Abstract：
:Direct labeling of RNA is an expedient method for labeling large quantities (e.g. micrograms) of target RNA for microarray analysis. We have developed an efficient labeling system that uses T4 RNA ligase to attach a 3'-biotinylated donor molecule to target RNA. Microarray analyses indicate that directly labeled RNA is uniformly labeled, has higher signal intensity than comparable labeling methods and achieves high transcript detection sensitivity. The labeled donor molecule we have developed allows the attachment of multiple biotins, which increases target signal intensity up to 30%. We have used this direct-labeling method to detect previously discovered class predictor genes for two types of cancer: acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). In order to test the sensitivity of direct RNA labeling, we analyzed the AML and ALL expression profiles for predictor genes that were previously found to show elevated expression in the disease state. Direct labeling of AML poly(A) RNA detects 90% of the class predictor genes that are detected by the IVT-based target amplification method used to discover the genes. These results indicate that the detection sensitivity, simplicity (single tube reaction) and speed (2 h) of this direct labeling protocol may be ideal for diagnostic applications that do not require target amplification.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Cole K,Truong V,Barone D,McGall Gdoi
10.1093/nar/gnh085keywords:
subject
Has Abstractpub_date
2004-06-17 00:00:00pages
e86issue
11eissn
0305-1048issn
1362-4962pii
32/11/e86journal_volume
32pub_type
杂志文章abstract：:Isolated yeast mitochondria incorporate added UTP into RNA. Amongst the products formed are the two rRNAs, 4S RNA and several components presumed to be mRNAs. In omega+ strains (containing an intervening sequence in the 21S rRNA gene) besides mature 21S rRNA a transcript could be detected still containing nucleotide s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.23.6369
更新日期：1981-12-11 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：:DNA from healthy Malaysian newborns was studied on gene maps after digestion with different restriction endonucleases. Of 65 newborns, two were found to be carriers of two different variants of triplicated alpha-globin loci. In variant no. 1, found in an Malay, the three alpha-globin genes are in an elongated DNA frag...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.15.3707
更新日期：1981-08-11 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：:We describe an interactive computer program (ANALYSEQ) that is used from a simple graphics terminal. The main purpose of the program is to determine the function of nucleic acid sequences but it also offers the simpler listing, searching and counting options. It contains methods to locate genes by looking for the effe...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.1part2.521
更新日期：1984-01-11 00:00:00
abstract：:DXZ4 is an X-linked macrosatellite composed of 12-100 tandemly arranged 3-kb repeat units. In females, it adopts opposite chromatin arrangements at the two alleles in response to X-chromosome inactivation. In males and on the active X chromosome, it is packaged into heterochromatin, but on the inactive X chromosome (X...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr964
更新日期：2012-02-01 00:00:00
abstract：:DNA-PKcs and Ku are essential components of the complex that catalyzes non-homologous end joining (NHEJ) of DNA double-strand breaks (DSBs). Ku, a heterodimeric protein, binds to DNA ends and facilitates recruitment of the catalytic subunit, DNA-PKcs. We have investigated the effect of DNA strand orientation and seque...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki157
更新日期：2005-01-07 00:00:00
abstract：:The nucleotide sequence of the Anacystis nidulans 23S rRNA gene, including the 5'- and 3'-flanking regions has been determined. The gene is 2876 nucleotides long and shows higher primary sequence homology to the 23S rRNAs of plastids (84.5%) than to that of E. coli (79%). The predicted rRNA transcript also shares many...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.7.3373
更新日期：1984-04-11 00:00:00
abstract：:Mouse DNA contains two equally abundant, homologous subfamilies of MspI 3.6 and 5 kb repeated fragments. The first subfamily corresponds to the previously described (1) Bam 4 kb repeats, the second one to Bam repeated fragments of higher molecular weight. These subfamilies account for the vast majority of long Bam rep...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.3.1593
更新日期：1984-02-10 00:00:00
abstract：:Transcriptional regulatory networks specify regulatory proteins controlling the context-specific expression levels of genes. Inference of genome-wide regulatory networks is central to understanding gene regulation, but remains an open challenge. Expression-based network inference is among the most popular methods to i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw963
更新日期：2017-02-28 00:00:00
abstract：:Mouse embryo fibroblasts (MEFs) are convenient sources for biochemical studies when cell number in mouse embryos is limiting. To derive the imprinting signature of MEFs and potentially detect novel imprinted genes we performed strand- and allele-specific RNA deep sequencing. We used sequenom allelotyping in embryo and...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1042
更新日期：2014-02-01 00:00:00
abstract：:After ionising radiation double-strand breaks (dsb) are lethal if not repaired or misrepaired. Cell killing is greatly enhanced by hyperthermia and it is questioned here whether heat not only affects dsb repair capacity but also fidelity in a chromosomal context. dsb repair experiments were designed so as to mainly sc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.9.1960
更新日期：2001-05-01 00:00:00
abstract：:Nematode.net (http://nematode.net) is a publicly available resource dedicated to the study of parasitic nematodes. In 2000, the Genome Center at Washington University (GC) joined a consortium including the Nematode Genomics group in Edinburgh, and the Pathogen Sequencing Unit of the Sanger Institute to generate expres...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn744
更新日期：2009-01-01 00:00:00
