Abstract:
:A study of the activity of deoxyribonucleotide-substituted analogs of the hammerhead domain of RNA catalysis has led to the design of a 14mer oligomer composed entirely of deoxyribonucleotides that promotes the cleavage of an RNA substrate. Characterization of this reaction with sequence variants and mixed DNA/RNA oligomers shows that, although the all-deoxyribonucleotide oligomer is less efficient in catalysis, the DNA/substrate complex shares many of the properties of the all-RNA hammerhead domain such as multiple turnover kinetics and dependence on Mg2+ concentration. On the other hand, the values of kinetic parameters distinguish the DNA oligomer from the all-RNA oligomer. In addition, an analog of the oligomer having a single ribonucleotide in a strongly conserved position of the hammerhead domain is associated with more efficient catalysis than the all-RNA oligomer.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Chartrand P,Harvey SC,Ferbeyre G,Usman N,Cedergren Rdoi
10.1093/nar/23.20.4092subject
Has Abstractpub_date
1995-10-25 00:00:00pages
4092-6issue
20eissn
0305-1048issn
1362-4962pii
5j0396journal_volume
23pub_type
杂志文章abstract::ZFP57 is necessary for maintaining repressive epigenetic modifications at Imprinting control regions (ICRs). In mouse embryonic stem cells (ESCs), ZFP57 binds ICRs (ICRBS) and many other loci (non-ICRBS). To address the role of ZFP57 on all its target sites, we performed high-throughput and multi-locus analyses of inb...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw505
更新日期:2016-09-30 00:00:00
abstract::Sequence-specific DNA-binding proteins play a key role in many fundamental biological processes, such as transcription, DNA replication and recombination. Very often, these DNA-binding proteins introduce structural changes to the target DNA-binding sites including DNA bending, twisting or untwisting and wrapping, whic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq078
更新日期:2010-06-01 00:00:00
abstract::UV-irradiation (lambda = 254 nm) of liquid aqueous solutions of deoxyguanosine in the presence of oxygen at pH less than 7 causes an intensive degradation of nucleoside. The quantum yield estimated from A254 decrease for the reaction mixture was found to be 1.5X10(-4) at doses to 150 E/mole. The rate of A254 decrease ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.4.955
更新日期:1977-04-01 00:00:00
abstract::Spliced leader (SL) trans-splicing is a critical element of gene expression in a number of eukaryotic groups. This process is arguably best understood in nematodes, where biochemical and molecular studies in Caenorhabditis elegans and Ascaris suum have identified key steps and factors involved. Despite this, the preci...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx500
更新日期:2017-08-21 00:00:00
abstract::Group II introns are self-splicing RNAs and retroelements found in bacteria and lower eukaryotic organelles. During the past several years, they have been uncovered in surprising numbers in bacteria due to the genome sequencing projects; however, most of the newly sequenced introns are not correctly identified. We hav...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg049
更新日期:2003-01-01 00:00:00
abstract::An algorithm is presented which compares two restriction maps, yielding a measure of distance between the maps and relating the maps by an alignment. This new algorithm finds the minimum weighted sum of genetic events required to convert one map into the other, where the genetic events are the appearance/disappearance...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.1part1.237
更新日期:1984-01-11 00:00:00
abstract::MLL, the trithorax ortholog, is a well-characterized histone 3 lysine 4 methyltransferase that is crucial for proper regulation of the Hox genes during embryonic development. Chromosomal translocations, disrupting the Mll gene, lead to aggressive leukemia with poor prognosis. However, the functions of MLL in cellular ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku458
更新日期:2014-07-01 00:00:00
abstract::Upon activation of the ERK and p38 MAPK pathways, the MSK1/2-mediated nucleosomal response, including H3 phosphorylation at serine 28 or 10, is coupled with the induction of immediate-early (IE) gene transcription. The outcome of this response, varying with the stimuli and cellular contexts, ranges from neoplastic tra...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq030
更新日期:2010-06-01 00:00:00
abstract::We have used computer assisted dot matrix and oligonucleotide frequency analyses to identify highly recurring sequence elements of 7-11 base pairs in eukaryotic genes and viral DNAs. Such elements are found much more frequently than expected, often with an average spacing of a few hundred base pairs. Furthermore, the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.4.1835
更新日期:1987-02-25 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
pub_type: 杂志文章
doi:10.1093/nar/gkz949
更新日期:2020-01-08 00:00:00
abstract::Lens epithelium-derived growth factor/p75 (LEDGF/p75) is a transcriptional coactivator involved in stress response, autoimmune disease, cancer and HIV replication. A fusion between the nuclear pore protein NUP98 and LEDGF/p75 has been found in human acute and chronic myeloid leukemia and association of LEDGF/p75 with ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq410
更新日期:2010-10-01 00:00:00
abstract::Hepatitis C virus (HCV) is the major etiological agent of non-A, non-B hepatitis. Current therapies are not effective in all patients and can result in the generation of resistant mutants, leading to a need for new therapeutic options. HCV has an RNA genome that contains a well-defined and highly conserved secondary s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh706
更新日期:2004-07-19 00:00:00
abstract::A fundamental problem with applying Consensus, Weight-Matrix or hidden Markov models as search tools for biosequences is that there is no way to know, from the model, if the modeled sequences display any dependencies between positional identities. In some instances, these dependencies are crucial in correctly acceptin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki374
