A designed RNA selection: establishment of a stable complex between a target and selectant RNA via two coordinated interactions.


:In this paper, we describe a new method for selecting RNA aptamers that cooperatively bind to two specific sites within a target RNA. We designed a selection system in which two RNAs, a target RNA and a RNA pool, were assembled by employing a pre-organized GAAA tetraloop-11-nt receptor interaction. This allows us to select the binding sequence against a targeted internal loop as well as a linker region optimized for binding of the two binding sites. After the selection, the aptamers bound with dissociation constants in the nanomolar range, thereby forming a stable complex with the target RNA. Thus this method enables identification of aptamers for a specific binding site together with a linker for cooperative binding of the two RNAs. It appears that our new method can be applied generally to select RNAs that adhere tightly to a target RNA via two specific sites. The method can also be applicable for further engineering of both natural and artificial RNAs.


Nucleic Acids Res


Nucleic acids research


Shiohara T,Saito H,Inoue T




Has Abstract


2009-02-01 00:00:00














  • Guanine tracts enhance sequence directed DNA bends.

    abstract::Synthetic DNA fragments were constructed to determine the effect of G tracts, in conjunction with periodically spaced A tracts, on DNA bends. Relative length measurements showed that the G tracts spaced at the half helical turn enhanced the DNA bend. When the G tract was interrupted with a thymine or shortened to one ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Milton DL,Casper ML,Wills NM,Gesteland RF

    更新日期:1990-02-25 00:00:00

  • Inherited disorders of cobalamin metabolism disrupt nucleocytoplasmic transport of mRNA through impaired methylation/phosphorylation of ELAVL1/HuR.

    abstract::The molecular mechanisms that underlie the neurological manifestations of patients with inherited diseases of vitamin B12 (cobalamin) metabolism remain to date obscure. We observed transcriptomic changes of genes involved in RNA metabolism and endoplasmic reticulum stress in a neuronal cell model with impaired cobalam...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Battaglia-Hsu SF,Ghemrawi R,Coelho D,Dreumont N,Mosca P,Hergalant S,Gauchotte G,Sequeira JM,Ndiongue M,Houlgatte R,Alberto JM,Umoret R,Robert A,Paoli J,Jung M,Quadros EV,Guéant JL

    更新日期:2018-09-06 00:00:00

  • Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): an archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic poleta.

    abstract::Phylogenetic analysis of Y-family DNA polymerases suggests that it can be subdivided into several discrete branches consisting of UmuC/DinB/Rev1/Rad30/Rad30A and Rad30B. The most diverse is the DinB family that is found in all three kingdoms of life. Searches of the complete genome of the crenarchaeon Sulfolobus solfa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Boudsocq F,Iwai S,Hanaoka F,Woodgate R

    更新日期:2001-11-15 00:00:00

  • 5' flanking sequence and genomic structure of Egr-1, a murine mitogen inducible zinc finger encoding gene.

    abstract::Egr-1 is a murine zinc finger encoding cDNA whose expression is modulated by a variety of ligand-receptor interactions and is often coregulated with c-fos (1). This study reports the isolation of a mouse Egr-1 genomic clone, its intron-exon structure, and 935 bp of 5' flanking sequence. The gene spans about 3.8 kb and...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Tsai-Morris CH,Cao XM,Sukhatme VP

    更新日期:1988-09-26 00:00:00

  • Structural features and stability of an RNA triple helix in solution.

    abstract::A 30 nt RNA with a sequence designed to form an intramolecular triple helix was analyzed by one-and two-dimensional NMR spectroscopy and UV absorption measurements. NMR data show that the RNA contains seven pyrimidine-purine-pyrimidine base triples stabilized by Watson-Crick and Hoogsteen interactions. The temperature...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Holland JA,Hoffman DW

    更新日期:1996-07-15 00:00:00

  • The ATP-mediated formation of the YgjD-YeaZ-YjeE complex is required for the biosynthesis of tRNA t6A in Escherichia coli.

