Triggered amplification by hybridization chain reaction.

Abstract:

:We introduce the concept of hybridization chain reaction (HCR), in which stable DNA monomers assemble only upon exposure to a target DNA fragment. In the simplest version of this process, two stable species of DNA hairpins coexist in solution until the introduction of initiator strands triggers a cascade of hybridization events that yields nicked double helices analogous to alternating copolymers. The average molecular weight of the HCR products varies inversely with initiator concentration. Amplification of more diverse recognition events can be achieved by coupling HCR to aptamer triggers. This functionality allows DNA to act as an amplifying transducer for biosensing applications.

authors

Dirks RM,Pierce NA

doi

10.1073/pnas.0407024101

keywords:

subject

Has Abstract

pub_date

2004-10-26 00:00:00

pages

15275-8

issue

43

eissn

0027-8424

issn

1091-6490

pii

0407024101

journal_volume

101

pub_type

杂志文章
  • Doping evolution of the Mott-Hubbard landscape in infinite-layer nickelates.

    abstract::The recent observation of superconductivity in [Formula: see text] has raised fundamental questions about the hierarchy of the underlying electronic structure. Calculations suggest that this system falls in the Mott-Hubbard regime, rather than the charge-transfer configuration of other nickel oxides and the supercondu...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2007683118

    authors: Goodge BH,Li D,Lee K,Osada M,Wang BY,Sawatzky GA,Hwang HY,Kourkoutis LF

    更新日期:2021-01-12 00:00:00

  • An NQO1- and PARP-1-mediated cell death pathway induced in non-small-cell lung cancer cells by beta-lapachone.

    abstract::Lung cancer is the number one cause of cancer-related deaths in the world. Patients treated with current chemotherapies for non-small-cell lung cancers (NSCLCs) have a survival rate of approximately 15% after 5 years. Novel approaches are needed to treat this disease. We show elevated NAD(P)H:quinone oxidoreductase-1 ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0702176104

    authors: Bey EA,Bentle MS,Reinicke KE,Dong Y,Yang CR,Girard L,Minna JD,Bornmann WG,Gao J,Boothman DA

    更新日期:2007-07-10 00:00:00

  • Protein dynamics investigated by inherent structure analysis.

    abstract::Molecular dynamics (MD) simulations provide essential information about the thermodynamics and dynamics of proteins. To construct the free-energy surface from equilibrium trajectories, it is necessary to group the individual snapshots in a meaningful way. The inherent structures (IS) are shown to provide an appropriat...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0915087107

    authors: Rao F,Karplus M

    更新日期:2010-05-18 00:00:00

  • PDGF-CC blockade inhibits pathological angiogenesis by acting on multiple cellular and molecular targets.

    abstract::The importance of identifying VEGF-independent pathways in pathological angiogenesis is increasingly recognized as a result of the emerging drug resistance to anti-VEGF therapies. PDGF-CC is the third member of the PDGF family discovered after more than two decades of studies on PDGF-AA and PDGF-BB. The biological fun...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1004143107

    authors: Hou X,Kumar A,Lee C,Wang B,Arjunan P,Dong L,Maminishkis A,Tang Z,Li Y,Zhang F,Zhang SZ,Wardega P,Chakrabarty S,Liu B,Wu Z,Colosi P,Fariss RN,Lennartsson J,Nussenblatt R,Gutkind JS,Cao Y,Li X

    更新日期:2010-07-06 00:00:00

  • Evolution in the hypervariable environment of Madagascar.

    abstract::We show that the diverse ecoregions of Madagascar share one distinctive climatic feature: unpredictable intra- or interannual precipitation compared with other regions with comparable rainfall. Climatic unpredictability is associated with unpredictable patterns of fruiting and flowering. It is argued that these featur...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0704346104

    authors: Dewar RE,Richard AF

    更新日期:2007-08-21 00:00:00

  • Protein database searches for multiple alignments.

    abstract::Protein database searches frequently can reveal biologically significant sequence relationships useful in understanding structure and function. Weak but meaningful sequence patterns can be obscured, however, by other similarities due only to chance. By searching a database for multiple as opposed to pairwise alignment...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.87.14.5509

    authors: Altschul SF,Lipman DJ

    更新日期:1990-07-01 00:00:00

  • Characteristic temperatures of folding of a small peptide.