abstract：:DNA labeled for 15 minutes during UV induced repair synthesis is two-fold more sensitive to micrococcal nuclease than the bulk nuclear DNA. As the length of the labeling period increases from 15 minutes to 4 hours the nuclease sensitivity of repair labeled DNA approaches that of bulk chromatin. Pulse-chase experiments...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.1.203
更新日期：1981-01-10 00:00:00
abstract：:DNA synthesized by in vitro transcription on rat interferon (IFN) mRNA has been cloned and amplified as recombinant DNA. The nucleotide sequence of these rat IFN cDNA clones revealed i. the partial presence of the coding region of the gene and ii all cDNA clones were derived from the same subtype of rat IFN-alpha mRNA...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.2.1227
更新日期：1984-01-25 00:00:00
abstract：:In the brome mosaic virus (BMV) virion, the coat protein (CP) selectively contacts the RNA motifs that regulate translation and RNA replication (Hoover et al., 2016. J. Virol. 90, 7748). We hypothesize that the unstructured N-terminal arm (NTA) of the BMV CP can specifically recognize RNA motifs. Using ion mobility sp...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1087
更新日期：2018-01-09 00:00:00
abstract：:During DNA replication, the presence of 8-oxoguanine (8-oxoG) lesions in the template strand cause the high-fidelity (HiFi) DNA polymerase (Pol) to stall. An early response to 8-oxoG lesions involves 'on-the-fly' translesion synthesis (TLS), in which a specialized TLS Pol is recruited and replaces the stalled HiFi Pol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa803
更新日期：2020-11-04 00:00:00
abstract：:We have used temperature gradient gel electrophoresis (TGGE) to measure the progress of local denaturation in closed circular topoisomer DNA as a function of temperature and superhelicity (sigma). We describe the versatility of this method as a tool for detecting various conformational modifications of plasmid DNAs. T...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.11.e51
更新日期：2000-06-01 00:00:00
abstract：:DNA was purified from double minutes isolated from MTX-resistant EL4/8 mouse lymphoma cells, digested to completion with Bam H1 restriction endonuclease and cloned in lambda-1059. The properties of the library suggest that the DNA from which it was made was not detectably contaminated with non-dm chromosome material, ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.21.6597
更新日期：1982-11-11 00:00:00
abstract：:The design of a family shuffling strategy (CLERY: Combinatorial Libraries Enhanced by Recombination in Yeast) associating PCR-based and in vivo recombination and expression in yeast is described. This strategy was tested using human cytochrome P450 CYP1A1 and CYP1A2 as templates, which share 74% nucleotide sequence id...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.20.e88
更新日期：2000-10-15 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：:Expression of the wild-type p53 tumor suppressor gene has been found to play an important role in the regulation of cellular proliferation and differentiation. In addition, in many transformed cells and primary tumors, the gene has undergone allelic deletions and mutant forms of the p53 gene are expressed at elevated ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.2.345
更新日期：1993-01-25 00:00:00
abstract：:The modulation of GLI2, an oncogenic transcription factor commonly upregulated in cancer, is in many cases not due to genetic defects, suggesting dysregulation through alternative mechanisms. The identity of these molecular events remains for the most part unknown. Here, we identified TFII-I as a novel repressor of GL...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa476
更新日期：2020-07-27 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：:Three peaks of methyltransferase activity specific for MNNG alkylated DNA have been identified from extracts of chemically adapted M. luteus. They are designated as TI to TIII in order to their elution from a Sephadex G-75 column. The first one of these peaks has been purified to homogeneity. TI, is an inducible, unus...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.22.9471
更新日期：1987-11-25 00:00:00
abstract：:A key complication in comparative genomics for reliable gene function prediction is the existence of duplicated genes. To study the effect of gene duplication on function prediction, we analyze orthologs between pairs of genomes where in one genome the orthologous gene has duplicated after the speciation of the two ge...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki913
更新日期：2005-10-27 00:00:00
abstract：:Pentatricopeptide repeat (PPR) proteins are helical-repeat proteins that offer a promising scaffold for the engineering of proteins to bind specified RNAs. PPR tracts bind RNA in a modular 1-repeat, 1-nucleotide fashion. An amino acid code specifying the bound nucleotide has been elucidated. However, this code does no...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1288
更新日期：2018-03-16 00:00:00
abstract：:In order to study the effects of DNA structure on cellular processes such as transcription, we have made a series of plasmids that locate several different kinds of DNA structure (stiff, flexible or curved) near the sites of cleavage by commonly-used restriction enzymes. One can use these plasmids to place any DNA reg...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.22.9447
更新日期：1989-11-25 00:00:00
abstract：:Comparisons of proteins show that they evolve through the movement of domains. However, in many cases, the underlying mechanisms remain unclear. Here, we observed the movements of DNA recognition domains between non-orthologous proteins within a prokaryote genome. Restriction-modification (RM) systems, consisting of a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks681
更新日期：2012-10-01 00:00:00
abstract：:A cDNA that encodes a transcription factor able to recognize the thyroglobulin gene promoter in vitro was isolated from a dog thyroid cDNA expression library in lambda gt11. The library was screened with a multimerized 20 bp-oligonucleotide probe corresponding to the -126 to -107 bp region of the bovine thyroglobulin ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.5.1121
更新日期：1991-03-11 00:00:00