    abstract::The essential and universal N(6)-threonylcarbamoyladenosine (t(6)A) modification at position 37 of ANN-decoding tRNAs plays a pivotal role in translational fidelity through enhancement of the cognate codon recognition and stabilization of the codon-anticodon interaction. In Escherichia coli, the YgjD (TsaD), YeaZ (Tsa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhang W,Collinet B,Perrochia L,Durand D,van Tilbeurgh H

    更新日期:2015-02-18 00:00:00

  • The transposable element Mdg3 in Drosophila melanogaster is flanked with the perfect direct and mismatched inverted repeats.

    abstract::MDg3 is a family of mobile dispersed genetic elements represented by 15 copies in the haploid genome of D. melanogaster and flanked, like other similar elements, by the regions of homology. In the present work, these regions of mdg3 have been sequenced. The existence of perfect direct repeats 268 base pairs long has b...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bayev AA Jr,Krayev AS,Lyubomirskaya NV,Ilyin YV,Skryabin KG,Georgiev GP

    更新日期:1980-08-11 00:00:00

  • Human microRNA hsa-miR-125a-5p interferes with expression of hepatitis B virus surface antigen.

    abstract::MicroRNAs are small non-coding RNAs that modulate gene expression at post-transcriptional level, playing a crucial role in cell differentiation and development. Recently, some reports have shown that a limited number of mammalian microRNAs are also involved in anti-viral defense. In this study, the analysis of the hep...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Potenza N,Papa U,Mosca N,Zerbini F,Nobile V,Russo A

    更新日期:2011-07-01 00:00:00

  • The EcoCyc and MetaCyc databases.

    abstract::EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, and-a new addition-its transport proteins. MetaCyc is a new metabolic-pathway database that describes pathways and enzymes of many different organisms, with a microbial...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Karp PD,Riley M,Saier M,Paulsen IT,Paley SM,Pellegrini-Toole A

    更新日期:2000-01-01 00:00:00

  • Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations.

    abstract::Ribonucleoprotein (RNP) granules are membraneless organelles (MLOs), which majorly consist of RNA and RNA-binding proteins and are formed via liquid-liquid phase separation (LLPS). Experimental studies investigating the drivers of LLPS have shown that intrinsically disordered proteins (IDPs) and nucleic acids like RNA...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Regy RM,Dignon GL,Zheng W,Kim YC,Mittal J

    更新日期:2020-12-16 00:00:00

  • Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV).

    abstract::The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa;...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lefkowitz EJ,Dempsey DM,Hendrickson RC,Orton RJ,Siddell SG,Smith DB

    更新日期:2018-01-04 00:00:00

  • PhiReX: a programmable and red light-regulated protein expression switch for yeast.

    abstract::Highly regulated induction systems enabling dose-dependent and reversible fine-tuning of protein expression output are beneficial for engineering complex biosynthetic pathways. To address this, we developed PhiReX, a novel red/far-red light-regulated protein expression system for use in Saccharomyces cerevisiae. PhiRe...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hochrein L,Machens F,Messerschmidt K,Mueller-Roeber B

    更新日期:2017-09-06 00:00:00

  • Activating-transcription-factor (ATF) regulates human 7S L RNA transcription by RNA polymerase III in vivo and in vitro.

    abstract::The gene-external part of the human 7S L promoter was analyzed by transcription in vitro and in vivo. Compared to the wild type promoter (-178), a -66 5'deletion mutant revealed full activity in vitro but was inefficiently transcribed in vivo. Further deletion to -37 reduced template activity to 50% in vitro and to ba...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bredow S,Sürig D,Müller J,Kleinert H,Benecke BJ

    更新日期:1990-12-11 00:00:00

  • DNA polymerase δ stalls on telomeric lagging strand templates independently from G-quadruplex formation.

    abstract::Previous evidence indicates that telomeres resemble common fragile sites and present a challenge for DNA replication. The precise impediments to replication fork progression at telomeric TTAGGG repeats are unknown, but are proposed to include G-quadruplexes (G4) on the G-rich strand. Here we examined DNA synthesis and...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lormand JD,Buncher N,Murphy CT,Kaur P,Lee MY,Burgers P,Wang H,Kunkel TA,Opresko PL

    更新日期:2013-12-01 00:00:00

  • HeLa DNA polymerase alpha activity in vitro: specific stimulation by a non-enzymic protein factor.

