Abstract:
:The presence of a homing endonuclease gene (HEG) within a microbial intron or intein empowers the entire element with the ability to invade genomic targets. The persistence of a homing endonuclease lineage depends in part on conservation of its DNA target site. One such rDNA sequence has been invaded both in archaea and in eukarya, by LAGLIDADG and His-Cys box homing endonucleases, respectively. The bases encoded by this target include a universally conserved ribosomal structure, termed helix 69 (H69) in the large ribosomal subunit. This region forms the 'B2a' intersubunit bridge to the small ribosomal subunit, contacts bound tRNA in the A- and P-sites, and acts as a trigger for ribosome disassembly through its interactions with ribosome recycling factor. We have determined the DNA-bound structure and specificity profile of an archaeal LAGLIDADG homing endonuclease (I-Vdi141I) that recognizes this target site, and compared its specificity with the analogous eukaryal His-Cys box endonuclease I-PpoI. These homodimeric endonuclease scaffolds have arrived at similar specificity profiles across their common biological target and analogous solutions to the problem of accommodating conserved asymmetries within the DNA sequence, but with differences at individual base pairs that are fine-tuned to the sequence conservation of archaeal versus eukaryal ribosomes.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Nomura N,Nomura Y,Sussman D,Klein D,Stoddard BLdoi
10.1093/nar/gkn846subject
Has Abstractpub_date
2008-12-01 00:00:00pages
6988-98issue
22eissn
0305-1048issn
1362-4962pii
gkn846journal_volume
36pub_type
杂志文章abstract::The B-subunits associated with the replicative DNA polymerases are conserved from Archaea to humans, whereas the corresponding catalytic subunits are not related. The latter belong to the B and D DNA polymerase families in eukaryotes and archaea, respectively. Sequence analysis places the B-subunits within the calcine...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh558
更新日期:2004-04-30 00:00:00
abstract::We developed a framework for quick and reliable construction of complex gene circuits for genetically engineering mammalian cells. Our hierarchical framework is based on a novel nucleotide addressing system for defining the position of each part in an overall circuit. With this framework, we demonstrate construction o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt605
更新日期:2013-09-01 00:00:00
abstract::The environmental carcinogen benzo[a]pyrene (BP) is metabolized to reactive diol epoxides that bind to cellular DNA by predominantly forming N2-guanine adducts (G*). Mutation hotspots for these adducts are frequently found in 5'- ... GG ... dinucleotide sequences, but their origins are poorly understood. Here we used ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm022
更新日期:2007-01-01 00:00:00
abstract::Conflicts between replication and transcription challenge chromosome duplication. Escherichia coli replisome movement along transcribed DNA is promoted by Rep and UvrD accessory helicases with Δrep ΔuvrD cells being inviable under rapid growth conditions. We have discovered that mutations in a tRNA gene, aspT, in an a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1254
更新日期:2017-03-17 00:00:00
abstract::Influenza A viruses are hosted by numerous avian and mammalian species, which have shaped their evolution into distinct lineages worldwide. The viral genome consists of eight RNA segments that are frequently exchanged between different viruses via a process known as genetic reassortment. A complete genotype nomenclatu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm365
更新日期:2007-07-01 00:00:00
abstract::Previous evidence indicates that telomeres resemble common fragile sites and present a challenge for DNA replication. The precise impediments to replication fork progression at telomeric TTAGGG repeats are unknown, but are proposed to include G-quadruplexes (G4) on the G-rich strand. Here we examined DNA synthesis and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt813
更新日期:2013-12-01 00:00:00
abstract::We have developed a simple method to measure RNA synthesis in real time. In this technique, transcription reactions are performed in the presence of molecular beacons that possess a 2'-O-methylribonucleotide backbone. These probes become fluorescent as they hybridize to nascent RNA during the course of synthesis. We f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh068
更新日期:2004-05-20 00:00:00
