SeqA structures behind Escherichia coli replication forks affect replication elongation and restart mechanisms.

abstract：:Furvina®, also denominated G1 (MW 297), is a synthetic nitrovinylfuran [2-bromo-5-(2-bromo-2-nitrovinyl)-furan] antibiotic with a broad antimicrobial spectrum. An ointment (Dermofural®) containing G1 as the only active principle is currently marketed in Cuba and successfully used to treat dermatological infections. He...

journal_title：Nucleic acids research

authors： Fabbretti A,Brandi L,Petrelli D,Pon CL,Castañedo NR,Medina R,Gualerzi CO

更新日期：2012-11-01 00:00:00

abstract：:Immature oocytes from Xenopus laevis contain a 42S ribonucleoprotein particle (RNP) containing 5S RNA, tRNA, a 43 kDa protein, and a 48 kDa protein. A particle containing 5S RNA and the 43 kDa protein (p43-5S) liberated from the 42S particle upon brief treatment with urea can be purified by anion exchange chromatograp...

journal_title：Nucleic acids research

authors： Sands MS,Bogenhagen DF

更新日期：1991-04-25 00:00:00

abstract：:Transcriptionally non-co-linear (NCL) transcripts can originate from trans-splicing (trans-spliced RNA; 'tsRNA') or cis-backsplicing (circular RNA; 'circRNA'). While numerous circRNAs have been detected in various species, tsRNAs remain largely uninvestigated. Here, we utilize integrative transcriptome sequencing of p...

journal_title：Nucleic acids research

authors： Chuang TJ,Chen YJ,Chen CY,Mai TL,Wang YD,Yeh CS,Yang MY,Hsiao YT,Chang TH,Kuo TC,Cho HH,Shen CN,Kuo HC,Lu MY,Chen YH,Hsieh SC,Chiang TW

更新日期：2018-04-20 00:00:00

abstract：:Pairing of a given E3 ubiquitin ligase with different E2s allows synthesis of ubiquitin conjugates of different topologies. While this phenomenon contributes to functional diversity, it remains largely unknown how a single E3 ubiquitin ligase recognizes multiple E2s, and whether identical structural requirements deter...

journal_title：Nucleic acids research

authors： Lok GT,Sy SM,Dong SS,Ching YP,Tsao SW,Thomson TM,Huen MS

更新日期：2012-01-01 00:00:00

abstract：:The enzyme endonuclease V nicks uracil-containing DNA at the second or third phosphodiester bond 3' to uracil sites. I applied the enzyme to random fragmentation of DNA to revise the complex DNA shuffling protocol. The merit of using endonuclease V is that cleavage occurs at random sites and the length of the fragment...

journal_title：Nucleic acids research

authors： Miyazaki K

更新日期：2002-12-15 00:00:00

abstract：:The MED1/TRAP220 subunit of the Mediator plays a key role in facilitating ligand-dependent interactions of this multisubunit coactivator complex with nuclear receptors through their ligand binding domains. The isolated MED1/TRAP220 protein previously was shown to interact with glucocorticoid receptor (GR) in a ligand-...

journal_title：Nucleic acids research

authors： Chen W,Roeder RG

更新日期：2007-01-01 00:00:00

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：:The isolation and characterization of deletion mutants of the bacteriocinogenic plasmid Clo DF13 is described. To construct these deletion mutants, DNA of Clo DF13::Tn901 and Clo DF13-rep3::Tn901 plasmids was digested with restriction endonucleases, ligated with T4 ligase and introduced by transformation into Escheric...

journal_title：Nucleic acids research

authors： Stuitje AR,Veltkamp E,van den Elzen PJ,Nijkamp HJ

更新日期：1978-06-01 00:00:00

abstract：:Gene rewiring is a common evolutionary phenomenon in nature that may lead to extinction for living organisms. Recent studies on synthetic biology demonstrate that cells can survive genetic rewiring. This survival (adaptation) is often linked to the stochastic expression of rewired genes with random transcriptional cha...

journal_title：Nucleic acids research

authors： Murakami Y,Matsumoto Y,Tsuru S,Ying BW,Yomo T

更新日期：2015-01-01 00:00:00

abstract：:We describe the characterisation of four thermo-stable NAD(+)-dependent DNA ligases, from Thermus thermophilus (Tth), Thermus scotoductus (Ts), Rhodothermus marinus (Rm) and Thermus aquaticus (Taq), by an assay which measures ligation rate and mismatch discrimination. Complete libraries of octa-, nona- and decanucleot...

