Cassette labeling for facile construction of energy transfer fluorescent primers.

Abstract:

:DNA primer sets, labeled with two fluorescent dyes to exploit fluorescence energy transfer (ET), can be efficiently excited with a single laser line and emit strong fluorescence at distinctive wavelengths. Such ET primers are superior to single fluorophore-labeled primers for DNA sequencing and other multiple color-based analyses [J. Ju, C. Ruan, C. W. Fuller, A. N. Glazer and R. A. Mathies (1995) Proc. Natl. Acad. Sci. USA 92, 4347-4351]. We describe here a novel method of constructing fluorescent primers using a universal ET cassette that can be incorporated by conventional synthesis at the 5'-end of an oligonucleotide primer of any sequence. In this cassette, the donor and acceptor fluorophores are separated by a polymer spacer (S6) formed by six 1',2'-dideoxyribose phosphate monomers (S). The donor is attached to the 5' side of the ribose spacer and the acceptor to a modified thymidine attached to the 3' end of the ribose spacer in the ET cassette. The resulting primers, labeled with 6-carboxy-fluorescein as the donor and other fluorescein and rhodamine dyes as acceptors, display well-separated acceptor emission spectra with 2-12-fold enhanced fluorescence intensity relative to that of the corresponding single dye-labeled primers. With single- stranded M13mp18DNA as the template, a typical run with these ET primers on a capillary sequencer provides DNA sequences with 99% accuracy in the first 550 bases using the same amount of DNA template as that typically required using a four-color slab gel automated sequencer.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Ju J,Glazer AN,Mathies RA

doi

10.1093/nar/24.6.1144

subject

Has Abstract

pub_date

1996-03-15 00:00:00

pages

1144-8

issue

6

eissn

0305-1048

issn

1362-4962

pii

5j0660

journal_volume

24

pub_type

杂志文章
  • Teolenn: an efficient and customizable workflow to design high-quality probes for microarray experiments.

    abstract::Despite the development of new high-throughput sequencing techniques, microarrays are still attractive tools to study small genome organisms, thanks to sample multiplexing and high-feature densities. However, the oligonucleotide design remains a delicate step for most users. A vast array of software is available to de...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq110

    authors: Jourdren L,Duclos A,Brion C,Portnoy T,Mathis H,Margeot A,Le Crom S

    更新日期:2010-06-01 00:00:00

  • Multiple isoform recovery (MIR)-PCR: a simple method for the isolation of related mRNA isoforms.

    abstract::We present a rapid and efficient method for the detection of related transcripts with different expression levels. This approach combines the rapid amplification of cDNA ends (RACE) method with a cDNA subtractive technique. The strategy is based on successive subtractions of prevalent isoforms resulting in enrichment ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.8.2031

    authors: Fagotti A,Gabbiani G,Pascolini R,Neuville P

    更新日期:1998-04-15 00:00:00

  • An RNasin-resistant ribonuclease selective for interleukin 2 mRNA.

    abstract::Interleukin 2 (IL2) mRNA has a short half-life in the cytoplasm of T lymphocytes, relative to most mRNA. We have discovered a candidate ribonuclease to account for the rapid turnover of IL2 mRNA in the cytosol of the human T lymphocyte cell line Jurkat. In partially purified form, this RNase is about 7 times as active...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.1.155

    authors: Hua J,Garner R,Paetkau V

    更新日期:1993-01-11 00:00:00

  • The E3 ubiquitin ligase UBE3A is an integral component of the molecular circadian clock through regulating the BMAL1 transcription factor.

    abstract::Post-translational modifications (such as ubiquitination) of clock proteins are critical in maintaining the precision and robustness of the evolutionarily conserved circadian clock. Ubiquitination of the core clock transcription factor BMAL1 (brain and muscle Arnt-like 1) has recently been reported. However, it remain...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku225

    authors: Gossan NC,Zhang F,Guo B,Jin D,Yoshitane H,Yao A,Glossop N,Zhang YQ,Fukada Y,Meng QJ

    更新日期:2014-05-01 00:00:00

  • LGA: A method for finding 3D similarities in protein structures.

