Abstract：
:Molecular beacons (MBs) have the potential to provide a powerful tool for rapid RNA detection in living cells, as well as monitoring the dynamics of RNA expression in response to external stimuli. To exploit this potential, it is necessary to distinguish true signal from background signal due to non-specific interactions. Here, we show that, when cyanine-dye labeled 2'-deoxy and 2'-O-methyl oligonucleotide probes are inside living cells for >5 h, most of their signals co-localize with mitochondrial staining. These probes include random-sequence MB, dye-labeled single-strand linear oligonucleotide and dye-labeled double-stranded oligonucleotide. Using carbonyl cyanide m-chlorophenyl hydrazone treatment, we found that the non-specific accumulation of oligonucleotide probes at mitochondria was driven by mitochondrial membrane potential. We further demonstrated that the dye-labeled oligonucleotide probes were likely on/near the surface of mitochondria but not inside mitochondrial inner membrane. Interestingly, oligonucleotides probes labeled respectively with Alexa Fluor 488 and Alexa Fluor 546 did not accumulate at mitochondria, suggesting that the non-specific interaction between dye-labeled ODN probes and mitochondria is dye-specific. These results may help design and optimize fluorescence imaging probes for long-time RNA detection and monitoring in living cells.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Rhee WJ,Bao Gdoi
10.1093/nar/gkq050subject
Has Abstractpub_date
2010-05-01 00:00:00pages
e109issue
9eissn
0305-1048issn
1362-4962pii
gkq050journal_volume
38pub_type
杂志文章abstract：:The PAH Mutation Analysis Consortium (81 investigators, 26 countries) is engaged in mutation detection at the human PAH locus. Ascertainment of probands occurs largely through newborn screening for hyperphenylalaninemia. A relational database records allelic variation (disease-producing and polymorphic) at the locus. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.1.127
更新日期：1996-01-01 00:00:00
abstract：:In order to systematically analyze the effects of nucleoside modification of sugar moieties in DNA polymerase reactions, we synthesized 16 modified templates containing 2',4'-bridged nucleotides and three types of 2',4'-bridged nucleoside-5'-triphospates with different bridging structures. Among the five types of ther...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn404
更新日期：2008-08-01 00:00:00
abstract：:The POU domain transcription factor, Oct-2, is essential for the B cell-specific expression of CD36 in mouse B cells. In order to determine how Oct-2 mediates expression of CD36 in B cells, we cloned and analysed the mouse CD36 promoter. In contrast to the human CD36 promoter, the mouse promoter contains a consensus o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.8.1767
更新日期：2002-04-15 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：:Vascular endothelial growth factor A (VEGF-A) is a master regulator of angiogenesis, vascular development and function. In this study we investigated the transcriptional regulation of VEGF-A-responsive genes in primary human aortic endothelial cells (HAECs) and human umbilical vein endothelial cells (HUVECs) using gen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1036
更新日期：2014-11-10 00:00:00
abstract：:HIV-1 Tat protein reprograms cellular gene expression of infected as well as uninfected cells apart from its primary function of transactivating HIV-1 long terminal repeat (LTR) promoter by binding to a nascent RNA stem-loop structure known as the transactivator response region (TAR). Tat also induces chromatin remode...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh289
更新日期：2004-02-23 00:00:00
abstract：:We have constructed deletion mutants of simian virus 40 (SV40) lacking the two tandemly repeated copies or all three copies of the 21-bp repeated sequence located in the origin region. The mutants were viable, but had lower infectivities compared to the wild type. The mutant lacking two copies of the 21-bp repeat grew...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.5.1601
更新日期：1983-03-11 00:00:00
abstract：:Four phage clones which hybridize with U1 small nuclear RNA were obtained from a rat gene library. Two clones contain a presumed pseudogene. A third clone includes two gene candidates that are co-linear with the rat U1-RNA, 3.6kb apart and in the opposite orientation. The two genes are surrounded by identical sequence...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.6.1791
更新日期：1983-03-25 00:00:00
abstract：:Human immunodeficiency virus type 2 (HIV-2) reverse transcription is initiated from cellular tRNA(Lys3) partially annealed to the RNA viral genome at the primer binding site (PBS). This annealing involves interactions between two highly structured RNA molecules. In contrast to HIV-1, in which the reverse transcription...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.13.2757
更新日期：2001-07-01 00:00:00
abstract：:The RSC complex of Saccharomyces cerevisiae is closely related to the SWI/SNF complex. Both complexes are involved in remodeling chromatin structure and they share conserved components. The RSC proteins Sth1, Rsc8/Swh3, Sfh1 and Rsc6 are homologs of the SWI/SNF proteins Swi2/Snf2, Swi3, Snf5 and Swp73 respectively. To...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.16.3739
更新日期：1998-08-15 00:00:00
abstract：:The effect of different levels of mercury substitution on the rate and extent of hybridisation of globin mRNA with a complementary DNA (cDNA) copy has been investigated. It was found that mercuration significantly reduces both the rate of hybridisation and the extent of the reaction, but that these effects are abolish...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/7.8.2357
更新日期：1979-12-20 00:00:00
abstract：:The excision of specific DNA sequences from integrated transgenes in insects permits the dissection in situ of structural elements that may be important in controlling gene expression. Furthermore, manipulation of potential control elements in the context of a single integration site mitigates against insertion site i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gng148
更新日期：2003-11-15 00:00:00
abstract：:Minichromosome maintenance (MCM) proteins facilitate replication by licensing origins and unwinding the DNA double strand. Interestingly, the number of MCM hexamers greatly exceeds the number of firing origins suggesting additional roles of MCMs. Here we show a hitherto unanticipated function of MCM2 in cilia formatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky945
更新日期：2019-01-10 00:00:00
