and two proteins (p48 and p43) to form a 42S particle. It has b...

journal_title：Nucleic acids research

authors： Barrett P,Sommerville J

更新日期：1987-11-11 00:00:00

abstract：:Sequences of 3279 sequences of tRNA genes and tRNAs published up to December 1996 are included in the compilation. Alignment of the sequences, which is most compatible with the tRNA phylogeny and known three-dimensional structures of tRNA, is used. Sequences and references are available under http://www.uni-bayreuth. ...

journal_title：Nucleic acids research

authors： Sprinzl M,Horn C,Brown M,Ioudovitch A,Steinberg S

更新日期：1998-01-01 00:00:00

abstract：:The database of 3D interacting domains (3did) is a collection of protein interactions for which high-resolution 3D structures are known. 3did exploits structural information to provide the crucial molecular details necessary for understanding how protein interactions occur. Besides interactions between globular domain...

journal_title：Nucleic acids research

authors： Stein A,Panjkovich A,Aloy P

更新日期：2009-01-01 00:00:00

abstract：:In fragile X syndrome, hypermethylation of the expanded CGG repeat and of the upstream promoter leads to transcriptional silencing of the FMR1 gene. Absence of the FMR1 protein results in mental retardation. We previously proved that treatment with 5-azadeoxycytidine (5-azadC) of fragile X cell lines results in reacti...

journal_title：Nucleic acids research

authors： Pietrobono R,Pomponi MG,Tabolacci E,Oostra B,Chiurazzi P,Neri G

更新日期：2002-07-15 00:00:00

abstract：:The binding of two symmetric bis-benzimidazole compounds, 2,2-bis-[4'-(3"-dimethylamino-1"-propyloxy)phenyl]-5,5-bi-1H-benzimidazole and its piperidinpropylphenyl analog, to the minor groove of DNA, have been studied by DNA footprinting, surface plasmon resonance (SPR) methods and molecular dynamics simulations in exp...

journal_title：Nucleic acids research

authors： Bailly C,Chessari G,Carrasco C,Joubert A,Mann J,Wilson WD,Neidle S

更新日期：2003-03-01 00:00:00

abstract：:We have developed a PCR-based short interfering RNA (siRNA) quantification method based on competition between siRNA and a homologous DNA primer for annealing to template DNA, avoiding the requirement for prior conversion of RNA to cDNA. Primers and probe were designed to amplify regions of the human papillomavirus E6...

journal_title：Nucleic acids research

authors： Liu WL,Stevenson M,Seymour LW,Fisher KD

更新日期：2009-01-01 00:00:00

abstract：:The structures of the termini and their flanking regions of two human KpnI family members were investigated. The two differed in length, but the starting sequence at one terminal (defined as the 5' terminal) was found to be common to both members. The Alu family sequence was found in the 5' flanking regions. The KpnI ...

journal_title：Nucleic acids research

authors： Miyake T,Migita K,Sakaki Y

更新日期：1983-10-11 00:00:00

abstract：:LNA oligonucleotides constitute a class of bicyclic RNA analogues having an exceptionally high affinity for their complementary DNA and RNA target molecules. We here report a novel method for highly efficient isolation of intact poly(A)+ RNA using an LNA-substituted oligo(dT) affinity ligand, based on the increased af...

journal_title：Nucleic acids research

authors： Jacobsen N,Nielsen PS,Jeffares DC,Eriksen J,Ohlsson H,Arctander P,Kauppinen S

更新日期：2004-04-19 00:00:00

abstract：:MicroRNAs (miRNAs) are small noncoding RNAs that attenuate expression of their mRNA targets. Here, we developed a new method and an R package, to easily infer candidate miRNA-mRNA target interactions that could be functional during a given biological process. Using this method, we described, for the first time, a comp...

journal_title：Nucleic acids research

authors： Kassambara A,Jourdan M,Bruyer A,Robert N,Pantesco V,Elemento O,Klein B,Moreaux J