    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

    authors: Zemla A

    更新日期:2003-07-01 00:00:00

  • The influence of tertiary structural restraints on conformational transitions in superhelical DNA.

    abstract::This paper examines theoretically the effects that restraints on the tertiary structure of a superhelical DNA domain exert on the energetics of linking and the onset of conformational transitions. The most important tertiary constraint arises from the nucleosomal winding of genomic DNA in vivo. Conformational transiti...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审

    doi:10.1093/nar/15.23.9985

    authors: Benham CJ

    更新日期:1987-12-10 00:00:00

  • An efficient system for selectively altering genetic information within mRNAs.

    abstract::Site-directed RNA editing (SDRE) is a strategy to precisely alter genetic information within mRNAs. By linking the catalytic domain of the RNA editing enzyme ADAR to an antisense guide RNA, specific adenosines can be converted to inosines, biological mimics for guanosine. Previously, we showed that a genetically encod...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw738

    authors: Montiel-González MF,Vallecillo-Viejo IC,Rosenthal JJ

    更新日期:2016-12-01 00:00:00

  • RPA complexes in Caenorhabditis elegans meiosis; unique roles in replication, meiotic recombination and apoptosis.

    abstract::Replication Protein A (RPA) is a critical complex that acts in replication and promotes homologous recombination by allowing recombinase recruitment to processed DSB ends. Most organisms possess three RPA subunits (RPA1, RPA2, RPA3) that form a trimeric complex critical for viability. The Caenorhabditis elegans genome...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa1293

    authors: Hefel A,Honda M,Cronin N,Harrell K,Patel P,Spies M,Smolikove S

    更新日期:2021-01-21 00:00:00

  • The Arabidopsis Information Resource (TAIR): gene structure and function annotation.

    abstract::The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is the model organism database for the fully sequenced and intensively studied model plant Arabidopsis thaliana. Data in TAIR is derived in large part from manual curation of the Arabidopsis research literature and direct submissions from the research...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm965

    authors: Swarbreck D,Wilks C,Lamesch P,Berardini TZ,Garcia-Hernandez M,Foerster H,Li D,Meyer T,Muller R,Ploetz L,Radenbaugh A,Singh S,Swing V,Tissier C,Zhang P,Huala E

    更新日期:2008-01-01 00:00:00

  • Correlation between sequence conservation and the genomic context after gene duplication.

    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

    authors: Notebaart RA,Huynen MA,Teusink B,Siezen RJ,Snel B

    更新日期:2005-10-27 00:00:00

  • Rearrangement of repeated DNA sequences during development of macronucleus in Tetrahymena thermophila.

    abstract::Three clones of non-repetitive sequences and six clones containing repetitive sequences were obtained from micronuclear DNA of Tetrahymena thermophila. All the non-repetitive and three repetitive sequences had the same organization in micro- and macronuclear DNAs as revealed by blot hybridization. On the other hand, t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.14.4279

    authors: Iwamura Y,Sakai M,Muramatsu M

    更新日期:1982-07-24 00:00:00

  • Extensive RNA editing of U to C in addition to C to U substitution in the rbcL transcripts of hornwort chloroplasts and the origin of RNA editing in green plants.

    abstract::We cloned and sequenced a portion of chloroplast DNA from the hornwort Anthoceros formosae. A nucleotide sequence of 7556 bp contained structures similar to those of ndhK, ndhC, trnV, trnM, atpE, atpB, rbcL, trnR and accD. The arrangement of these was the same as that of other chloroplast DNA. However, two nonsense co...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/24.6.1008

    authors: Yoshinaga K,Iinuma H,Masuzawa T,Uedal K

    更新日期:1996-03-15 00:00:00

  • The nucleosome repeat length increases during erythropoiesis in the chick.

    abstract::During erythropoiesis in the chick, the nucleosome repeat length increases from 190 base pairs to 212 base pairs. This increase is correlated with a dramatic increase in the concentration of the red cell specific histone H5 (from 0.2 molecules per nucleosome to 1 molecule per nucleosome) and with no change in the conc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/5.4.1179

    authors: Weintraub H

    更新日期:1978-04-01 00:00:00

  • The structural basis for recognition of base J containing DNA by a novel DNA binding domain in JBP1.