    abstract::We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that the folding of a small peptide is a multistage process associated with two charact...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.94.20.10652

    authors: Hansmann UH,Masuya M,Okamoto Y

    更新日期:1997-09-30 00:00:00

  • Adversarial alignment enables competing models to engage in cooperative theory building toward cumulative science.

    abstract::Crises in science concern not only methods, statistics, and results but also, theory development. Beyond the indispensable refinement of tools and procedures, resolving crises would also benefit from a deeper understanding of the concepts and processes guiding research. Usually, theories compete, and some lose, incent...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1906720117

    authors: Ellemers N,Fiske ST,Abele AE,Koch A,Yzerbyt V

    更新日期:2020-04-07 00:00:00

  • Two-dimensional infrared spectra reveal relaxation of the nonnucleoside inhibitor TMC278 complexed with HIV-1 reverse transcriptase.

    abstract::The two nitrile groups at the wings of the nonnucleoside HIV-1 reverse transcriptase (RT) inhibitor TMC278 are both identified in high-sensitivity 2D IR spectroscopy experiments of the HIV-1 RT/TMC278 complex. The vibrational spectra indicate that the two arms of the inhibitor sense quite different environments within...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0709320104

    authors: Fang C,Bauman JD,Das K,Remorino A,Arnold E,Hochstrasser RM

    更新日期:2008-02-05 00:00:00

  • Two tail-anchored protein variants, differing in transmembrane domain length and intracellular sorting, interact differently with lipids.

    abstract::C-tail-anchored (TA) proteins often require a transmembrane domain of moderate hydrophobicity to maintain their endoplasmic reticulum residence, but the suggested role of protein-lipid interactions in this phenomenon has not been established. Here, we studied the interaction of TA proteins with lipids by differential ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0508157102

    authors: Ceppi P,Colombo S,Francolini M,Raimondo F,Borgese N,Masserini M

    更新日期:2005-11-08 00:00:00

  • Dipoles localized at helix termini of proteins stabilize charges.

    abstract::The charge-stabilization effect associated with alpha-helices in proteins has been reexamined by microscopic calculations without any a priori assumptions about the dielectric constant of the protein. The calculations reproduce the observed charge stabilization effect of a helix in two well-defined test cases: a histi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.5.2026

    authors: Aqvist J,Luecke H,Quiocho FA,Warshel A

    更新日期:1991-03-01 00:00:00

  • Chromosome 14 transfer and functional studies identify a candidate tumor suppressor gene, mirror image polydactyly 1, in nasopharyngeal carcinoma.

    abstract::Chromosome 14 allelic loss is common in nasopharyngeal carcinoma (NPC) and may reflect essential tumor suppressor gene loss in tumorigenesis. An intact chromosome 14 was transferred to an NPC cell line using a microcell-mediated chromosome transfer approach. Microcell hybrids (MCHs) containing intact exogenously trans...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0900198106

    authors: Cheung AK,Lung HL,Ko JM,Cheng Y,Stanbridge EJ,Zabarovsky ER,Nicholls JM,Chua D,Tsao SW,Guan XY,Lung ML

    更新日期:2009-08-25 00:00:00

  • Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single molecules.

    abstract::We use alternating-laser excitation to achieve fluorescence-aided molecule sorting (FAMS) and enable simultaneous analysis of biomolecular structure and interactions at the level of single molecules. This was performed by labeling biomolecules with fluorophores that serve as donor-acceptor pairs for Förster resonance ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0401690101

    authors: Kapanidis AN,Lee NK,Laurence TA,Doose S,Margeat E,Weiss S

    更新日期:2004-06-15 00:00:00

  • Replication and expression of thymidine kinase and human globin genes microinjected into mouse fibroblasts.

    abstract::A mixture of two recombinant plasmids was microinjected into mouse thymidine kinase-negative fibroblasts (L cells). One plasmid contained the thymidine kinase gene of herpes simplex virus type I and the other contained the human beta globin gene. Seven fibroblast colonies arising from injected cells incubated in hypox...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.77.9.5399

    authors: Anderson WF,Killos L,Sanders-Haigh L,Kretschmer PJ,Diacumakos EG

    更新日期:1980-09-01 00:00:00

  • Nicotinic cholinergic signaling in hippocampal astrocytes involves calcium-induced calcium release from intracellular stores.

