Two-tailed RT-qPCR: a novel method for highly accurate miRNA quantification.


:MicroRNAs are a class of small non-coding RNAs that serve as important regulators of gene expression at the posttranscriptional level. They are stable in body fluids and pose great potential to serve as biomarkers. Here, we present a highly specific, sensitive and cost-effective system to quantify miRNA expression based on two-step RT-qPCR with SYBR-green detection chemistry called Two-tailed RT-qPCR. It takes advantage of novel, target-specific primers for reverse transcription composed of two hemiprobes complementary to two different parts of the targeted miRNA, connected by a hairpin structure. The introduction of a second probe ensures high sensitivity and enables discrimination of highly homologous miRNAs irrespectively of the position of the mismatched nucleotide. Two-tailed RT-qPCR has a dynamic range of seven logs and a sensitivity sufficient to detect down to ten target miRNA molecules. It is capable to capture the full isomiR repertoire, leading to accurate representation of the complete miRNA content in a sample. The reverse transcription step can be multiplexed and the miRNA profiles measured with Two-tailed RT-qPCR show excellent correlation with the industry standard TaqMan miRNA assays (r2 = 0.985). Moreover, Two-tailed RT-qPCR allows for rapid testing with a total analysis time of less than 2.5 hours.


Nucleic Acids Res


Nucleic acids research


Androvic P,Valihrach L,Elling J,Sjoback R,Kubista M




Has Abstract


2017-09-06 00:00:00














  • DynOmics: dynamics of structural proteome and beyond.

    abstract::DynOmics ( is a portal developed to leverage rapidly growing structural proteomics data by efficiently and accurately evaluating the dynamics of structurally resolved systems, from individual molecules to large complexes and assemblies, in the context of their physiological environment. At the core o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Li H,Chang YY,Lee JY,Bahar I,Yang LW

    更新日期:2017-07-03 00:00:00

  • The major form of MeCP2 has a novel N-terminus generated by alternative splicing.

    abstract::MeCP2 is a methyl-CpG binding protein that can repress transcription of nearby genes. In humans, mutations in the MECP2 gene are the major cause of Rett syndrome. By searching expressed sequence tag (EST) databases we have found a novel MeCP2 splice isoform (MeCP2alpha) which encodes a distinct N-terminus. We demonstr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kriaucionis S,Bird A

    更新日期:2004-03-19 00:00:00

  • Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium.

    abstract::The Protein Folding Database (PFD) is a publicly accessible repository of thermodynamic and kinetic protein folding data. Here we describe the first major revision of this work, featuring extensive restructuring that conforms to standards set out by the recently formed International Foldeomics Consortium. The database...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Fulton KF,Bate MA,Faux NG,Mahmood K,Betts C,Buckle AM

    更新日期:2007-01-01 00:00:00

  • Functional analysis of a C. elegans trans-splice acceptor.

    abstract::The rol-6 gene is trans-spliced to the 22 nt leader, SL1, 173 nt downstream of the transcription start. We have analyzed splicing in transformants carrying extrachromosomal arrays of rol-6 with mutations in the trans-splice acceptor site. This site is a close match to the consensus, UUUCAG, that is highly conserved in...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Conrad R,Liou RF,Blumenthal T

    更新日期:1993-02-25 00:00:00

  • Gene-specific mutagenesis enables rapid continuous evolution of enzymes in vivo.

    abstract::Various in vivo mutagenesis methods have been developed to facilitate fast and efficient continuous evolution of proteins in cells. However, they either modify the DNA region that does not match the target gene, or suffer from low mutation rates. Here, we report a mutator, eMutaT7 (enhanced MutaT7), with very fast in ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Park H,Kim S

    更新日期:2021-01-06 00:00:00

  • Stability of the primary organization of nucleosome core particles upon some conformational transitions.

    abstract::The sequential arrangement of histones along DNA in nucleosome core particles was determined between 0.5 and 600 mM salt and from 0 to 8 M urea. These concentrations of salt and urea up to 6 M had no significant effect on the linear order of histones along DNA but 8 M urea caused the rearrangement of histones. Conform...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zayetz VW,Bavykin SG,Karpov VL,Mirzabekov AD