    abstract::The J-binding protein 1 (JBP1) is essential for biosynthesis and maintenance of DNA base-J (β-d-glucosyl-hydroxymethyluracil). Base-J and JBP1 are confined to some pathogenic protozoa and are absent from higher eukaryotes, prokaryotes and viruses. We show that JBP1 recognizes J-containing DNA (J-DNA) through a 160-res...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr125

    authors: Heidebrecht T,Christodoulou E,Chalmers MJ,Jan S,Ter Riet B,Grover RK,Joosten RP,Littler D,van Luenen H,Griffin PR,Wentworth P Jr,Borst P,Perrakis A

    更新日期:2011-07-01 00:00:00

  • Metal sensing and regulation of adaptive responses to manganese limitation by MtsR is critical for group A streptococcus virulence.

    abstract::Pathogenic bacteria encounter host-imposed manganese (Mn) limitation during infection. Herein we report that in the human pathogen Streptococcus pyogenes, the adaptive response to Mn limitation is controlled by a DtxR family metalloregulator, MtsR. Genes upregulated by MtsR during Mn limitation include Mn (mtsABC) and...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz524

    authors: Do H,Makthal N,Chandrangsu P,Olsen RJ,Helmann JD,Musser JM,Kumaraswami M

    更新日期:2019-08-22 00:00:00

  • Microcomputer programs for back translation of protein to DNA sequences and analysis of ambiguous DNA sequences.

    abstract::Three computer programs are described which may be used to translate a DNA sequence into a protein sequence, back translate the protein sequence into an ambiguous DNA sequence, and then do pattern searching in the ambiguous sequence. The programs are written in the C programming language, have been compiled to run on ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.1part2.819

    authors: Mount DW,Conrad B

    更新日期:1984-01-11 00:00:00

  • The 5' and 3' splice sites come together via a three dimensional diffusion mechanism.

    abstract::We present evidence that the splice sites in mammalian pre-mRNAs are brought together via a three dimensional diffusion mechanism. We tested two mechanisms for splice site pairing: a lateral diffusion ('scanning') model and the currently favored three dimensional diffusion ('jumping') model. Two lines of evidence that...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/24.9.1638

    authors: Pasman Z,Garcia-Blanco MA

    更新日期:1996-05-01 00:00:00

  • Evolution of a highly functional circular DNA aptamer in serum.

    abstract::Circular DNA aptamers are powerful candidates for therapeutic applications given their dramatically enhanced biostability. Herein we report the first effort to evolve circular DNA aptamers that bind a human protein directly in serum, a complex biofluid. Targeting human thrombin, this strategy has led to the discovery ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa800

    authors: Mao Y,Gu J,Chang D,Wang L,Yao L,Ma Q,Luo Z,Qu H,Li Y,Zheng L

    更新日期:2020-11-04 00:00:00

  • Evidence for cross-linking DNA by bis-intercalators with rigid and extended linkers is provided by knotting and catenation.

    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

    authors: Annan NK,Cook PR,Mullins ST,Lowe G

    更新日期:1992-03-11 00:00:00

  • A cDNA fragment of hepatitis C virus isolated from an implicated donor of post-transfusion non-A, non-B hepatitis in Japan.

    abstract::Recently, a cDNA from the hepatitis C virus (HCV) RNA genome has been isolated in the USA from a chronically infected chimpanzee. In order to isolate HCV cDNA derived from human material, RNA was extracted from plasma of a Japanese blood donor implicated in post-transfusion non-A, non-B hepatitis and HCV cDNA was synt...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/17.24.10367

    authors: Kubo Y,Takeuchi K,Boonmar S,Katayama T,Choo QL,Kuo G,Weiner AJ,Bradley DW,Houghton M,Saito I

    更新日期:1989-12-25 00:00:00

  • 'Compensatory slippage' in the evolution of ribosomal RNA genes.

    abstract::The distribution patterns of shared short repetitive motifs in the expansion segments of the large subunit rRNA genes of different species show that these segments are coevolving as a set and that in two examined vertebrate species the RNA secondary structures are conserved as a consequence of runs of motifs in one re...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/18.20.5949

    authors: Hancock JM,Dover GA

    更新日期:1990-10-25 00:00:00

  • Dynamic binding of Ku80, Ku70 and NF90 to the IL-2 promoter in vivo in activated T-cells.

    abstract::IL-2 gene expression in activated T-cells is initiated by chromatin remodeling at the IL-2 proximal promoter and conversion of a transcriptional repressor into a potent transcriptional activator. A purine-box regulator complex was purified from activated Jurkat T-cell nuclei based on sequence-specific DNA binding to t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm117

    authors: Shi L,Qiu D,Zhao G,Corthesy B,Lees-Miller S,Reeves WH,Kao PN

    更新日期:2007-01-01 00:00:00

  • Glycyl-tRNA synthetase specifically binds to the poliovirus IRES to activate translation initiation.