更新日期：2017-06-02 00:00:00

abstract：:Benzo[c]phenanthrene dihydrodiol epoxide (B[c] PhDE) is well known as an important environmental chemical carcinogen that preferentially modifies DNA in adenine residues. However, the molecular mechanism by which B[c]PhDE induces tumorigenesis is not fully understood. In this report, we demonstrate that DNA mismatch r...

journal_title：Nucleic acids research

authors： Wu J,Zhu BB,Yu J,Zhu H,Qiu L,Kindy MS,Gu L,Seidel A,Li GM

更新日期：2003-11-15 00:00:00

abstract：:Zar1 was one of the earliest mammalian maternal-effect genes to be identified. Embryos derived from Zar1-null female mice are blocked before zygotic genome activation; however, the underlying mechanism remains unclear. By knocking out Zar1 and its homolog Zar2 in mice, we revealed a novel function of these genes in oo...

journal_title：Nucleic acids research

authors： Rong Y,Ji SY,Zhu YZ,Wu YW,Shen L,Fan HY

更新日期：2019-12-02 00:00:00

abstract：:Enzymes involved in nucleic acid transactions often have a helicase-like ATPase coordinating and driving their functional activities, but our understanding of the mechanistic details of their coordination is limited. For example, DNA cleavage by the antiphage defense system Type ISP restriction-modification enzyme req...

journal_title：Nucleic acids research

authors： Chand MK,Carle V,Anuvind KG,Saikrishnan K

更新日期：2020-03-18 00:00:00

abstract：:The effect of temperature and primer concentration on oligonucleotide-primed transcription has been studied using the separated strands of a well-defined natural DNA as template. Results were similar to those obtained in the homopolymer-directed model systems. At high temperature and excess primer concentration mainly...

journal_title：Nucleic acids research

authors： Van Kreijl CF,Beelen RH,Borst P

更新日期：1977-02-01 00:00:00

abstract：:Abasic (AP) sites, the most common DNA lesions are frequently associated with double strand breaks (DSBs) and can pose a block to the final ligation. In many prokaryotes, nonhomologous end joining (NHEJ) repair of DSBs relies on a two-component machinery constituted by the ring-shaped DNA-binding Ku that recruits the ...

journal_title：Nucleic acids research

authors： de Ory A,Carabaña C,de Vega M

更新日期：2019-06-04 00:00:00

abstract：:The COXPRESdb (http://coxpresdb.jp) provides gene coexpression relationships for animal species. Here, we report the updates of the database, mainly focusing on the following two points. For the first point, we added RNAseq-based gene coexpression data for three species (human, mouse and fly), and largely increased th...

journal_title：Nucleic acids research

authors： Okamura Y,Aoki Y,Obayashi T,Tadaka S,Ito S,Narise T,Kinoshita K

更新日期：2015-01-01 00:00:00

abstract：:Mutations in the gene of human RNase T2 are associated with white matter disease of the human brain. Although brain abnormalities (bilateral temporal lobe cysts and multifocal white matter lesions) and clinical symptoms (psychomotor impairments, spasticity and epilepsy) are well characterized, the pathomechanism of RN...

journal_title：Nucleic acids research

authors： Thorn A,Steinfeld R,Ziegenbein M,Grapp M,Hsiao HH,Urlaub H,Sheldrick GM,Gärtner J,Krätzner R

更新日期：2012-09-01 00:00:00

abstract：:Recent advances in next-generation sequencing technologies and genome assembly algorithms have enabled the accumulation of a huge volume of genome sequences from various species. This has provided new opportunities for large-scale comparative genomics studies. Identifying and utilizing synteny blocks, which are genomi...

journal_title：Nucleic acids research

authors： Lee J,Hong WY,Cho M,Sim M,Lee D,Ko Y,Kim J

更新日期：2016-07-08 00:00:00

abstract：:A new restriction endonuclease Bse SI has been isolated from Bacillus stearothermophilus Jo10-553. Bse SI recognizes a degenerate hexanucleotide sequence 5'-G(G/T)GC(A/C)C-3' and cleaves DNA to produce 3[prime]-protruding tetranucleotide ends. ...

journal_title：Nucleic acids research

authors： Steponaviciene D,Maneliene Z,Petrusyte M,Janulaitis A

更新日期：1999-07-01 00:00:00