    更新日期:1981-03-11 00:00:00

  • Increased levels of E2F-1-dependent DNA binding activity after UV- or gamma-irradiation.

    abstract::In mammalian cells, DNA damage induces robust changes in gene expression and these changes contribute to the proper execution of cellular responses to DNA damage, including DNA repair, cell cycle arrest and apoptosis. The transcription factor E2F-1 has been suggested to play a key role in the regulation of cell cycle-...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Höfferer M,Wirbelauer C,Humar B,Krek W

    更新日期:1999-01-15 00:00:00

  • GAM: a web-service for integrated transcriptional and metabolic network analysis.

    abstract::Novel techniques for high-throughput steady-state metabolomic profiling yield information about changes of nearly thousands of metabolites. Such metabolomic profiles, when analyzed together with transcriptional profiles, can reveal novel insights about underlying biological processes. While a number of conceptual appr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sergushichev AA,Loboda AA,Jha AK,Vincent EE,Driggers EM,Jones RG,Pearce EJ,Artyomov MN

    更新日期:2016-07-08 00:00:00

  • Distribution of DNA-condensing protein complexes in the adenovirus core.

    abstract::Genome packing in adenovirus has long evaded precise description, since the viral dsDNA molecule condensed by proteins (core) lacks icosahedral order characteristic of the virus protein coating (capsid). We show that useful insights regarding the organization of the core can be inferred from the analysis of spatial di...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Pérez-Berná AJ,Marion S,Chichón FJ,Fernández JJ,Winkler DC,Carrascosa JL,Steven AC,Šiber A,San Martín C

    更新日期:2015-04-30 00:00:00

  • Anti-prion activity of an RNA aptamer and its structural basis.

    abstract::Prion proteins (PrPs) cause prion diseases, such as bovine spongiform encephalopathy. The conversion of a normal cellular form (PrP(C)) of PrP into an abnormal form (PrP(Sc)) is thought to be associated with the pathogenesis. An RNA aptamer that tightly binds to and stabilizes PrP(C) is expected to block this conversi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mashima T,Nishikawa F,Kamatari YO,Fujiwara H,Saimura M,Nagata T,Kodaki T,Nishikawa S,Kuwata K,Katahira M

    更新日期:2013-01-01 00:00:00

  • KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions.

    abstract::KUPS (The University of Kansas Proteomics Service) provides high-quality protein-protein interaction (PPI) data for researchers developing and evaluating computational models for predicting PPIs by allowing users to construct ready-to-use data sets of interacting protein pairs (IPPs), non-interacting protein pairs (NI...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chen XW,Jeong JC,Dermyer P

    更新日期:2011-01-01 00:00:00

  • The FurA regulon in Anabaena sp. PCC 7120: in silico prediction and experimental validation of novel target genes.

    abstract::In the filamentous cyanobacterium Anabaena sp. PCC 7120, the ferric uptake regulator FurA functions as a global transcriptional regulator. Despite several analyses have focused on elucidating the FurA-regulatory network, the number of target genes described for this essential transcription factor is limited to a handf...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: González A,Angarica VE,Sancho J,Fillat MF

    更新日期:2014-04-01 00:00:00

  • RNAMST: efficient and flexible approach for identifying RNA structural homologs.

    abstract::RNA molecules fold into characteristic secondary structures for their diverse functional activities such as post-translational regulation of gene expression. Searching homologs of a pre-defined RNA structural motif, which may be a known functional element or a putative RNA structural motif, can provide useful informat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chang TH,Huang HD,Chuang TN,Shien DM,Horng JT

    更新日期:2006-07-01 00:00:00

  • A comparison between mammalian and avian fast skeletal muscle alkali myosin light chain genes: regulatory implications.

    abstract::A single locus in the mouse, rat and chicken encodes both alkali myosin light chains, MLC1F and MLC3F. This gene has two distinct promoters and gives rise to two different primary transcripts, which are processed by alternative and different modes of splicing to form MLC1F and MLC3F mRNAs. The MLC1F/MLC3F gene is very...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Daubas P,Robert B,Garner I,Buckingham M