journal_title：Nucleic acids research

authors： Housby JN,Thorbjarnardóttir SH,Jónsson ZO,Southern EM

更新日期：2000-02-01 00:00:00

abstract：:A short histone-like fusion RNA, generated when the RNA 3' processing signal from a mouse histone H4 gene is inserted into a heterologous transcription unit, becomes correctly down-regulated in G1-arrested cells of a temperature-sensitive mouse mastocytoma cell cycle mutant (21-Tb; Stauber et al., EMBO J. 5, 3297-3303...

journal_title：Nucleic acids research

authors： Stauber C,Schümperli D

更新日期：1988-10-25 00:00:00

abstract：:Labeling of a covalently closed circular double-stranded DNA was achieved using a so-called 'padlock oligonucleotide'. The oligonucleotide was targeted to a sequence which is present in the replication origin of phage f1 and thus in numerous commonly used plasmids. After winding around the double-stranded target DNA s...

journal_title：Nucleic acids research

authors： Roulon T,Coulaud D,Delain E,Le Cam E,Hélène C,Escudé C

更新日期：2002-02-01 00:00:00

abstract：:A simplified and economical method for the attachment of 2'-deoxyribo, ribo and arabinonucleosides onto long-chain alkylamidopropanoic acid controlled-pore glass (LCAAP-CPG, P-3) is described. In this procedure, 5'-O-tritylated nucleosides are coupled directly to LCAAP-CPG in excellent yields using 1-(3-dimethylaminop...

journal_title：Nucleic acids research

authors： Damha MJ,Giannaris PA,Zabarylo SV

更新日期：1990-07-11 00:00:00

abstract：:The reactions between purified anti-poly A. poly U and-poly I. poly C. antibodies (IgG and IgM), and synthetic and natural polynucleotides were visualized at the molecular level. This was achieved by the use of fine tungsten bidirectional shadowing of molecules adsorbed onto thin carbon films, combined with dark field...

journal_title：Nucleic acids research

authors： Nahon-Merlin E,Delain E,Coulaud D,Lacour F

更新日期：1980-04-25 00:00:00

abstract：:The HIV-1 viral infectivity factor (Vif) allows productive infection of non-permissive cells (including most natural HIV-1 targets) by counteracting the cellular cytosine deaminases APOBEC-3G (hA3G) and hA3F. The Vif-induced degradation of these restriction factors by the proteasome has been extensively studied, but l...

journal_title：Nucleic acids research

authors： Mercenne G,Bernacchi S,Richer D,Bec G,Henriet S,Paillart JC,Marquet R

更新日期：2010-01-01 00:00:00

abstract：:From a recombinant lambda phage, we have determined a 387 bp sequence containing a mouse lysine tRNA gene. The putative lys tRNA (anticodon UUU) differs from rabbit liver lys tRNA at five positions. The flanking regions of the mouse gene are not generally homologous to published human and Drosophila lys tRNA genes. Ho...

journal_title：Nucleic acids research

authors： Han JH,Harding JD

更新日期：1983-04-11 00:00:00

abstract：:The human telomeric DNA sequence with four repeats can fold into a parallel-stranded propeller-type topology. NMR structures solved under molecular crowding experiments correlate with the crystal structures found with crystal-packing interactions that are effectively equivalent to molecular crowding. This topology has...

journal_title：Nucleic acids research

authors： Islam B,Sgobba M,Laughton C,Orozco M,Sponer J,Neidle S,Haider S

更新日期：2013-02-01 00:00:00

abstract：:Two DNA hexadecamers containing one central 5'-GC-3' base step have been examined by footprinting methodology in the presence and absence of actinomycin D. The results of these studies, coupled with imino proton NMR measurements indicate that the antitumor drug causes a change in DNA conformation at a distance from th...

journal_title：Nucleic acids research

authors： Huang YQ,Rehfuss RP,LaPlante SR,Boudreau E,Borer PN,Lane MJ

更新日期：1988-12-09 00:00:00

abstract：:Reagents for proteome research must of necessity be generated by high throughput methods. Aptamers are potentially useful as reagents to identify and quantitate individual proteins, yet are currently produced for the most part by manual selection procedures. We have developed automated selection methods, but must stil...

journal_title：Nucleic acids research

authors： Cox JC,Hayhurst A,Hesselberth J,Bayer TS,Georgiou G,Ellington AD

更新日期：2002-10-15 00:00:00

abstract：:DNA-damage response machinery is crucial to maintain the genomic integrity of cells, by enabling effective repair of even highly lethal lesions such as DNA double-strand breaks (DSBs). Defects in specific genes acquired through mutations, copy-number alterations or epigenetic changes can alter the balance of these pat...