    abstract::A non-enzymic protein factor that increases the in vitro rate of synthesis by HeLa DNA polymerase alpha 15- to 30-fold with denatured DNA as template has been partially purified from the cytoplasmic fraction of HeLa cells. The stimulatory effect is highly specific for HeLa DNA polymerase alpha and for DNA templates th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Novak B,Baril EF

    更新日期:1978-01-01 00:00:00

  • The Rat Genome Database 2009: variation, ontologies and pathways.

    abstract::The Rat Genome Database (RGD, http://rgd.mcw.edu) was developed to provide a core resource for rat researchers combining genetic, genomic, pathway, phenotype and strain information with a focus on disease. RGD users are provided with access to structured and curated data from the molecular level through to the level o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Dwinell MR,Worthey EA,Shimoyama M,Bakir-Gungor B,DePons J,Laulederkind S,Lowry T,Nigram R,Petri V,Smith J,Stoddard A,Twigger SN,Jacob HJ,RGD Team.

    更新日期:2009-01-01 00:00:00

  • Resolution of a Holliday junction by vaccinia topoisomerase requires a spacer DNA segment 3' of the CCCTT/ cleavage sites.

    abstract::Vaccinia virus DNA topoisomerase catalyzes resolution of synthetic Holliday junctions in vitro. The mechanism entails concerted transesterifications at two recognition sites, 5'-CCCTT/, that are opposed within a partially mobile four-way junction. Efficient resolution occurs on a junction with a 10 bp segment of branc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sekiguchi J,Cheng C,Shuman S

    更新日期:2000-07-15 00:00:00

  • Large-scale profiling of microRNAs for The Cancer Genome Atlas.

    abstract::The comprehensive multiplatform genomics data generated by The Cancer Genome Atlas (TCGA) Research Network is an enabling resource for cancer research. It includes an unprecedented amount of microRNA sequence data: ~11 000 libraries across 33 cancer types. Combined with initiatives like the National Cancer Institute G...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chu A,Robertson G,Brooks D,Mungall AJ,Birol I,Coope R,Ma Y,Jones S,Marra MA

    更新日期:2016-01-08 00:00:00

  • A conserved U-rich RNA region implicated in regulation of translation in Plasmodium female gametocytes.

    abstract::Translational repression (TR) plays an important role in post-transcriptional regulation of gene expression and embryonic development in metazoans. TR also regulates the expression of a subset of the cytoplasmic mRNA population during development of fertilized female gametes of the unicellular malaria parasite, Plasmo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Braks JA,Mair GR,Franke-Fayard B,Janse CJ,Waters AP

    更新日期:2008-03-01 00:00:00

  • UV stalled replication forks restart by re-priming in human fibroblasts.

    abstract::Restarting stalled replication forks is vital to avoid fatal replication errors. Previously, it was demonstrated that hydroxyurea-stalled replication forks rescue replication either by an active restart mechanism or by new origin firing. To our surprise, using the DNA fibre assay, we only detect a slightly reduced for...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Elvers I,Johansson F,Groth P,Erixon K,Helleday T

    更新日期:2011-09-01 00:00:00

  • Antisense inhibition of gene expression in cells by oligonucleotides incorporating locked nucleic acids: effect of mRNA target sequence and chimera design.

    abstract::Use of antisense oligonucleotides is a versatile strategy for achieving control of gene expression. Unfortunately, the interpretation of antisense-induced phenotypes is sometimes difficult, and chemical modifications that improve the potency and specificity of antisense action would be useful. The introduction of lock...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Braasch DA,Liu Y,Corey DR

    更新日期:2002-12-01 00:00:00

  • The rat poly pyrimidine tract binding protein (PTB) interacts with a single-stranded DNA motif in a liver-specific enhancer.

    abstract::We characterized and purified a protein from rat liver which specifically binds to a DNA motif present in a liver-specific enhancer of the rat tyrosine aminotransferase (TAT) gene, when offered as single-stranded DNA. Binding is highly sequence-specific and coincides with a region known to be essential for function of...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Jansen-Dürr P,Boshart M,Lupp B,Bosserhoff A,Frank RW,Schütz G

