Abstract：
:Cellular RNA labeling strategies based on bioorthogonal chemical reactions are much less developed in comparison to glycan, protein and DNA due to its inherent instability and lack of effective methods to introduce bioorthogonal reactive functionalities (e.g. azide) into RNA. Here we report the development of a simple and modular posttranscriptional chemical labeling and imaging technique for RNA by using a novel toolbox comprised of azide-modified UTP analogs. These analogs facilitate the enzymatic incorporation of azide groups into RNA, which can be posttranscriptionally labeled with a variety of probes by click and Staudinger reactions. Importantly, we show for the first time the specific incorporation of azide groups into cellular RNA by endogenous RNA polymerases, which enabled the imaging of newly transcribing RNA in fixed and in live cells by click reactions. This labeling method is practical and provides a new platform to study RNA in vitro and in cells.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Sawant AA,Tanpure AA,Mukherjee PP,Athavale S,Kelkar A,Galande S,Srivatsan SGdoi
10.1093/nar/gkv903subject
Has Abstractpub_date
2016-01-29 00:00:00pages
e16issue
2eissn
0305-1048issn
1362-4962pii
gkv903journal_volume
44pub_type
杂志文章abstract：:Three new proteins which selectively bind to UV-damaged DNA were identified and purified to near homogeneity from UV-irradiated Drosophila melanogaster embryos through several column chromatographies. These proteins, tentatively designated as D-DDB P1, P2 and P3, can be identified as different complex bands in a gel s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.14.2600
更新日期：1995-07-25 00:00:00
abstract：:By putting heterologous genomic regulatory systems into contact, chromosome addition lines derived from interspecific or intergeneric crosses allow the investigation of transcriptional regulation in new genomic environments. Here, we report the transcriptional and epigenetic adaptation of stably inherited alien maize ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky209
更新日期：2018-06-01 00:00:00
abstract：:Replication protein A (RPA) plays a critical role in all eukaryotic DNA processing involving single-stranded DNA (ssDNA). Contrary to the notion that RPA provides solely inert protection to transiently formed ssDNA, the RPA-ssDNA complex acts as a dynamic DNA processing unit. Here, we studied the diffusion of RPA alon...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz1202
更新日期：2020-02-28 00:00:00
abstract：:Escherichia coli Exonuclease I (ExoI) digests single-stranded DNA (ssDNA) in the 3'-5' direction in a highly processive manner. The crystal structure of ExoI, determined previously in the absence of DNA, revealed a C-shaped molecule with three domains that form a central positively charged groove. The active site is a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt278
更新日期：2013-06-01 00:00:00
abstract：:Meiotic cells possess surveillance mechanisms that monitor critical events such as recombination and chromosome synapsis. Meiotic defects resulting from the absence of the synaptonemal complex component Zip1 activate a meiosis-specific checkpoint network resulting in delayed or arrested meiotic progression. Pch2 is an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw506
更新日期：2016-09-19 00:00:00
abstract：:Triethylammonium uridine-3',5'-cyclic phosphorothioate crystallizes in space group P2(1)2(1)2(1), a = 7.177(1), b = 13.155(6), c = 21.114(7) A, C15H26N3O7PS, MW 423.4, Z = 4, dx = 1.41g/cm3. The crystal structure was solved by direct methods on the basis of 1493 counter X-ray diffraction data (CuK alpha) and refined t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.12.4945
更新日期：1987-06-25 00:00:00
abstract：:The primary structures of two overlapping novel alpha-tubulin cDNA clones isolated from a Macaca fascicularis testis cDNA library and the corresponding human gene are presented. Although the general structure of the human gene conforms to that of previously described mammalian alpha-tubulin genes, there is a surprisin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.1.199
更新日期：1987-01-12 00:00:00
abstract：:Two similar, but not identical, models have been proposed for the amino acid-base pair contacts in the CAP-DNA complex ('Model I,' Weber, I. and Steitz, T., Proc. Natl. Acad. Sci. USA, 81, 3973-3977, 1984; 'Model II,' Ebright, et al., Proc. Natl. Acad. Sci. USA, 81, 7274-7278, 1984). One difference between the two mod...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.23.6853
