Abstract:
:The photostability and narrow emission spectra of non-organic quantum dot fluorophores (QDs) make them desirable candidates for fluorescent in situ hybridization (FISH) to study the expression of specific mRNA transcripts. We developed a novel method for direct QD labeling of modified oligonucleotide probes through streptavidin and biotin interactions, as well as protocols for their use in multiple-label FISH. We validated this technique in mouse brainstem sections. The subcellular localization of the vesicular monoamine transporter (Vmat2) mRNA corresponds when using probes labeled with two different QDs in the same hybridization. We developed protocols for combined direct QD FISH and QD immunohistochemical labeling within the same neurons as well as for simultaneous study of the subcellular distribution of multiple mRNA targets. We demonstrated increased sensitivity of FISH using QDs in comparison with organic fluorophores. These techniques gave excellent histological results both for multiplex FISH and combined FISH and immunohistochemistry. This approach can facilitate the ultrasensitive simultaneous study of multiple mRNA and protein markers in tissue culture and histological section.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Chan P,Yuen T,Ruf F,Gonzalez-Maeso J,Sealfon SCdoi
10.1093/nar/gni162keywords:
subject
Has Abstractpub_date
2005-10-13 00:00:00pages
e161issue
18eissn
0305-1048issn
1362-4962pii
33/18/e161journal_volume
33pub_type
杂志文章abstract::Impaired DNA damage repair, especially deficient transcription-coupled nucleotide excision repair, leads to segmental progeroid syndromes in human patients as well as in rodent models. Furthermore, DNA double-strand break signalling has been pinpointed as a key inducer of cellular senescence. Several recent findings s...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkm1065
更新日期:2007-01-01 00:00:00
abstract::Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and ecosystem health. To combat infection greater comparative knowledge is required on the pathogenic process in multiple species. The Pathogen-Host Interactions database (PHI-bas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1165
更新日期:2015-01-01 00:00:00
abstract::Orthology is a widely used concept in comparative and evolutionary genomics. In addition to prokaryotic orthology, delineating eukaryotic orthology has provided insight into the evolution of higher organisms. Indeed, many eukaryotic ortholog databases have been established for this purpose. However, unlike prokaryotes...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn227
更新日期:2008-06-01 00:00:00
abstract::Two new crescent-shaped unsymmetrical cyanine dyes have been synthesised and their interactions with DNA have been investigated by different spectroscopic methods. These dyes are analogues to a minor groove binding unsymmetrical cyanine dye, BEBO, recently reported by us. In this dye, the structure of the known interc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg821
更新日期:2003-11-01 00:00:00
abstract::A new series of DNA bis-intercalators is reported in which acridine moieties are connected by rigid and extended pyridine-based linkers of varied length. Cross-linking of DNA by bis-intercalation is inferred from the unwinding and folding of linear DNA induced by the compounds; after ligation and removal of the bis-in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.5.983
更新日期:1992-03-11 00:00:00
abstract::We identify a new subgroup of Type I Restriction-Modification enzymes that modify cytosine in one DNA strand and adenine in the opposite strand for host protection. Recognition specificity has been determined for ten systems using SMRT sequencing and each recognizes a novel DNA sequence motif. Previously characterized...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw743
更新日期:2016-11-02 00:00:00
abstract::Repression of cellular reprogramming in germ cells is critical to maintaining cell fate and fertility. When germ cells mis-express somatic genes they can be directly converted into other cell types, resulting in loss of totipotency and reproductive potential. Identifying the molecular mechanisms that coordinate these ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa174
更新日期:2020-05-07 00:00:00
abstract::This work presents the Apo-Holo DataBase (AH-DB, http://ahdb.ee.ncku.edu.tw/ and http://ahdb.csbb.ntu.edu.tw/), which provides corresponding pairs of protein structures before and after binding. Conformational transitions are commonly observed in various protein interactions that are involved in important biological f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr940
更新日期:2012-01-01 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::The complete nucleotide sequences of the various precursor 5S RNA species occurring in Bacillus licheniformis have been elucidated. The B. licheniformis precursors contain a 5'-precursor-specific segment of 95 nucleotides which is four times as long as the corresponding segment of the p5S RNAs from the closely related...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.19.4535
更新日期:1980-10-10 00:00:00
abstract::We have reported on the differences in site-specific cleavage between DNA and DNA-RNA hybrids by various prototypic DNA cleavers (accompanying paper). In the case of bleomycin (BLM), degradation at 5'-GC-3'sites was suppressed relative to the same sequence in double-stranded DNA, while 5'-GT-3' damage remained constan...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.9.1846
更新日期:1997-05-01 00:00:00
abstract::Previous studies have implicated the DE-1 (-111/-106) and alpha A-CRYBP1 (-66/-57) sites for activity of the mouse alpha A-crystallin promoter in transiently transfected lens cells. Here we have used the bacterial chloramphenicol acetyltransferase (CAT) reporter gene to test the functional importance of the putative D...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.11.2633
更新日期:1993-06-11 00:00:00
abstract::Allostery is comprehensively studied for natural macromolecules, such as proteins and nucleic acids. Here, we present controllable allostery of synthetic DNA nanostructure-enzyme systems. Rational designs of the synthetic allosteric systems are based on an in-depth understanding of allosteric sites with several types ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa488
更新日期:2020-07-27 00:00:00
