Abstract：
:RNA molecules of > 20 nucleotides have been the focus of numerous recent NMR structural studies. Several investigators have used the UNCG family of hairpins to ensure proper folding. We show that th UUCG hairpin has a minimum requirement of a two base-pair stem. Hairpins with a CG loop closing base pair and an initial 5'CG or 5'GC base pair have a melting temperature approximately 55 degrees C in 10 mM sodium phosphate. The high stability of even such small hairpins suggests that the hairpin can serve as a nucleation site for folding. For high resolution NMR work, the UNCG loop family (UACG in particular) provides excellent spectroscopic markers in one-dimensional exchangeable spectra, in two-dimensional COSY spectra and in NOESY spectra that clearly define it as forming a hairpin. This allows straightforward initiation of chemical shift assignments.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Molinaro M,Tinoco I Jrdoi
10.1093/nar/23.15.3056subject
Has Abstractpub_date
1995-08-11 00:00:00pages
3056-63issue
15eissn
0305-1048issn
1362-4962pii
4j0839journal_volume
23pub_type
杂志文章abstract：:Laser microirradiation is a powerful tool for real-time single-cell analysis of the DNA damage response (DDR). It is often found, however, that factor recruitment or modification profiles vary depending on the laser system employed. This is likely due to an incomplete understanding of how laser conditions/dosages affe...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv976
更新日期：2016-02-18 00:00:00
abstract：:Re-sequencing, the identification of the specific variants in a sequence of interest compared with a known genomic sequence, is a ubiquitous task in today's biology. Universal arrays, which interrogate all possible oligonucleotides of a certain length in a target sequence, have been suggested for computationally deter...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg757
更新日期：2003-10-01 00:00:00
abstract：:MS²PIP is a data-driven tool that accurately predicts peak intensities for a given peptide's fragmentation mass spectrum. Since the release of the MS²PIP web server in 2015, we have brought significant updates to both the tool and the web server. In addition to the original models for CID and HCD fragmentation, we hav...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz299
更新日期：2019-07-02 00:00:00
abstract：:Simian virus 40 (SV40) nucleoprotein complexes were extracted from nuclei of infected monkey cells and fractionated on neutral sucrose density gradients. Complexes which contained replicating SV40 DNA (95S) separated well from those containing closed circular supercoiled viral DNA (75S). DNA polymerase activity was as...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.5.1715
更新日期：1978-05-01 00:00:00
abstract：:Proper cytokine gene expression is essential in development, homeostasis and immune responses. Studies on the transcriptional control of cytokine genes have mostly focused on highly researched transcription factors (TFs) and cytokines, resulting in an incomplete portrait of cytokine gene regulation. Here, we used enha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1055
更新日期：2020-12-02 00:00:00
abstract：:The mini-exon, a short segment found at the 5' end of trypanosome mRNAs, is contributed by a small RNA, the mini-exon donor (medRNA). In vivo 32P-labeled medRNA, a set of smaller RNAs related to it, and mRNA, were purified from Trypanosoma brucei by hybrid selection and gel electrophoresis. Using RNA fingerprinting an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.23.9861
更新日期：1987-12-10 00:00:00
abstract：:Targeted delivery of antisense oligonucleotides (ASO) to hepatocytes via the asialoglycoprotein receptor (ASGR) has improved the potency of ASO drugs ∼30-fold in the clinic (1). In order to fully characterize the effect of GalNAc valency, oligonucleotide length, flexibility and chemical composition on ASGR binding, we...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx060
更新日期：2017-03-17 00:00:00
abstract：:DNA molecules with covalently sealed (hairpin) ends are probable intermediates in V(D)J recombination. According to current models hairpin ends are opened to produce short single-stranded extensions that are thought to be precursors of a particular type of extra nucleotides, termed P nucleotides, which are frequently ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.19.3872
更新日期：1995-10-11 00:00:00
abstract：:Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current versi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr201
更新日期：2011-07-01 00:00:00
abstract：:With the improved secreted protein prediction approach and comprehensive data sources, including Swiss-Prot, TrEMBL, RefSeq, Ensembl and CBI-Gene, we have constructed secretomes of human, mouse and rat, with a total of 18 152 secreted proteins. All the entries are ranked according to the prediction confidence. They we...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki093
更新日期：2005-01-01 00:00:00
abstract：:The Gibbs Motif Sampler is a software package for locating common elements in collections of biopolymer sequences. In this paper we describe a new variation of the Gibbs Motif Sampler, the Gibbs Recursive Sampler, which has been developed specifically for locating multiple transcription factor binding sites for multip...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg608
更新日期：2003-07-01 00:00:00
abstract：:The nucleotide sequence of Neurospora crassa 5.8 S rDNA and adjacent regions has been determined. The deduced 5.8 S rRNA sequence of Neurospora differs from the 5.8 S rRNA sequence of Saccharomyces cerevisiae at 13 of 158 residues. Nine of these differences are clustered in a segment capable of forming a short hairpin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.7.2561
更新日期：1979-06-11 00:00:00
abstract：:Many cellular proteins are methylated on lysine residues and this has been most intensively studied for histone proteins. Lysine methylations on non-histone proteins are also frequent, but in most cases the functional significance of the methylation event, as well as the identity of the responsible lysine (K) specific...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx432
更新日期：2017-08-21 00:00:00