journal_title：Nucleic acids research

authors： Liu C,Srihari S,Cao KA,Chenevix-Trench G,Simpson PT,Ragan MA,Khanna KK

更新日期：2014-06-01 00:00:00

abstract：:Transgenic mice suitable for the in vivo assay of suspected mutagens at the chromosome level have been constructed by stable integration of a lambda phage shuttle vector. The shuttle vector, which contains a beta-galactosidase (beta-gal) target gene, can be rescued from genomic DNA with in vitro packaging extracts. Mu...

journal_title：Nucleic acids research

authors： Kohler SW,Provost GS,Kretz PL,Dycaico MJ,Sorge JA,Short JM

更新日期：1990-05-25 00:00:00

abstract：:A growing number of whole genome sequencing projects, in combination with development of phylogenetic methods for reconstructing gene evolution, have provided us with a window into genomes that existed millions, and even billions, of years ago. Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehe...

journal_title：Nucleic acids research

authors： Huang X,Albou LP,Mushayahama T,Muruganujan A,Tang H,Thomas PD

更新日期：2019-01-08 00:00:00

abstract：:The primary rRNA transcript contains a large external transcribed spacer (ETS) approximately 4,000 nucleotides in length. We have used subcloned DNA probes derived from the 5' end of the ETS in conjunction with Northern blot analysis of murine nuclear RNA to examine processing of this region. In agreement with the res...

journal_title：Nucleic acids research

authors： Fetherston J,Werner E,Patterson R

更新日期：1984-09-25 00:00:00

abstract：:To enhance our knowledge regarding biological pathway regulation, we took an integrated approach, using the biomedical literature, ontologies, network analyses and experimental investigation to infer novel genes that could modulate biological pathways. We first constructed a novel gene network via a pairwise compariso...

journal_title：Nucleic acids research

authors： Qin T,Matmati N,Tsoi LC,Mohanty BK,Gao N,Tang J,Lawson AB,Hannun YA,Zheng WJ

更新日期：2014-10-01 00:00:00

abstract：:Polyadenylation is a co-transcriptional process that modifies mRNA 3'-ends in eukaryotes. In yeast, CF IA and CPF constitute the core 3'-end maturation complex. CF IA comprises Rna14p, Rna15p, Pcf11p and Clp1p. CF IA interacts with the C-terminal domain of RNA Pol II largest subunit via Pcf11p which links pre-mRNA 3'-...

journal_title：Nucleic acids research

authors： Haddad R,Maurice F,Viphakone N,Voisinet-Hakil F,Fribourg S,Minvielle-Sébastia L

更新日期：2012-02-01 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：:RecBCD enzyme acts in the major pathway of homologous recombination of linear DNA in Escherichia coli. The enzyme unwinds DNA and is an ATP-dependent double-strand and single-strand exonuclease and a single-strand endonuclease; it acts at Chi recombination hotspots (5'-GCTGGTGG-3') to produce a recombinogenic single-s...

journal_title：Nucleic acids research

authors： Amundsen SK,Taylor AF,Smith GR

更新日期：1998-05-01 00:00:00

abstract：:Highly conserved sequences present at an identical position near the 3' ends of eukaryotic and prokaryotic 5S rRNAs are complementary to the 5' strand of the m2(6)A hairpin structure near the 3' ends of 18S rRNA and 16S rRNA, respectively. The extent of base-pairing and the calculated stabilities of the hybrids that c...

journal_title：Nucleic acids research

authors： Azad AA

更新日期：1979-12-11 00:00:00

abstract：:The International Mouse Phenotyping Consortium (IMPC) web portal (http://www.mousephenotype.org) provides the biomedical community with a unified point of access to mutant mice and rich collection of related emerging and existing mouse phenotype data. IMPC mouse clinics worldwide follow rigorous highly structured and ...

journal_title：Nucleic acids research

authors： Koscielny G,Yaikhom G,Iyer V,Meehan TF,Morgan H,Atienza-Herrero J,Blake A,Chen CK,Easty R,Di Fenza A,Fiegel T,Grifiths M,Horne A,Karp NA,Kurbatova N,Mason JC,Matthews P,Oakley DJ,Qazi A,Regnart J,Retha A,Santos

更新日期：2014-01-01 00:00:00

abstract：:DNA-PKcs and Ku are essential components of the complex that catalyzes non-homologous end joining (NHEJ) of DNA double-strand breaks (DSBs). Ku, a heterodimeric protein, binds to DNA ends and facilitates recruitment of the catalytic subunit, DNA-PKcs. We have investigated the effect of DNA strand orientation and seque...

journal_title：Nucleic acids research

authors： Pawelczak KS,Andrews BJ,Turchi JJ

更新日期：2005-01-07 00:00:00