更新日期：1990-12-11 00:00:00
abstract：:Planarian flatworms are in the midst of a renaissance as a model system for regeneration and stem cells. Besides two well-studied model species, hundreds of species exist worldwide that present a fascinating diversity of regenerative abilities, tissue turnover rates, reproductive strategies and other life history trai...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1148
更新日期：2016-01-04 00:00:00
abstract：:Coralyne is a small crescent-shaped molecule known to intercalate duplex and triplex DNA. We report that coralyne can cause the complete and irreversible disproportionation of duplex poly(dT)*poly(dA). That is, coralyne causes the strands of duplex poly(dT)*poly(dA) to repartition into equal molar equivalents of tripl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.4.983
更新日期：2002-02-15 00:00:00
abstract：:Overexpression of the flap endonuclease FEN1 has been observed in a variety of cancer types and is a marker for poor prognosis. To better understand the cellular consequences of FEN1 overexpression we utilized a model of its Saccharomyces cerevisiae homolog, RAD27. In this system, we discovered that flap endonuclease ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky313
更新日期：2018-06-20 00:00:00
abstract：:We have isolated an eight kilobase fragment of Bacillus subtilis DNA by specific integration and excision of a plasmid containing a sequence adjacent to ribosomal operon rrn O. The genetic locus of the cloned fragment was verified by linkage of the integrated vector to nearby genetic markers using both transduction an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.15.6307
更新日期：1984-08-10 00:00:00
abstract：:Besides orthologs of other eukaryotic mismatch-repair (MMR) proteins, plants encode MSH7, a paralog of MSH6. The Arabidopsis thaliana recognition heterodimers AtMSH2*MSH6 (AtMutSalpha) and AtMSH2*MSH3 (AtMutSbeta) were previously found to bind the same subsets of mismatches as their counterparts in other eukaryotes--r...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg780
更新日期：2003-10-15 00:00:00
abstract：:Transcription of the human adenovirus 5 genome in transformed rat embryo cells (DFK3) was investigated using two different approaches. Preferential digestion of transcribed viral sequences by DNase I was analysed using kinetics of renaturation of 32P-labeled Ad5 HpaI restriction fragments in the presence of material w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.1.1
更新日期：1978-01-01 00:00:00
abstract：:Protein species interacting with newly replicated DNA were analyzed using a photo cross-linking technique. Nascent DNA was labeled in vitro with [alpha-32P]dCTP and BrdUTP in SV40-infected CV-1 cells made permeable with saponin. The labeled cells were then irradiated with UV light (254 nm) and were treated extensively...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.14.4793
更新日期：1983-07-25 00:00:00
abstract：:Alternative first exons diversify the transcriptomes of eukaryotes by producing variants of the 5' Untranslated Regions (5'UTRs) and N-terminal coding sequences. Accurate transcriptome-wide detection of alternative first exons typically requires specialized experimental approaches that are designed to identify the 5' ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky053
更新日期：2018-05-04 00:00:00
abstract：:Two residues are invariant in all bZip basic regions: asparagine -18 and arginine -10 (we define the first leucine of the leucine zipper of GCN4 as +1). X-ray structures of two specific GCN4-DNA complexes (Ellenberger et al., Cell, 71, 1223-1237, 1992; König & Richmond, J. Mol. Biol., 233, 139-154, 1993) demonstrate t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.21.4395
更新日期：1994-10-25 00:00:00
abstract：:Gene-order-based comparison of multiple genomes provides signals for functional analysis of genes and the evolutionary process of genome organization. Gene clusters are regions of co-localized genes on genomes of different species. The rapid increase in sequenced genomes necessitates bioinformatics tools for finding g...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw843
更新日期：2016-11-16 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
pub_type： 杂志文章
doi：10.1093/nar/4.2.445
更新日期：1977-02-01 00:00:00