abstract::A very mild and efficient procedure has been developed for the preparation of C-5 substituted deoxyuridines. The substituent carries a masked primary aliphatic amino group. These compounds are readily converted into their phosphoramidites and can be used to prepare oligonucleotides carrying one or more aliphatic amino...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.12.4857
更新日期:1987-06-25 00:00:00
abstract::Many proteins of the SNF2 family, which share a similar DNA-dependent ATPase/putative helicase domain, are involved in global transcriptional control and processing of DNA damage. We report here the partial cloning and characterization of 89B helicase, a gene encoding a new Drosophila melanogaster member of the SNF2 f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.16.3121
更新日期:1996-08-15 00:00:00
abstract::Ribonuclease MRP is an endonuclease, related to RNase P, which functions in eukaryotic pre-rRNA processing. In Saccharomyces cerevisiae, RNase MRP comprises an RNA subunit and ten proteins. To improve our understanding of subunit roles and enzyme architecture, we have examined protein-protein and protein-RNA interacti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm553
更新日期:2007-01-01 00:00:00
abstract::Acinetobacter sp. strain ADP1 is a nutritionally versatile soil bacterium closely related to representatives of the well-characterized Pseudomonas aeruginosa and Pseudomonas putida. Unlike these bacteria, the Acinetobacter ADP1 is highly competent for natural transformation which affords extraordinary convenience for ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh910
更新日期:2004-10-28 00:00:00
abstract::PAHdb (http://www.mcgill.ca/pahdb ) is a curated relational database (Fig. 1) of nucleotide variation in the human PAH cDNA (GenBank U49897). Among 328 different mutations by state (Fig. 2) the majority are rare mutations causing hyperphenylalaninemia (HPA) (OMIM 261600), the remainder are polymorphic variants without...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.1.220
更新日期:1998-01-01 00:00:00
abstract::PIR-International is an association of macromolecular sequence data collection centers dedicated to fostering international cooperation as an essential element in the development of scientific databases. A major objective of PIR-International is to continue the development of the Protein Sequence Database as an essent...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:
更新日期:1994-09-01 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
pub_type: 杂志文章
doi:10.1093/nar/gks1197
更新日期:2013-02-01 00:00:00
abstract::As opposed to the vast majority of prokaryotic repressors, the immunity repressor of temperate Escherichia coli phage P2 (C) recognizes non-palindromic direct repeats of DNA rather than inverted repeats. We have determined the crystal structure of P2 C at 1.8 Å. This constitutes the first structure solved from the fam...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq626
更新日期:2010-11-01 00:00:00
abstract::Recruitment of RAD18 to stalled replication forks facilitates monoubiquitination of PCNA during S-phase, promoting translesion synthesis at sites of UV irradiation-induced DNA damage. In this study, we show that RAD18 is also recruited to ionizing radiation (IR)-induced sites of DNA double-strand breaks (DSBs) forming...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp082
更新日期:2009-04-01 00:00:00
abstract::The behaviour of highly purified bacterial expressed rat O6-methylguanine-DNA methyltransferase (MGMT) towards the repair of CGCm6GAGCTCGCG and CGCe6GAGCTCGCG (km6G/ke6G = 1.45, where k is the second order repair rate constant determined, m6G and e6G are O6-methyl and O6-ethylguanine) is similar to that of E. coli 39k...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.9.1613
更新日期:1994-05-11 00:00:00
abstract::A DNA fragment d(GCGAAAGCT), known to adopt a stable mini-hairpin structure in solution, has been crystallized in the space group I4(1)22 with the unit-cell dimensions a = b = 53.4 A and c = 54.0 A, and the crystal structure has been determined at 2.5 A resolution. The four nucleotide residues CGAA of the first half o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf639
更新日期:2002-12-01 00:00:00
abstract::Transcription factor IIIA (TFIIIA) and p43 zinc finger protein form distinct complexes with 5S ribosomal RNA in Xenopus oocytes. Additionally, TFIIIA binds the internal promoter of the 5S RNA gene and supports assembly of a transcription initiation complex. Both proteins have nine tandemly repeated zinc fingers with a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.3.703