abstract：:MicroRNAs (miRNA) are short single-stranded RNA molecules derived from hairpin-forming precursors that play a crucial role as post-transcriptional regulators in eukaryotes and viruses. In the past years, many microRNA target genes (MTGs) have been identified experimentally. However, because of the high costs of experi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1085
更新日期：2017-01-25 00:00:00
abstract：:The first step in DNA cleavage at V(D)J recombination signals by RAG1 and RAG2 is creation of a nick at the heptamer/coding flank border. Under proper conditions in vitro the second step, hairpin formation, requires two signals with spacers of 12 and 23 bp, a restriction referred to as the 12/23 rule. Under these cond...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.21.4370
更新日期：1997-11-01 00:00:00
abstract：:For the analysis of protein-DNA interactions by coupled gel-shift/footprinting, DNA fragments need to be extracted from polyacrylamide gels and subsequently separated on high resolution gels. Due to impurities in the extracted DNA, single nucleotide resolution is frequently not achieved. We now describe an improved ex...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.2.453
更新日期：1997-01-15 00:00:00
abstract：:Adaptation to the host cell environment to efficiently take-over the host cell's machinery is crucial in particular for small RNA viruses like picornaviruses that come with only small RNA genomes and replicate exclusively in the cytosol. Their Internal Ribosome Entry Site (IRES) elements are specific RNA structures th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks182
更新日期：2012-07-01 00:00:00
abstract：:Algae are a diverse, polyphyletic group of photosynthetic eukaryotes spanning nearly all eukaryotic lineages of life and collectively responsible for ∼50% of photosynthesis on Earth. Sequenced algal genomes, critical to understanding their complex biology, are growing in number and require efficient tools for analysis...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa898
更新日期：2021-01-08 00:00:00
abstract：:We present the LGA (Local-Global Alignment) method, designed to facilitate the comparison of protein structures or fragments of protein structures in sequence dependent and sequence independent modes. The LGA structure alignment program is available as an online service at http://PredictionCenter.llnl.gov/local/lga. D...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg571
更新日期：2003-07-01 00:00:00
abstract：:Specific DNA restriction endonuclease fragments can be identified after electrophoresis in agarose gels by hybridization in the gel (in situ) to radioactive homologous RNA. RNA-DNA hybrids are detected by autoradiography of the gel. Comparison of band patterns of the autoradiogram and the ethidium bromide stained gel ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.10.1911
更新日期：1975-10-01 00:00:00
abstract：:The small nucleolar RNA U3 is essential for viability in yeast. We have previously shown that U3 can be cross-linked in vivo to the pre-rRNA in the 5' external transcribed spacer (ETS), at +470. This ETS region contains 10 nucleotides of perfect complementarity to U3. In a genetic background where the mutated rDNA is ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.20.4057
更新日期：1994-10-11 00:00:00
abstract：:Two triple helix structures (15-mers containing only T.A-T triplets or containing mixed T.A-T and C.G-C triplets) have been studied by uranyl mediated DNA photocleavage to probe the accessibility of the phosphates of the DNA backbone. Whereas the phosphates of the pyrimidine strand are at least as accessible as in dou...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.11.2735
更新日期：1992-06-11 00:00:00
abstract：:DNA strand exchange, the central step of homologous recombination, is considered to occur approximately independently of DNA sequence content. However, certain prokaryotic and eukaryotic genomic loci display either an enhanced or reduced frequency of genetic exchange. Here we show that the Homo sapiens DNA strand exch...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl355
更新日期：2006-05-24 00:00:00
abstract：:A specific segment of mitochondrial DNA from 18 people was examined by two methods of direct DNA sequencing. This segment includes a small noncoding region (V) shown before by restriction analysis to exhibit length polymorphism. All 11 of the human mtDNAs previously reported to have a deletion in this region proved to...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.2.529
更新日期：1987-01-26 00:00:00
abstract：:Intestinal apolipoprotein B mRNA is edited at nucleotide 6666 by a C to U transition resulting in a translational stop codon. The enzymatic properties of the editing activity were characterised in vitro using rat enterocyte cytosolic extract. The editing activity has no nucleotide or ion cofactor requirement. It shows...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.13.3569
更新日期：1991-07-11 00:00:00
abstract：:The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz943
更新日期：2020-01-08 00:00:00
abstract：:The principal early promoter of human papillomaviruses (HPVs), designated P97 in the case of HPV-16, contains four characteristically aligned cis-responsive elements, namely one binding site for Sp1, two for the viral E2 proteins, and the TATA box. The Sp1 binding site is needed to mediate activation of P97 by the rem...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.2.251
更新日期：1992-01-25 00:00:00
abstract：:Ribosomes transit between two conformational states, non-rotated and rotated, through the elongation cycle. Here, we present evidence that an internal loop in the essential yeast ribosomal protein rpL10 is a central controller of this process. Mutations in this loop promote opposing effects on the natural equilibrium ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1107
更新日期：2014-02-01 00:00:00
abstract：:Advancement in the field of computational research has made it possible for the in silico methods to offer significant benefits to both regulatory needs and requirements for risk assessments, and pharmaceutical industry to assess the safety profile of a chemical. Here, we present ProTox-II that incorporates molecular ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky318
更新日期：2018-07-02 00:00:00
abstract：:Cells continuously monitor protein synthesis to prevent accumulation of aberrant polypeptides. Insufficient capacity of cellular degradative systems, chaperone shortage or high levels of mistranslation by ribosomes can result in proteotoxic stress and endanger proteostasis. One of the least explored reasons for mistra...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa068
更新日期：2020-04-17 00:00:00