    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

    authors: Andreev DE,Hirnet J,Terenin IM,Dmitriev SE,Niepmann M,Shatsky IN

    更新日期:2012-07-01 00:00:00

  • SWEET-DB: an attempt to create annotated data collections for carbohydrates.

    abstract::Complex carbohydrates are known as mediators of complex cellular events. Concerning their structural diversity, their potential of information content is several orders of magnitude higher in a short sequence than any other biological macromolecule. SWEET-DB (http://www.dkfz.de/spec2/sweetdb/) is an attempt to use mod...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/30.1.405

    authors: Loss A,Bunsmann P,Bohne A,Loss A,Schwarzer E,Lang E,von der Lieth CW

    更新日期:2002-01-01 00:00:00

  • Yeast mitochondrial RNase P, RNase Z and the RNA degradosome are part of a stable supercomplex.

    abstract::Initial steps in the synthesis of functional tRNAs require 5'- and 3'-processing of precursor tRNAs (pre-tRNAs), which in yeast mitochondria are achieved by two endonucleases, RNase P and RNase Z. In this study, using a combination of detergent-free Blue Native Gel Electrophoresis, proteomics and in vitro testing of p...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr941

    authors: Daoud R,Forget L,Lang BF

    更新日期:2012-02-01 00:00:00

  • A deafness-associated tRNA mutation caused pleiotropic effects on the m1G37 modification, processing, stability and aminoacylation of tRNAIle and mitochondrial translation.

    abstract::Defects in the posttranscriptional modifications of mitochondrial tRNAs have been linked to human diseases, but their pathophysiology remains elusive. In this report, we investigated the molecular mechanism underlying a deafness-associated tRNAIle 4295A>G mutation affecting a highly conserved adenosine at position 37,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa1225

    authors: Meng F,Zhou M,Xiao Y,Mao X,Zheng J,Lin J,Lin T,Ye Z,Cang X,Fu Y,Wang M,Guan MX

    更新日期:2021-01-25 00:00:00

  • Crystal structure of the DdrB/ssDNA complex from Deinococcus radiodurans reveals a DNA binding surface involving higher-order oligomeric states.

    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

    authors: Sugiman-Marangos SN,Peel JK,Weiss YM,Ghirlando R,Junop MS

    更新日期:2013-11-01 00:00:00

  • The malaria parasite Plasmodium falciparum encodes members of the Puf RNA-binding protein family with conserved RNA binding activity.

    abstract::A novel class of RNA-binding proteins, Puf, regulates translation and RNA stability by binding to specific sequences in the 3'-untranslated region of target mRNAs. Members of this protein family share a conserved Puf domain consisting of eight 36 amino acid imperfect repeats. Here we report two Puf family member genes...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkf600

    authors: Cui L,Fan Q,Li J

    更新日期:2002-11-01 00:00:00

  • Subtractive cDNA cloning using oligo(dT)30-latex and PCR: isolation of cDNA clones specific to undifferentiated human embryonal carcinoma cells.

    abstract::The human embryonal carcinoma cell line NEC14 can be induced to differentiate by the addition of 10(-2)M N,N'-hexamethylene-bis-acetamide (HMBA). A subtractive cDNA library specific to undifferentiated NEC14 cells was constructed using oligo(dT)30-Latex and polymerase chain reaction (PCR). The method was designed to i...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.25.7097

    authors: Hara E,Kato T,Nakada S,Sekiya S,Oda K

    更新日期:1991-12-01 00:00:00

  • Enhancement of ribosomal frameshifting by oligonucleotides targeted to the HIV gag-pol region.

    abstract::The pol gene of all retroviruses is expressed as a gag-pol fusion protein which is proteolytically processed to produce all viral enzymes. In the human immunodeficiency virus (HIV), the gag and pol genes overlap by 241 nucleotides with pol in the -1 phase with respect to gag. The gag-pol fusion is produced via a -1 ri...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.15.3945

    authors: Vickers TA,Ecker DJ

    更新日期:1992-08-11 00:00:00