更新日期:1998-02-01 00:00:00
abstract::The deoxyoligonucleotide 5' AATCGGGCATGGATT (15-mer) was synthesized containing 12 phosphoramidate linkages derived from 2 primary and 2 secondary amines. The oligonucleotides were purified by reverse phase HPLC and characterized by PAGE. The thermal stability of the duplexes derived from these compounds, when hybridi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.11.4831
更新日期:1988-06-10 00:00:00
abstract::Apurinic/apyrimidinic endonuclease 1 (APE1), an essential protein in mammals, is involved in base excision DNA repair (BER) and in regulation of gene expression, acting as a redox co-activator of several transcription factors. Recent findings highlight a novel role for APE1 in RNA metabolism, which is modulated by nuc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq691
更新日期:2010-12-01 00:00:00
abstract::Virtually the whole region of the mobile dispersed genetic element mdg1 including the direct repeats that frame mdg1 /1/ is transcribed. The end of the transcriptional unit is located within the direct repeat. Although the transcription of mdg1 is symmetric, one direction is transcribed preferentially and is a full-le...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.22.5347
更新日期:1980-11-25 00:00:00
abstract::Stable protein complexes, including those formed with RNA, are major building blocks of every living cell. Escherichia coli has been the leading bacterial organism with respect to global protein-protein networks. Yet, there has been no global census of RNA/protein complexes in this model species of microbiology. Here,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa676
更新日期:2020-09-18 00:00:00
abstract::We have assessed the ability of nucleosomes to influence the formation of mammalian topoisomerase II-DNA complexes by mapping the sites of cleavage induced by four unrelated topoisomerase II inhibitors in naked versus nucleosome-reconstituted SV40 DNA. DNA fragments were reconstituted with histone octamers from HeLa c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.15.4553
更新日期:1990-08-11 00:00:00
abstract::A new way of studying RNA-protein complexes, using neutron small angle scattering in solution, is described and was applied in the case of the system, yeast valyl-tRNA synthetase, interacting with its cognate and non cognate yeast tRNAs. It was shown that, when limited amounts of tRNA (either cognate or non cognate) a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.7.2421
更新日期:1977-07-01 00:00:00
abstract::Chloroplast DNA, isolated from a synchronized culture of Chlamydomonas reinhardii, was digested with restriction endonucleases and examined in the electron microscope. Restriction fragments containing displacement loops (D-loop) were photographed and measured to determine the position of replicated sequences in relati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.9.3843
更新日期:1984-05-11 00:00:00
abstract::In previous studies, we reported that fractionation of HeLa cell nuclear extracts on glycerol gradients revealed an endogenous ∼10S particle that contained galectin-3 and U1 snRNP and this particle was sufficient to load the galectin polypeptide onto a pre-mRNA substrate. We now document that this interaction between ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw303
更新日期:2016-07-27 00:00:00
abstract::The triphosphate of the nucleoside deoxyribosyl dihydropyrimido[4,5-c][1,2]oxazin-7-one (dP) is known to be incorporated into DNA efficiently by Taq polymerase and is a useful tool for polymerase-mediated in vitro mutagenesis. It is shown here that dP is a potent mutagen in Escherichia coli and Salmonella typhimurium ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.8.1548
更新日期:1997-04-15 00:00:00
abstract::The EcoCyc database describes the genome and gene products of Escherichia coli, its metabolic and signal-transduction pathways, and its tRNAs. The database describes 4391 genes of E.coli, 695 enzymes encoded by a subset of these genes, 904 metabolic reactions that occur in E.coli, and the organization of these reactio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.1.55
更新日期:1999-01-01 00:00:00
abstract::Using the quenched flow technique the mechanism of seryl tRNA synthetase action has been investigated with respect to the presteady state kinetics of individual steps. Under conditions where the strong binding sites of the enzyme are nearly saturated and the steady state turnover number is about 1 s-1, rate constants ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.17.4021
更新日期:1980-09-11 00:00:00