Abstract:
:The advent of jellyfish green fluorescent protein and its spectral variants, together with promising new fluorescent proteins from other classes of the Cnidarian phylum (coral and anemones), has greatly enhanced and promises to further boost the detection and localization of proteins in cell biology. It has been less widely appreciated that highly sensitive methods have also recently been developed for detecting the movement and localization in living cells of the very molecules that precede proteins in the gene expression pathway, i.e. RNAs. These approaches include the microinjection of fluorescent RNAs into living cells, the in vivo hybridization of fluorescent oligonucleotides to endogenous RNAs and the expression in cells of fluorescent RNA-binding proteins. This new field of 'fluorescent RNA cytochemistry' is summarized in this article, with emphasis on the biological insights it has already provided. These new techniques are likely to soon collaborate with other emerging approaches to advance the investigation of RNA birth, RNA-protein assembly and ribonucleoprotein particle transport in systems such as oocytes, embryos, neurons and other somatic cells, and may even permit the observation of viral replication and transcription pathways as they proceed in living cells, ushering in a new era of nucleic acids research in vivo.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Pederson Tdoi
10.1093/nar/29.5.1013keywords:
subject
Has Abstractpub_date
2001-03-01 00:00:00pages
1013-6issue
5eissn
0305-1048issn
1362-4962journal_volume
29pub_type
杂志文章,评审abstract::The complete nucleotide sequence of the mitochondrial DNA of the amphioxus Branchiostoma lanceolatum has been determined. This mitochondrial genome is small (15 076 bp) because of the short size of the two rRNA genes and the tRNA genes. In addition, this genome contains a very short non-coding region (57 bp) with no s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.13.3279
更新日期:1998-07-01 00:00:00
abstract::CeR-2 RNA is one of the newly identified Caenorhabditis elegans noncoding RNAs (ncRNAs). The characterization of CeR-2 by RNomic studies has failed to classify it into any known ncRNA family. In this study, we examined the spatiotemporal expression patterns of CeR-2 to gain insight into its function. CeR-2 is expresse...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq335
更新日期:2010-09-01 00:00:00
abstract::The DNA sequence was determined for the narL gene of Escherichia coli. This gene is involved in global regulation of a number of nitrate controlled genes including frdABCD, tor, narGHJI, and adhE which are associated with bacterial respiration and fermentation. Comparison of the deduced amino acid sequence of narL to ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.5.1965
更新日期:1989-03-11 00:00:00
abstract::The ability of Deinococcus radiodurans to recover from extensive DNA damage is due in part to its ability to efficiently repair its genome, even following severe fragmentation by hundreds of double-strand breaks. The single-strand annealing pathway plays an important role early during the recovery process, making use ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt759
更新日期:2013-11-01 00:00:00
abstract::We present a www server for AUGUSTUS, a novel software program for ab initio gene prediction in eukaryotic genomic sequences. Our method is based on a generalized Hidden Markov Model with a new method for modeling the intron length distribution. This method allows approximation of the true intron length distribution m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh379
更新日期:2004-07-01 00:00:00
abstract::The activation of a telomere maintenance mechanism is required for cancer development in humans. While most tumors achieve this by expressing the enzyme telomerase, a fraction (5-15%) employs a recombination-based mechanism termed alternative lengthening of telomeres (ALT). Here we show that loss of the single-strande...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm738
更新日期:2007-01-01 00:00:00
abstract::The nucleotide sequences of the LTRs and their adjacent regions from 19 type C and one type B retrovirus were compared. Salient features are: (a) The R regions in the genomes of most of the type C retroviruses begin with GC and end with CA. (b) The mammalian type C retroviruses have a polyadenylation signal "AATAAA" i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.4.1767
更新日期:1984-02-24 00:00:00
abstract::The Cox protein from bacteriophage P2 forms oligomeric filaments and it has been proposed that DNA can be wound up around these filaments, similar to how histones condense DNA. We here use fluorescence microscopy to study single DNA-Cox complexes in nanofluidic channels and compare how the Cox homologs from phages P2 ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw352
更新日期:2016-09-06 00:00:00
abstract::A precursor of modified nucleoside Q isolated from E. coli methyl-deficient tRNA was determined to be 7-(aminomethyl)-7-deazaguanosine. The structure was deduced by means of its chromatographic and electrophoretic mobilities, and UV and mass spectra, in addition to comparison with the synthesized authentic compound. T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.7.2289
更新日期:1978-07-01 00:00:00
abstract::Multi-modal interactions are frequently observed in intrinsically disordered regions (IDRs) of proteins upon binding to their partners. In many cases, post-translational modifications in IDRs are accompanied by coupled folding and binding. From both molecular simulations and biochemical experiments with mutational stu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1297
更新日期:2018-03-16 00:00:00
abstract::Virulence factor database (VFDB) was set up in 2004 dedicated for providing current knowledge of virulence factors (VFs) from various medical significant bacterial pathogens to facilitate pathogenomic research. Nowadays, complete genome sequences of almost all the major pathogenic microbes have been determined, which ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm951
更新日期:2008-01-01 00:00:00
abstract::The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing infor...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl793
更新日期:2007-01-01 00:00:00