    更新日期:1985-07-11 00:00:00

  • A central fragment of ribosomal protein S26 containing the eukaryote-specific motif YxxPKxYxK is a key component of the ribosomal binding site of mRNA region 5' of the E site codon.

    abstract::The eukaryotic ribosomal protein S26e (rpS26e) lacking eubacterial counterparts is a key component of the ribosomal binding site of mRNA region 5' of the codon positioned at the exit site. Here, we determined the rpS26e oligopeptide neighboring mRNA on the human 80S ribosome using mRNA analogues bearing perfluoropheny...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sharifulin D,Khairulina Y,Ivanov A,Meschaninova M,Ven'yaminova A,Graifer D,Karpova G

    更新日期:2012-04-01 00:00:00

  • SuperSweet--a resource on natural and artificial sweetening agents.

    abstract::A vast number of sweet tasting molecules are known, encompassing small compounds, carbohydrates, d-amino acids and large proteins. Carbohydrates play a particularly big role in human diet. The replacement of sugars in food with artificial sweeteners is common and is a general approach to prevent cavities, obesity and ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ahmed J,Preissner S,Dunkel M,Worth CL,Eckert A,Preissner R

    更新日期:2011-01-01 00:00:00

  • Absolute quantitative measurement of transcriptional kinetic parameters in vivo.

    abstract::mRNA expression involves transcription initiation, elongation and degradation. In cells, these dynamic processes are highly regulated. However, experimental characterization of the dynamic processes in vivo is difficult due to the paucity of methods capable of direct measurements. We present a highly sensitive and ver...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Iyer S,Park BR,Kim M

    更新日期:2016-10-14 00:00:00

  • Effect of 5-methylcytosine on the stability of triple-stranded DNA--a thermodynamic study.

    abstract::We have previously shown that the pyrimidine oligonucleotide 5'CTTCCTCCTCT (Y11) recognizes the double-helical stem of hairpin 5'GAAGGAGGAGA-T4-TCTCCTCCTTC (h26) by triple-helix formation (1). In this paper, we report the effect on triplex formation of substituting the cytosine residues of Y11 with 5-methylcytosines (...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Xodo LE,Manzini G,Quadrifoglio F,van der Marel GA,van Boom JH

    更新日期:1991-10-25 00:00:00

  • GenBank.

    abstract::GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or st...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Benson DA,Karsch-Mizrachi I,Lipman DJ,Ostell J,Wheeler DL

    更新日期:2008-01-01 00:00:00

  • Two zinc finger proteins from Xenopus laevis bind the same region of 5S RNA but with different nuclease protection patterns.

    abstract::Immature oocytes from Xenopus laevis contain a 42S ribonucleoprotein particle (RNP) containing 5S RNA, tRNA, a 43 kDa protein, and a 48 kDa protein. A particle containing 5S RNA and the 43 kDa protein (p43-5S) liberated from the 42S particle upon brief treatment with urea can be purified by anion exchange chromatograp...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sands MS,Bogenhagen DF

    更新日期:1991-04-25 00:00:00

  • Glycosyl conformational and inductive effects on the acid catalysed hydrolysis of purine nucleosides.

    abstract::The log kobs vs. pH profiles were determined in the intermediate acidity region for the glycosyl hydrolysis of guanosine and its 8-amino, 8-monomethylamino, 8-dimethylamino and 8-bromo derivatives. The decreased rate of the 8-amino and enhanced rate of the 8-bromo compound compared to guanosine support an A type mecha...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Jordan F,Niv H

    更新日期:1977-03-01 00:00:00

  • New rapid methods for DNA sequencing based in exonuclease III digestion followed by repair synthesis.

    abstract::We describe improve enzymatic methods for sequencing method for sequencing DNA. They are based on partial digestion of duplex DNA with exonuclease III to produce DNA molecules with 3' ends shortened to varying lengths, followed by repair synthesis to extend and label the 3' ends. After asymmetrical cleavage of the DNA...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Guo LH,Wu R

    更新日期:1982-03-25 00:00:00

  • Reversal of methylation-mediated repression with short-chain fatty acids: evidence for an additional mechanism to histone deacetylation.

