Abstract：
:The availability of protein fluorophores with appropriate spectral properties has made it possible to employ fluorescence resonance energy transfer (FRET) to assess interactions between three proteins microscopically. Flow cytometry offers excellent sensitivity, effective signal separation and the capacity to assess a large number of events, and, therefore, should be an ideal means to explore protein interactions in living cells. Here, we report a flow-cytometric FRET technique that employed both direct energy transfer from CFP-->YFP-->mRFP and donor quenching to assess TRAF2 trimerization in living cells. Initially, a series of fusion proteins incorporating CFP, YFP and mRFP with spacers that did or did not permit FRET were employed to document the magnitude of CFP-->YFP and YFP-->mRFP FRET and to calculate the efficiency of CFP-->YFP-->mRFP two-step FRET. Based upon this, TRAF2 homotrimerization could be detected. This method should have great utility in studying the dynamics of interactions between three specific proteins in vivo.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
He L,Wu X,Simone J,Hewgill D,Lipsky PEdoi
10.1093/nar/gni057keywords:
subject
Has Abstractpub_date
2005-04-01 00:00:00pages
e61issue
6eissn
0305-1048issn
1362-4962pii
33/6/e61journal_volume
33pub_type
杂志文章abstract：:The sequences coding for DNA[cytosine-N4]methyltransferases MvaI (from Micrococcus varians RFL19) and Cfr9I (from Citrobacter freundii RFL9) have been determined. The predicted methylases are proteins of 454 and 300 amino acids, respectively. Primary structure comparison of M.Cfr9I and another m4C-forming methylase, M...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.23.9823
更新日期：1989-12-11 00:00:00
abstract：:Upon activation of the ERK and p38 MAPK pathways, the MSK1/2-mediated nucleosomal response, including H3 phosphorylation at serine 28 or 10, is coupled with the induction of immediate-early (IE) gene transcription. The outcome of this response, varying with the stimuli and cellular contexts, ranges from neoplastic tra...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq030
更新日期：2010-06-01 00:00:00
abstract：:Topoisomerases catalyse changes in the topological state of DNA and are required for many aspects of DNA metabolism. While the functions of topoisomerases I and II in eukaryotes are well established, the role of topoisomerase III remains poorly defined. We have identified a gene in the fission yeast Schizosaccharomyce...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.20.4050
更新日期：1999-10-15 00:00:00
abstract：:To confirm the activity of an initial small molecule 'hit compound' from an activity screening, one needs to probe the structure-activity relationships by testing close analogs. The multi-fingerprint browser presented here (http://dcb-reymond23.unibe.ch:8080/MCSS/) enables one to rapidly identify such close analogs am...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku379
更新日期：2014-07-01 00:00:00
abstract：:The sigma(54) factor associates with core RNA polymerase (RNAP) to form a holoenzyme that is unable to initiate transcription unless acted on by an activator protein. sigma(54) is closely involved in many steps of activator-dependent transcription, such as core RNAP binding, promoter recognition, activator interaction...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp419
更新日期：2009-07-01 00:00:00
abstract：:During the last years, the demand for custom-made cDNA chips/arrays as well as whole genome chips is increasing rapidly. The efficient selection of gene-specific primers/oligomers is of the utmost importance for the successful production of such chips. We developed GenomePRIDE, a highly flexible and scalable software ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg752
更新日期：2003-10-01 00:00:00
abstract：:Active DNA demethylation is crucial for epigenetic control, but the underlying enzymatic mechanisms are incompletely understood. REPRESSOR OF SILENCING 1 (ROS1) is a 5-methylcytosine (5-meC) DNA glycosylase/lyase that initiates DNA demethylation in plants through a base excision repair process. The enzyme binds DNA no...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt625
更新日期：2013-10-01 00:00:00
abstract：:PomBase (http://www.pombase.org) is the model organism database for the fission yeast Schizosaccharomyces pombe. PomBase provides a central hub for the fission yeast community, supporting both exploratory and hypothesis-driven research. It provides users easy access to data ranging from the sequence level, to molecula...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1040
更新日期：2015-01-01 00:00:00
abstract：:The lytic-lysogenic decision in bacteriophage 186 is governed by the 186 CI repressor protein in a unique way. The 186 CI is proposed to form a wheel-like oligomer that can mediate either wrapped or looped nucleoprotein complexes to provide the cooperative and competitive interactions needed for regulation. Although c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt298
更新日期：2013-06-01 00:00:00
abstract：:We have studied the role of the C-terminal domain of the alpha subunit (alphaCTD) of Escherichia coli RNA polymerase during transcription initiation at promoters lacking an UP-element. The temperature requirement for open complex formation was used as an indication of the kinetics of this process. We have previously s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.9.2051
更新日期：1999-05-01 00:00:00
abstract：:Chromosome stability is primarily determined by telomere length. TRF1 is the core subunit of shelterin that plays a critical role in telomere organization and replication. However, the dynamics of TRF1 in scenarios of telomere-processing activities remain elusive. Using single-molecule magnetic tweezers, we here inves...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1222
更新日期：2021-01-25 00:00:00
abstract：:MicroRNAs (miRNAs) are small RNAs ∼22 nt in length that are involved in the regulation of a variety of physiological and pathological processes. Advances in high-throughput small RNA sequencing (smRNA-seq), one of the next-generation sequencing applications, have reshaped the miRNA research landscape. In this study, w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1238
更新日期：2013-01-01 00:00:00
abstract：:The 5' portions and flanking sequences of genes encoding types 1, 12, 24, and 6 M proteins were compared. Although the DNA sequences encoding the amino-termini of the mature M proteins had no obvious similarity, upstream sequences, and those encoding the signal peptides (leader sequences) of the four M protein genes h...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.10.4667