    abstract::In this report we provide evidence that neuronal nicotinic acetylcholine receptors (nAChRs) are present on hippocampal astrocytes and their activation produces rapid currents and calcium transients. Our data indicate that these responses obtained from astrocytes are primarily mediated by an AChR subtype that is functi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.071540198

    authors: Sharma G,Vijayaraghavan S

    更新日期:2001-03-27 00:00:00

  • Equilibrium phase diagram of a randomly pinned glass-former.

    abstract::We use computer simulations to study the thermodynamic properties of a glass-former in which a fraction c of the particles has been permanently frozen. By thermodynamic integration, we determine the Kauzmann, or ideal glass transition, temperature [Formula: see text] at which the configurational entropy vanishes. This...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1500730112

    authors: Ozawa M,Kob W,Ikeda A,Miyazaki K

    更新日期:2015-06-02 00:00:00

  • Quantitative noise analysis for gene expression microarray experiments.

    abstract::A major challenge in DNA microarray analysis is to effectively dissociate actual gene expression values from experimental noise. We report here a detailed noise analysis for oligonuleotide-based microarray experiments involving reverse transcription, generation of labeled cRNA (target) through in vitro transcription, ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.222164199

    authors: Tu Y,Stolovitzky G,Klein U

    更新日期:2002-10-29 00:00:00

  • Sequential activation of the three protomers in the Moloney murine leukemia virus Env.

    abstract::Viral membrane fusion proteins of class I are trimers in which the protomeric unit is a complex of a surface subunit (SU) and a fusion active transmembrane subunit (TM). Here we have studied how the protomeric units of Moloney murine leukemia virus envelope protein (Env) are activated in relation to each other, sequen...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1617264114

    authors: Sjöberg M,Löving R,Lindqvist B,Garoff H

    更新日期:2017-03-07 00:00:00

  • Inhibition of N-methyl-N-nitrosourea-induced mutagenicity and DNA methylation by ellagic acid.

    abstract::Ellagic acid, a naturally occurring plant phenol, inhibits the activity of the direct-acting mutagen N-methyl-N-nitrosourea (MeNU) in Salmonella typhimurium TA100. Ellagic acid at 0.10, 0.25, 0.50, and 1.00 mM inhibited the mutagenicity of MeNU (0.40 mM) by 3%, 13%, 45%, and 60%, respectively. Ellagic acid (3 mM) also...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.83.21.8039

    authors: Dixit R,Gold B

    更新日期:1986-11-01 00:00:00

  • Subunit interactions change the heme active-site geometry in p-cresol methylhydroxylase.

    abstract::The enzyme p-cresol methylhydroxylase [4-cresol: (acceptor) oxidoreductase (methyl-hydroxylating), EC 1.17.99.1] contains two subunits: a cytochrome c (electron transfer) subunit (cytochrome cpc) and a flavin (catalytic) subunit. When these subunits are separated by isoelectric focusing, a stable cytochrome subunit is...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.21.9463

    authors: McLendon GL,Bagby S,Charman JA,Driscoll PC,McIntire WS,Mathews FS,Hill HA

    更新日期:1991-11-01 00:00:00

  • Crystal structure of an RNA.DNA hybrid reveals intermolecular intercalation: dimer formation by base-pair swapping.

    abstract::An intermolecular intercalation of base pairs was found at the CA step in the I222 crystal structure of the RNA.DNA hybrid, r(CAAAGAAAAG).d(CTTTTCTTTG), which contains two-thirds of the polypurine tract sequence of HIV-1 with a substitution of cytosine for the initial adenine. This sequence crystallized in both P21212...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1533326100

    authors: Han GW,Kopka ML,Langs D,Sawaya MR,Dickerson RE

    更新日期:2003-08-05 00:00:00

  • A channeled tRNA cycle during mammalian protein synthesis.

    abstract::In earlier studies it was shown that the mammalian translation system is highly organized in vivo and that the intermediates in the process, aminoacyl-tRNAs, are channeled--i.e., they are directly transferred from the aminoacyl-tRNA synthetases to the elongation factor to the ribosomes without dissociating into the ce...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.92.16.7158

    authors: Stapulionis R,Deutscher MP

    更新日期:1995-08-01 00:00:00

  • A ribosome-dependent GTPase from yeast distinct from elongation factor 2.