    abstract::We have constructed a stable cell line, human embryonal kidney 293M+, containing a lacZ reporter gene controlled by an in vitro methylated hormone-responsive enhancer. Methylation of the enhancer-promoter abolishes lacZ expression controlled by ponasterone A (an analogue of ecdysone). Ponasterone A-induced expression ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Benjamin D,Jost JP

    更新日期:2001-09-01 00:00:00

  • Generating compatible translation initiation regions for heterologous gene expression in Escherichia coli by exhaustive periShine-Dalgarno mutagenesis. Human glutathione reductase cDNA as a model.

    abstract::Adaptation of eucaryotic cDNA to heterologous expression was studied by mutating the translation initiation (TI) region upstream (mTI) and downstream (MTI) of the start codon. In the mTI subregion the 8 bases flanking the invariant Shine-Dalgarno motif GG-AG were mutagenized exhaustively, while the MTI subregion was s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bücheler US,Werner D,Schirmer RH

    更新日期:1992-06-25 00:00:00

  • Structural probing of the HIV-1 polypurine tract RNA:DNA hybrid using classic nucleic acid ligands.

    abstract::The interactions of archetypical nucleic acid ligands with the HIV-1 polypurine tract (PPT) RNA:DNA hybrid, as well as analogous DNA:DNA, RNA:RNA and swapped hybrid substrates, were used to probe structural features of the PPT that contribute to its specific recognition and processing by reverse transcriptase (RT). Re...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Turner KB,Brinson RG,Yi-Brunozzi HY,Rausch JW,Miller JT,Le Grice SF,Marino JP,Fabris D

    更新日期:2008-05-01 00:00:00

  • Synthesis and coding properties of dinucleoside diphosphates containing alky pyrimidines which are formed by the action of carcinogens on nucleic acids.

    abstract::Dinucleoside diphosphates of the general type pGpN have been prepared enzymatically using ribonuclease N1. Alkylated uridines or cytidines, which are products of carcinogens acting on nucleic acids, were tested in dinucleoside diphosphates for their ability to stimulate the binding of Ala- or Val-tRNA to ribosomes. O2...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Singer B,Pergolizzi RG,Grunberger D

    更新日期:1979-04-01 00:00:00

  • X chromosome inactivation of the human TIMP gene.

    abstract::X chromosome inactivation results in the cis-limited inactivation of most, but not all, genes on one of the two X chromosomes in mammalian females. The molecular basis for inactivation is unknown. In order to examine the transcriptional activity of human X-linked genes, a series of mouse-human somatic cell hybrids und...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Brown CJ,Flenniken AM,Williams BR,Willard HF

    更新日期:1990-07-25 00:00:00

  • Use of a cellular polyadenylation signal by viral transcripts in polyoma virus transformed cells.

    abstract::The DNA sequences at and around the junctions between viral and cellular DNA in the polyoma virus transformed mouse cell line, TS-A-3T3, have been determined. No common sequence specificity or structural features at the joins have been observed. The sequence indicates that the 94K truncated large T antigen found in TS...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ruley HE,Lania L,Chaudry F,Fried M

    更新日期:1982-08-11 00:00:00

  • Role of interaction energy in the specificity of transcription. II-The Watson Crick A-U base pair template.

    abstract::In continuation with work regarding the evaluation of the energy of association of various RNA bases with various base pairs, the results of the computations of the electrostatic interaction energy of A-U base pair with four RNA bases viz. Adenine, Uracil, Guanine and Cytosine have been reported. Non bonded induced po...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sanyal NK,Kumar U,Roychoudhury M

    更新日期:1980-09-11 00:00:00

  • Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning.

    abstract::Nucleosomes are the most abundant protein-DNA complexes in eukaryotes that provide compaction of genomic DNA and are implicated in regulation of transcription, DNA replication and repair. The details of DNA positioning on the nucleosome and the DNA conformation can provide key regulatory signals. Hydroxyl-radical foot...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Shaytan AK,Xiao H,Armeev GA,Wu C,Landsman D,Panchenko AR

    更新日期:2017-09-19 00:00:00