    更新日期:1992-03-25 00:00:00

  • LEDGF/p75 interacts with divergent lentiviral integrases and modulates their enzymatic activity in vitro.

    abstract::Transcriptional co-activator LEDGF/p75 is the major cellular interactor of HIV-1 integrase (IN), critical to efficient viral replication. In this work, a series of INs from the Betaretrovirus, Gammaretrovirus, Deltaretrovirus, Spumavirus and Lentivirus retroviral genera were tested for interaction with the host factor...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Cherepanov P

    更新日期:2007-01-01 00:00:00

  • KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns.

    abstract::Due to the importance of protein phosphorylation in cellular control, many researches are undertaken to predict the kinase-specific phosphorylation sites. Referred to our previous work, KinasePhos 1.0, incorporated profile hidden Markov model (HMM) with flanking residues of the kinase-specific phosphorylation sites. H...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Wong YH,Lee TY,Liang HK,Huang CM,Wang TY,Yang YH,Chu CH,Huang HD,Ko MT,Hwang JK

    更新日期:2007-07-01 00:00:00

  • Distribution of 5-methylcytosine in the DNA of somatic and germline cells from bovine tissues.

    abstract::Genomic DNA of calf thymus contains 1.5 times as much 5-methylcytosine as similar sperm DNA, but the major EcoRI repeat fragment from satellite I of thymus contains ten times as much 5-methylcytosine as the corresponding fragment from sperm DNA. Restriction enzyme analyses of the total DNA and the satellite I fragment...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sturm KS,Taylor JH

    更新日期:1981-09-25 00:00:00

  • Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism.

    abstract::The endonuclease activity within the influenza virus cap-snatching process is a proven therapeutic target. The anti-influenza drug baloxavir is highly effective, but is associated with resistance mutations that threaten its clinical efficacy. The endonuclease resides within the N-terminal domain of the PA subunit (PAN...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kumar G,Cuypers M,Webby RR,Webb TR,White SW

    更新日期:2021-01-19 00:00:00

  • Structures of apo IRF-3 and IRF-7 DNA binding domains: effect of loop L1 on DNA binding.

    abstract::Interferon regulatory factors IRF-3 and IRF-7 are transcription factors essential in the activation of interferon-β (IFN-β) gene in response to viral infections. Although, both proteins recognize the same consensus IRF binding site AANNGAAA, they have distinct DNA binding preferences for sites in vivo. The X-ray struc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: De Ioannes P,Escalante CR,Aggarwal AK

    更新日期:2011-09-01 00:00:00

  • The modulation of topoisomerase I-mediated DNA cleavage and the induction of DNA-topoisomerase I crosslinks by crotonaldehyde-derived DNA adducts.

    abstract::Crotonaldehyde is a representative alpha,beta-unsaturated aldehyde endowed of mutagenic and carcinogenic properties related to its propensity to react with DNA. Cyclic crotonaldehyde-derived deoxyguanosine (CrA-PdG) adducts can undergo ring opening in duplex DNA to yield a highly reactive aldehydic moiety. Here, we de...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Dexheimer TS,Kozekova A,Rizzo CJ,Stone MP,Pommier Y

    更新日期:2008-07-01 00:00:00

  • High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions.

    abstract::The emergence of massively parallel sequencing technology has revolutionized microbial profiling, allowing the unprecedented comparison of microbial diversity across time and space in a wide range of host-associated and environmental ecosystems. Although the high-throughput nature of such methods enables the detection...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Amir A,Zeisel A,Zuk O,Elgart M,Stern S,Shamir O,Turnbaugh PJ,Soen Y,Shental N

    更新日期:2013-12-01 00:00:00

  • MethBank 3.0: a database of DNA methylomes across a variety of species.

    abstract::MethBank (http://bigd.big.ac.cn/methbank) is a database that integrates high-quality DNA methylomes across a variety of species and provides an interactive browser for visualization of methylation data. Here, we present an updated implementation of MethBank (version 3.0) by incorporating more DNA methylomes from multi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Li R,Liang F,Li M,Zou D,Sun S,Zhao Y,Zhao W,Bao Y,Xiao J,Zhang Z

    更新日期:2018-01-04 00:00:00