更新日期：1988-05-25 00:00:00
abstract：:A common goal in the discovery of rare functional DNA variants via medical resequencing is to incur a relatively lower proportion of false positive base-calls. We developed a novel statistical method for resequencing arrays (SRMA, sequence robust multi-array analysis) to increase the accuracy of detecting rare variant...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq750
更新日期：2011-01-01 00:00:00
abstract：:Lens epithelium-derived growth factor/p75 (LEDGF/p75) is a transcriptional coactivator involved in stress response, autoimmune disease, cancer and HIV replication. A fusion between the nuclear pore protein NUP98 and LEDGF/p75 has been found in human acute and chronic myeloid leukemia and association of LEDGF/p75 with ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq410
更新日期：2010-10-01 00:00:00
abstract：:Measuring minimal residual disease in cancer has applications for prognosis, monitoring treatment and detection of recurrence. Simple sequence-based methods to detect nucleotide substitution variants have error rates (about 10-3) that limit sensitive detection. We developed and characterized the performance of MASQ (m...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa090
更新日期：2020-04-17 00:00:00
abstract：:Plant orthologs of the yeast sucrose non-fermenting (Snf1) kinase and mammalian AMP-activated protein kinase (AMPK) represent an emerging class of important regulators of metabolic and stress signalling. The catalytic alpha-subunits of plant Snf1-related kinases (SnRKs) interact in the yeast two-hybrid system with dif...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.17.3685
更新日期：2001-09-01 00:00:00
abstract：:A total of 10 B-lymphocyte-specific DNase I hypersensitive sites located in the chicken Ig-beta locus were divided into four regions and combinations of deletions of these regions were carried out. A decrease in transcription of the Ig-beta gene to <3% was demonstrated in cells with deletions in all four regions. The ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl469
更新日期：2006-08-11 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：:Multicellular organismal development is controlled by a complex network of transcription factors, promoters and enhancers. Although reliable computational and experimental methods exist for enhancer detection, prediction of their target genes remains a major challenge. On the basis of available literature and ChIP-seq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1081
更新日期：2011-04-01 00:00:00
abstract：:Resolvase enzymes that cleave DNA four-way (Holliday) junctions are required for poxvirus replication, but clinically useful inhibitors have not been developed. Here, we report an assay for resolvase cleavage activity based on fluorescence polarization (FP) for high-throughput screening and mechanistic studies. Initia...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks325
更新日期：2012-09-01 00:00:00
abstract：:The multifunctional RNA-dependent RNA polymerase L protein of vesicular stomatitis virus catalyzes unconventional pre-mRNA capping via the covalent enzyme-pRNA intermediate formation, which requires the histidine-arginine (HR) motif in the polyribonucleotidyltransferase domain. Here, the effects of cap-defective mutat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku901
更新日期：2014-10-29 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：:Genotoxic stress induces alternative splicing of the oncogene MDM2 generating MDM2-ALT1, an isoform attributed with tumorigenic properties. However, the mechanisms underlying this event remain unclear. Here we explore MDM2 splicing regulation by utilizing a novel minigene that mimics endogenous MDM2 splicing in respon...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv223
更新日期：2015-04-30 00:00:00
abstract：:Dramatic improvements in ribozyme mimics have been achieved by employing the principles of small molecule catalysis to the design of macromolecular, biomimetic reagents. Ribozyme mimics derived from the ligand 2,9-dimethylphenanthroline (neocuproine) show at least 30-fold improvements in efficiency at sequence-specifi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.10.2199
更新日期：2001-05-15 00:00:00
abstract：:The frequencies of each of the 257 468 complete protein coding sequences (CDSs) have been compiled from the taxonomical divisions of the GenBank DNA sequence database. The sum of the codons used by 8792 organisms has also been calculated. The data files can be obtained from the anonymous ftp sites of DDBJ, Kazusa and ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.1.292
更新日期：2000-01-01 00:00:00
abstract：:In highly oncogenic adenovirus (Ad) 12-transformed cells, major histocompatibility complex (MHC) class I gene expression is down-regulated by the products of the viral E1A oncogene at the level of initiation of transcription. However, class I gene expression is unaltered or elevated in non-oncogenic Ad2- or Ad5-transf...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.22.4779
更新日期：1994-11-11 00:00:00
abstract：:The sxy (tfoX) gene product is the central regulator of DNA uptake by naturally competent gamma-proteobacteria such as Haemophilus influenzae, Vibrio cholerae and probably Escherichia coli. However, the mechanisms regulating sxy gene expression are not understood despite being key to understanding the physiological ro...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm915
更新日期：2008-01-01 00:00:00
abstract：:The DNA topoisomerase from Agrobacterium tumefaciens has been purified to apparent homogeneity. The enzyme is a single polypeptide of about 100,000 in molecular weight. No apparent separation of the nicking and sealing activities could be obtained in attempts to separate the two activities by a variety of methods, inc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.4.909
更新日期：1981-02-25 00:00:00
abstract：:Human immunodeficiency virus-1 (HIV-1) leader RNA, which contains double-stranded regions due to inverted repeats, was shown to activate the dsRNA-dependent enzymes associated with the interferon system. HIV-1 leader RNA produced in vitro using SP6 RNA polymerase was characterized using probes for antisense and sense-...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.3.969
更新日期：1989-02-11 00:00:00