abstract::To elucidate the response to oxidative stress in eukaryotic cells, the effect of an oxidized nucleotide, 8-oxo-2'-deoxyguanosine 5'-triphosphate (8-oxo-dGTP), generated from dGTP with an active oxygen, on DNA synthesis was studied using a cell-free DNA replication system derived from Xenopus egg lysates with a single-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.2.569
更新日期:2002-01-15 00:00:00
abstract::Substantial amounts of DNA (at least 25 microgram per cm2) can be stably bound to diazobenzyloxymethyl (DBM)-paper. Complementary RNA will hybridize to the DNA paper almost completely in 24 hours. Using several different conditions of hybridization and washing, the background of RNA bound non-specifically is very low ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.1.195
更新日期:1979-01-01 00:00:00
abstract::Transcription initiation complexes formed by bacterial RNA polymerases (RNAPs) exhibit dramatic species-specific differences in stability, leading to different strategies of transcription regulation. The molecular basis for this diversity is unclear. Promoter complexes formed by RNAP from Thermus aquaticus (Taq) are c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks973
更新日期:2012-12-01 00:00:00
abstract::PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface. Points...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz424
更新日期:2019-07-02 00:00:00
abstract::Cellular liquid-liquid phase separation (LLPS) results in the formation of dynamic granules that play an important role in many biological processes. On a molecular level, the clustering of proteins into a confined space results from an indefinite network of intermolecular interactions. Here, we introduce and exploit ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx353
更新日期:2017-06-20 00:00:00
abstract::The nucleotide excision repair pathway removes ultraviolet (UV) photoproducts from the human genome in the form of short oligonucleotides ∼ 30 nt in length. Because there are limitations to many of the currently available methods for investigating UV photoproduct repair in vivo, we developed a convenient non-radioisot...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1179
更新日期:2014-02-01 00:00:00
abstract::We have isolated and sequenced the complete murine I-E alpha immune response gene of the H-2db haplotype. The I-E alpha d gene consists of 5300 basepairs and is organized into five or possibly six exons that correspond to different domains of the alpha chain. The amino acid sequence deduced from the I-E alpha gene sho...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.15.5055
更新日期:1983-08-11 00:00:00
abstract::Poly 2'0-ethylcytidylic acid (poly (Ce)) was prepared by polymerization of 2'-0-ethylcytidine-5'-pyrophosphate with Escherichia coli polynucleotide phosphorylase in the presence of Mn++, and its properties compared with those of poly (rC), poly (Cm) and poly (dC). The neutral form of pOLY (Ce) exhibits properties simi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.3.817
更新日期:1976-03-01 00:00:00
abstract::As shown in the accompanying paper (5), the oligonucleotide composition of the E. coli genome is highly asymmetric for sequences up to 6 bp in length when ranked from highest to lowest abundance. We show here that this largely reflects codon usage because heavily used codons were found in the highly abundant oligomers...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.6.2627
更新日期:1987-03-25 00:00:00
abstract::Essential genes are genes that are indispensable to support cellular life. These genes constitute a minimal gene set required for a living cell. We have constructed a Database of Essential Genes (DEG), which contains all the essential genes that are currently available. The functions encoded by essential genes are con...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh024
更新日期:2004-01-01 00:00:00
abstract::Synchronous plasmodia of cycloheximide-sensitive and cycloheximide-resistant strains of Physarum polycephalum were labelled with 3[H]-deoxyadenosine in pulse and pulse-chase experiments in presence and absence of cycloheximide. The replication products were studied with alkaline sucrose gradient sedimentation analysis...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.2.405
更新日期:1977-02-01 00:00:00
abstract::Transcription of tRNA-encoding genes by RNA polymerase (Pol) III requires the six-subunit general transcription factor IIIC that uses subcomplexes τA and τB to recognize two gene-internal promoter elements named A- and B-box. The Schizosaccharomyces pombe τA subcomplex comprises subunits Sfc1, Sfc4 and Sfc7. The cryst...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt664
更新日期:2013-10-01 00:00:00
abstract::Robust estimation of allele frequencies in pools of DNA has the potential to reduce genotyping costs and/or increase the number of individuals contributing to a study where hundreds of thousands of genetic markers need to be genotyped in very large populations sample sets, such as genome wide association studies. In o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni142
更新日期:2005-09-30 00:00:00
abstract::This paper presents TurboFold II, an extension of the TurboFold algorithm for predicting secondary structures for multiple RNA homologs. TurboFold II augments the structure prediction capabilities of TurboFold by additionally providing multiple sequence alignments. Probabilities for alignment of nucleotide positions b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx815
更新日期:2017-11-16 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::The pattern of sites for cleavage mediated by topoisomerase II was determined in 830 kb of cloned DNA from the Drosophila X chromosome, with the objectives of comparing it with mapped structural and functional landmarks and examining if the correlations with such landmarks reported in individual loci can be generalize...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.11.2041
更新日期:1997-06-01 00:00:00
abstract::Various environmental oxidative stresses are sensed by redox-sensitive regulators through cysteine thiol oxidation or modification. A few zinc-containing anti-sigma (ZAS) factors in actinomycetes have been reported to respond sensitively to thiol oxidation, among which RsrA from Streptomyces coelicolor is best charact...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr477
更新日期:2011-09-01 00:00:00