abstract::GAP-43 is a membrane phosphoprotein that is important for the development and plasticity of neural connections. In undifferentiated PC12 pheochromocytoma cells, GAP-43 mRNA degrades rapidly ( t = 5 h), but becomes stable when cells are treated with nerve growth factor. To identify trans- acting factors that may influe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.6.1281
更新日期:1997-03-15 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::A molecular rotor thioflavin T (ThT) is usually used as a fluorescent ligand specific for G-quadruplexes. Here, we demonstrate that ThT can tightly bind non-G-quadruplex DNAs with several GA motifs and dimerize them in a parallel double-stranded mode, accompanied by over 100-fold enhancement in the fluorescence emissi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx942
更新日期:2017-12-01 00:00:00
abstract::We report thermodynamic values for binding of the guanosine nucleophile to the ribozyme derived from the Anabaena group I intron, and find that they are similar to those measured previously for the structurally distinct Tetrahymena ribozyme. The free energy of binding guanosine 5'-monophosphate (pG) at 30 degrees C is...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.19.3722
更新日期:1996-10-01 00:00:00
abstract::A novel method combining elements of suppression subtractive hybridization with high throughput differential screening permits the efficient and rapid cloning of rarely transcribed differentially expressed genes. The experimental strategy virtually excludes the possibility of isolating false positive clones. The poten...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.13.2598
更新日期:1997-07-01 00:00:00
abstract::The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130,000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77,000 Thalassiosira pseudonana ESTs from seven libraries...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn905
更新日期:2009-01-01 00:00:00
abstract::A set of programs is presented for the reconstruction of a DNA sequence from data generated by the M13 shotgun sequencing technique. Once the sequence has been established and stored other programs are used for its analysis. The programs have been written for the Apple II microcomputer. A minimum investment is require...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.1.39
更新日期:1982-01-11 00:00:00
abstract::Treatment of the ciliated protozoan Tetrahymena thermophila with 8-methoxypsoralen combined with long wavelength ultraviolet irradiation (UVA, lambda approximately 360 nm) resulted in a dose dependent equal inhibition of the synthesis of rRNA, 5.8S, 5S and tRNA. Similar results were obtained with 3-carbethoxy-8-methox...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.3.921
更新日期:1987-02-11 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::Conserved in a variety of evolutionarily divergent plant species, LOB DOMAIN (LBD) genes define a large, plant-specific family of largely unknown function. LBD genes have been implicated in a variety of developmental processes in plants, although to date, relatively few members have been assigned functions. LBD protei...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm775
更新日期:2007-01-01 00:00:00
abstract::The Epstein-Barr virus gene BRLF1 encodes the transcription factor R, which is a sequence-specific DNA-binding protein important for the switch from latency to a productive cycle. We have defined a repertoire of specific R-binding sites using a GST-R fusion protein and a pool of 23 bp random DNA sequences. The R-bound...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.7.1172
更新日期:1994-04-11 00:00:00
abstract::The FSSP database presents a continuously updated classification of 3-D protein folds based on an all-against-all comparison of structures currently in the Protein Data Bank (PDB) [Bernstein et al. (1977) J. Mol. Biol., 112, 535- 542]. The database currently contains an extended structural family for each of 600 repre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.1.206
更新日期:1996-01-01 00:00:00
abstract::Extrachromosomal circular DNA (eccDNA) is both a driver of eukaryotic genome instability and a product of programmed genome rearrangements, but its extent had not been surveyed in Oxytricha, a ciliate with elaborate DNA elimination and translocation during development. Here, we captured rearrangement-specific circular...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz725
更新日期:2019-10-10 00:00:00
abstract::Escherichia coli mRNA translation is facilitated by sequences upstream and downstream of the initiation codon, called Shine-Dalgarno (SD) and downstream box (DB) sequences, respectively. In E.coli enhancing the complementarity between the DB sequences and the 16S rRNA penultimate stem resulted in increased protein acc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.4.970
更新日期:2001-02-15 00:00:00
abstract::The interpretation of data-driven experiments in genomics often involves a search for biological categories that are enriched for the responder genes identified by the experiments. However, knowledge bases such as the Gene Ontology (GO) contain hundreds or thousands of categories with very high overlap between categor...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq045
更新日期:2010-06-01 00:00:00
abstract::The chemical shifts of the well-resolved ring nitrogen protons of uracil and a series of substituted uracils, including pseudouridine (5-ribosyl-uracil) and uridine (1-ribosyl-uracil) were determined using nuclear magnetic resonance (NMR). The observed chemical shifts suggest the existence of an atypical syn conformat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.8.2747
更新日期:1977-08-01 00:00:00
abstract::The novel deoxyribonucleotide alpha-[d(CpCpTpTpCpC)] and its complement beta-[d(GpGpApApGpG)] were synthesized by the phosphotriester method. 1H-NMR-NOE examination of the alpha-hexamer revealed that the cytosine and thymine bases appear to adopt anti conformations in this strand. In addition the deoxyribose of the th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.12.5019
更新日期:1986-06-25 00:00:00
abstract::We have developed a comprehensive resource devoted to biologists wanting to optimize the use of gene trap clones in their experiments. We have processed 300 602 such clones from both public and private projects to generate 28,199 'UniTraps', i.e. distinct collections of unambiguous insertions at the same subgenic regi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm825
更新日期:2008-01-01 00:00:00