更新日期:2005-07-01 00:00:00
abstract::The database of molecular motions, MolMovDB (http://molmovdb.org), has been in existence for the past decade. It classifies macromolecular motions and provides tools to interpolate between two conformations (the Morph Server) and predict possible motions in a single structure. In 2005, we expanded the services offered...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj046
更新日期:2006-01-01 00:00:00
abstract::Eukaryotic RNases H from Saccharomyces cerevisiae , Schizosaccharomyces pombe and Crithidia fasciculata , unlike the related Escherichia coli RNase HI, contain a non-RNase H domain with a common motif. Previously we showed that S.cerevisiae RNase H1 binds to duplex RNAs (either RNA-DNA hybrids or double-stranded RNA) ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.7.1834
更新日期:1998-04-01 00:00:00
abstract::An accurate and highly sensitive mutation detection assay has been developed. The assay is based on the detection of mispaired and unpaired bases by immobilized mismatch binding protein (Escherichia coli MutS). The assay can detect most mismatches and all single base substitution mutations, as well as small addition o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.19.3944
更新日期:1995-10-11 00:00:00
abstract::Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1195
更新日期:2021-01-11 00:00:00
abstract::Topoisomerases catalyse changes in the topological state of DNA and are required for many aspects of DNA metabolism. While the functions of topoisomerases I and II in eukaryotes are well established, the role of topoisomerase III remains poorly defined. We have identified a gene in the fission yeast Schizosaccharomyce...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.20.4050
更新日期:1999-10-15 00:00:00
abstract::The structure-specific Mus81-Eme1/Mms4 endonuclease contributes importantly to DNA repair and genome integrity maintenance. Here, using budding yeast, we have studied its function and regulation during the cellular response to DNA damage and show that this endonuclease is necessary for successful chromosome replicatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt645
更新日期:2013-10-01 00:00:00
abstract::Synthetic oligonucleotides were used to introduce mutations into the lacPUV5 promoter. Four mutations were obtained at positions -13, -14, and -15, with respect to the transcriptional start site. The effects of these mutations were measured in vivo and the results are discussed with respect to the consensus sequence a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.9.4011
更新日期:1984-05-11 00:00:00
abstract::We describe here a novel method for integrating gene and miRNA expression profiles in cancer using feed-forward loops (FFLs) consisting of transcription factors (TFs), miRNAs and their common target genes. The dChip-GemiNI (Gene and miRNA Network-based Integration) method statistically ranks computationally predicted ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks395
更新日期:2012-09-01 00:00:00
abstract::The crystal structure is reported of a complex between an ethyl derivative of the minor-groove drug furamidine and the dodecanucleotide duplex d(CGCGAATTCGCG)2, which has been refined to 1.85 A resolution and an R factor of 16.6% for data collected at -173 degreesC. An exceptionally large number (220) of water molecul...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.12.2873
更新日期:1998-06-15 00:00:00
abstract::We report the latest release (version 1.4) of the CATH protein domains database (http://www.biochem.ucl.ac.uk/bsm/cath). This is a hierarchical classification of 13 359 protein domain structures into evolutionary families and structural groupings. We currently identify 827 homologous families in which the proteins hav...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.1.275
更新日期:1999-01-01 00:00:00
abstract::Nuclei from frozen calf thymus suspended in buffer were analyzed for metal content prior to and after repeated washing. After three such extractions about 0.1 micrograms Zn/mg DNA and 0.025 micrograms Cu/mg DNA remained tightly associated with chromatin. This level of metal was essentially unchanged with subsequent wa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.21.5811
更新日期:1981-11-11 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::A method is presented for the purification of mRNAs and the identification of structural gene sequences in recombinant DNA molecules. RNA is hybridized to double-stranded linear DNA such that R-loops are formed between most DNAs and their complementary RNA sequences. These R-loops are purified from unhybridized RNAs b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.7.2483
更新日期:1979-06-11 00:00:00
abstract::O-GLYCBASE is a revised database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the sequence databases. Entries include information about species, sequence, glycosylation sites and glycan type and is fully cross-referenced. Compare...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.1.387
更新日期:1998-01-01 00:00:00
abstract::To organize data resulting from the phenotypic characterization of a library of 30,000 T-DNA enhancer trap (ET) insertion lines of rice (Oryza sativa L cv. Nipponbare), we developed the Oryza Tag Line (OTL) database (http://urgi.versailles.inra.fr/OryzaTagLine/). OTL structure facilitates forward genetic search for sp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm762
更新日期:2008-01-01 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
pub_type: 杂志文章
doi:10.1093/nar/gku379
更新日期:2014-07-01 00:00:00
abstract::High-throughput sequencing of 16S rRNA gene amplicons (16S-seq) has become a widely deployed method for profiling complex microbial communities but technical pitfalls related to data reliability and quantification remain to be fully addressed. In this work, we have developed and implemented a set of synthetic 16S rRNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw984
更新日期:2017-02-28 00:00:00