    abstract::Three proteins required for poly(U)-directed polyphenylalanine synthesis have been separated from yeast. Two of the factors correspond to the elongation factors 1 and 2 described for other eukaryotic systems, according to the criteria of phenylalanyl-tRNA binding and diphtheria toxin-catalyzed ADP-ribosylation. The th...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.73.1.73

    authors: Skogerson L,Wakatama E

    更新日期:1976-01-01 00:00:00

  • Echolocating bats accumulate information from acoustic snapshots to predict auditory object motion.

    abstract::Unlike other predators that use vision as their primary sensory system, bats compute the three-dimensional (3D) position of flying insects from discrete echo snapshots, which raises questions about the strategies they employ to track and intercept erratically moving prey from interrupted sensory information. Here, we ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2011719117

    authors: Salles A,Diebold CA,Moss CF

    更新日期:2020-11-17 00:00:00

  • Matrix mechanics controls FHL2 movement to the nucleus to activate p21 expression.

    abstract::Substrate rigidity affects many physiological processes through mechanochemical signals from focal adhesion (FA) complexes that subsequently modulate gene expression. We find that shuttling of the LIM domain (domain discovered in the proteins, Lin11, Isl-1, and Mec-3) protein four-and-a-half LIM domains 2 (FHL2) betwe...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1608210113

    authors: Nakazawa N,Sathe AR,Shivashankar GV,Sheetz MP

    更新日期:2016-11-01 00:00:00

  • Induction of erythroid differentiation and modulation of gene expression by tiazofurin in K-562 leukemia cells.

    abstract::Tiazofurin (2-beta-D-ribofuranosyl-4-thiazole-carboxamide; NSC 286193), an antitumor carbon-linked nucleoside that inhibits IMP dehydrogenase (IMP:NAD+ oxidoreductase; EC 1.1.1.205) and depletes guanylate levels, can activate the erythroid differentiation program of K-562 human leukemia cells. Tiazofurin-mediated cell...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.85.17.6533

    authors: Olah E,Natsumeda Y,Ikegami T,Kote Z,Horanyi M,Szelenyi J,Paulik E,Kremmer T,Hollan SR,Sugar J

    更新日期:1988-09-01 00:00:00

  • Influence of paced maternal breathing on fetal-maternal heart rate coordination.

    abstract::Pregnant mothers often report a special awareness of and bonding with their unborn child. Little is known about this relationship although it may offer potential for the assessment of the fetal condition. Recently we found evidence of short epochs of fetal-maternal heart rate synchronization under uncontrolled conditi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0901049106

    authors: Van Leeuwen P,Geue D,Thiel M,Cysarz D,Lange S,Romano MC,Wessel N,Kurths J,Grönemeyer DH

    更新日期:2009-08-18 00:00:00

  • Transcription of the white locus in Drosophila melanogaster.

    abstract::Genetic studies of the white locus have shown that it has a distal region where structural mutations occur and a proximal region where regulatory mutations occur. To better understand the molecular basis of this genetic organization we have analyzed white locus transcription. A 2.7-kilobase transcript comprising 0.000...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.80.22.6917

    authors: O'hare K,Levis R,Rubin GM

    更新日期:1983-11-01 00:00:00

  • Structural evidence that human liver and placental alkaline phosphatase isoenzymes are coded by different genes.

    abstract::Human liver alkaline phosphatase [ortho-phosphoric monoester phosphohydrolase (alkaline optimum), EC 3.1.3.1] was purified, and some of its physical and chemical properties were examined and compared to those of human placental alkaline phosphatase. The results indicated a different peptide structure for each, based u...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.73.7.2201

    authors: Badger KS,Sussman HH

    更新日期:1976-07-01 00:00:00

  • Human cytomegalovirus in a SCID-hu mouse: thymic epithelial cells are prominent targets of viral replication.

    abstract::Animal models of human cytomegalovirus (CMV) infections have not been available to study pathogenesis or to evaluate antiviral drugs. Severe combined immunodeficient mice implanted with human fetal tissues (SCID-hu) were found to support CMV replication and may provide a model for this species-specific virus. When con...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.90.1.104

    authors: Mocarski ES,Bonyhadi M,Salimi S,McCune JM,Kaneshima H

    更新日期:1993-01-01 00:00:00