abstract：:The distribution patterns of shared short repetitive motifs in the expansion segments of the large subunit rRNA genes of different species show that these segments are coevolving as a set and that in two examined vertebrate species the RNA secondary structures are conserved as a consequence of runs of motifs in one re...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.20.5949
更新日期：1990-10-25 00:00:00
abstract：:Poly A-containing RNA enriched in prolactin-coding sequences was isolated from female rate pituitaries after induction with diethylstilbesterol. Double stranded cDNA was synthesized from this RNA and inserted into plasmid pBR322 at the Pst I site via the poly(dG):polyy(dC) tailing method. E. coli was transformed with ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.3.915
更新日期：1979-03-01 00:00:00
abstract：:DNA glycosylases from the Fpg/Nei structural superfamily are base excision repair enzymes involved in the removal of a wide variety of mutagen and potentially lethal oxidized purines and pyrimidines. Although involved in genome stability, the recent discovery of synthetic lethal relationships between DNA glycosylases ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku613
更新日期：2014-01-01 00:00:00
abstract：:The putative role of double-strand breaks (DSBs) created in vitro by restriction enzyme cleavage in or near CGG*CCG or CTG*CAG repeat tracts on their genetic instabilities, both within the repeats and in their flanking sequences, was investigated in an Escherichia coli plasmid system. DSBs at TRS junctions with the ve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl612
更新日期：2006-01-01 00:00:00
abstract：:WebProAnalyst is a web-accessible analysis tool (http://wwwmgs.bionet.nsc.ru/mgs/programs/panalyst/) designed for scanning quantitative structure-activity relationships in protein families. The tool allows users to search correlations between protein activity and physicochemical characteristics (i.e. hydrophobicity or...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki421
更新日期：2005-07-01 00:00:00
abstract：:In a gene targeting experiment, the generation of a targeting construct often requires complex DNA manipulations. We developed a set of cassettes and plasmids useful for creating targeting vectors to modify the mammalian genome. A positive selection marker cassette (PGK/EM7p-npt), which included dual prokaryotic and e...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gni055
更新日期：2005-03-22 00:00:00
abstract：:The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), provided from EMBL-EBI, has for more than three decades been responsible for archiving the world's public sequencing data and presenting this important resource to the scientific community to support and accelerate the global research effort. Here, we o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1078
更新日期：2019-01-08 00:00:00
abstract：:The ribosomal frameshifting signal of the mouse embryonal carcinoma differentiation regulated (Edr) gene represents the sole documented example of programmed -1 frameshifting in mammalian cellular genes [Shigemoto,K., Brennan,J., Walls,E,. Watson,C.J., Stott,D., Rigby,P.W. and Reith,A.D. (2001), Nucleic Acids Res., 29...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki299
更新日期：2005-03-14 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh465
更新日期：2004-07-01 00:00:00
abstract：:PlantGDB (http://www.plantgdb.org/) is a genomics database encompassing sequence data for green plants (Viridiplantae). PlantGDB provides annotated transcript assemblies for >100 plant species, with transcripts mapped to their cognate genomic context where available, integrated with a variety of sequence analysis tool...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm1041
更新日期：2008-01-01 00:00:00
abstract：:RNA duplex stability depends strongly on ionic conditions, and inside cells RNAs are exposed to both monovalent and multivalent ions. Despite recent advances, we do not have general methods to quantitatively account for the effects of monovalent and multivalent ions on RNA stability, and the thermodynamic parameters f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks289
更新日期：2012-08-01 00:00:00
abstract：:With the high number of sequences and structures streaming in from genomic projects, there is a need for more powerful and sophisticated annotation tools. Most problematic of the annotation efforts is predicting gene and protein function. Over the past few years there has been considerable progress in automated protei...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl045
更新日期：2006-07-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt153
更新日期：2013-04-01 00:00:00
abstract：:In Trypanosoma brucei the genes are organised into long polycistronic transcription units and only three promoters for protein-encoding genes and a single terminator have been characterised. These promoters recruit a polI-like RNA polymerase for the transcription units encoding the two major stage-specific antigens of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.2.597
更新日期：2000-01-15 00:00:00
abstract：:The transcriptional shift from repression to activation of target genes is crucial for the fidelity of Notch responses through incompletely understood mechanisms that likely involve chromatin-based control. To activate silenced genes, repressive chromatin marks are removed and active marks must be acquired. Histone H3...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw105
更新日期：2016-06-02 00:00:00
abstract：:Hepatitis C virus (HCV) RNA is recognized and cleaved in vitro by RNase P enzyme near the AUG start codon. Because RNase P identifies transfer RNA (tRNA) precursors, it has been proposed that HCV RNA adopts structural similarities to tRNA. Here, we present experimental evidence of RNase P sensitivity conservation in n...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki290
更新日期：2005-03-08 00:00:00
abstract：:The Nucleolar Proteome Database (NOPdb) archives data on >700 proteins that were identified by multiple mass spectrometry (MS) analyses from highly purified preparations of human nucleoli, the most prominent nuclear organelle. Each protein entry is annotated with information about its corresponding gene, its domain st...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkj004
更新日期：2006-01-01 00:00:00