abstract：:In Escherichia coli transcription of individual genes generally requires concomitant translation, and thus the decay of mRNAs cannot be studied without the complication of translation. Here we have used T7 RNA polymerase to transcribe in vivo lacZ genes carrying ribosome binding sites of variable efficiency. We show t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.19.5787
更新日期：1990-10-11 00:00:00
abstract：:The sequence of 110 nucleotides adjacent to the 3'-end of Neurospora crassa 25S-rRNA has been derived by chemical sequencing methods. Sequences present between 40 and 85 nucleotides of the 3'-end were found to complement sequences at the 3'- and 5'-ends of 5.8S-rRNA. Interaction was shown to occur between 5.8S-rRNA an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.5.1111
更新日期：1981-03-11 00:00:00
abstract：:We have isolated a human cDNA (kup), encoding a new protein with two distantly spaced zinc fingers of the C2H2 type. This gene is highly conserved in mammals and is expressed mainly in hematopoietic cells and testis. Its expression was not higher in the various transformed cells tested than in the normal corresponding...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.7.1431
更新日期：1991-04-11 00:00:00
abstract：:During telomere replication in yeast, chromosome ends acquire a long single-stranded extension of the strand making the 3' end. Previous work showed that these 3' tails are generated late in S-phase, when conventional replication is virtually complete. In addition, the extensions were also observed in cells that lacke...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.23.5365
更新日期：1998-12-01 00:00:00
abstract：:NMR data from different experiments often contain errors; thus, automated backbone resonance assignment is a very challenging issue. In this paper, we present a method called GANA that uses a genetic algorithm to automatically perform backbone resonance assignment with a high degree of precision and recall. Precision ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki768
更新日期：2005-08-10 00:00:00
abstract：:Two models have been proposed for triggering release of the lagging strand polymerase at the replication fork, enabling cycling to the primer for the next Okazaki fragment--either collision with the 5'-end of the preceding fragment (collision model) or synthesis of a new primer by primase (signaling model). Specific p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1098
更新日期：2014-02-01 00:00:00
abstract：:Using a genetic selection for suppressors of a UGA nonsense mutation in trpA, we have isolated a G to A transition mutation at position 1491 in the decoding region of 16S rRNA. This suppressor displayed no codon specificity, suppressing UGA, UAG and UAA nonsense mutations and +1 and -1 frameshift mutations in lacZ. Su...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.21.4234
更新日期：1995-11-11 00:00:00
abstract：:DNA methylation plays a crucial role in the establishment of tissue-specific gene expression and the regulation of key biological processes. However, our present inability to predict the effect of genome sequence variation on DNA methylation precludes a comprehensive assessment of the consequences of non-coding variat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx177
更新日期：2017-06-20 00:00:00
abstract：:LINKER was developed as an online server to assist biomedical researchers to design linker sequences for constructing functional fusion proteins. The program automatically generates a set of peptide sequences that are known to adopt extended conformations as determined by X-ray crystallography and NMR. In addition to ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh422
更新日期：2004-07-01 00:00:00
abstract：:7SK snRNA, an abundant RNA discovered in human nucleus, regulates transcription by RNA polymerase II (RNAPII). It sequesters and inhibits the transcription elongation factor P-TEFb which, by phosphorylation of RNAPII, switches transcription from initiation to processive elongation and relieves pauses of transcription....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq660
更新日期：2010-11-01 00:00:00
abstract：:One of the master regulators of placental cell fusion in mammals leading to multi-nucleated syncytiotrophoblasts is the transcription factor GCMa. Recently, we proved that the cAMP-driven protein kinase A signaling pathway is fundamental for up-regulation of GCMa transcript levels and protein stability. Here, we show ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn306
更新日期：2008-06-01 00:00:00
