Orthogonal regulation of DNA nanostructure self-assembly and disassembly using antibodies.

Abstract:

:Here we report a rational strategy to orthogonally control assembly and disassembly of DNA-based nanostructures using specific IgG antibodies as molecular inputs. We first demonstrate that the binding of a specific antibody to a pair of antigen-conjugated split DNA input-strands induces their co-localization and reconstitution into a functional unit that is able to initiate a toehold strand displacement reaction. The effect is rapid and specific and can be extended to different antibodies with the expedient of changing the recognition elements attached to the two split DNA input-strands. Such an antibody-regulated DNA-based circuit has then been employed to control the assembly and disassembly of DNA tubular structures using specific antibodies as inputs. For example, we demonstrate that we can induce self-assembly and disassembly of two distinct DNA tubular structures by using DNA circuits controlled by two different IgG antibodies (anti-Dig and anti-DNP antibodies) in the same solution in an orthogonal way.

journal_name

Nat Commun

journal_title

Nature communications

authors

Ranallo S,Sorrentino D,Ricci F

doi

10.1038/s41467-019-13104-6

subject

Has Abstract

pub_date

2019-12-03 00:00:00

pages

5509

issue

1

issn

2041-1723

pii

10.1038/s41467-019-13104-6

journal_volume

10

pub_type

杂志文章
  • TruePrime is a novel method for whole-genome amplification from single cells based on TthPrimPol.

    abstract::Sequencing of a single-cell genome requires DNA amplification, a process prone to introducing bias and errors into the amplified genome. Here we introduce a novel multiple displacement amplification (MDA) method based on the unique DNA primase features of Thermus thermophilus (Tth) PrimPol. TthPrimPol displays a poten...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms13296

    authors: Picher ÁJ,Budeus B,Wafzig O,Krüger C,García-Gómez S,Martínez-Jiménez MI,Díaz-Talavera A,Weber D,Blanco L,Schneider A

    更新日期:2016-11-29 00:00:00

  • Disinhibition of olfactory bulb granule cells accelerates odour discrimination in mice.

    abstract::Granule cells are the dominant cell type of the olfactory bulb inhibiting mitral and tufted cells via dendrodendritic synapses; yet the factors regulating the strength of their inhibitory output, and, therefore, their impact on odour discrimination, remain unknown. Here we show that GABAAR β3-subunits are distributed ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms9950

    authors: Nunes D,Kuner T

    更新日期:2015-11-23 00:00:00

  • Oscillatory surface rheotaxis of swimming E. coli bacteria.

    abstract::Bacterial contamination of biological channels, catheters or water resources is a major threat to public health, which can be amplified by the ability of bacteria to swim upstream. The mechanisms of this 'rheotaxis', the reorientation with respect to flow gradients, are still poorly understood. Here, we follow individ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-11360-0

    authors: Mathijssen AJTM,Figueroa-Morales N,Junot G,Clément É,Lindner A,Zöttl A

    更新日期:2019-07-31 00:00:00

  • Emergent honeycomb network of topological excitations in correlated charge density wave.

    abstract::When two periodic potentials compete in materials, one may adopt the other, which straightforwardly generates topological defects. Of particular interest are domain walls in charge-, dipole-, and spin-ordered systems, which govern macroscopic properties and important functionality. However, detailed atomic and electro...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-11981-5

    authors: Park JW,Cho GY,Lee J,Yeom HW

    更新日期:2019-09-06 00:00:00

  • Replication of flexible polymer membranes with geometry-controllable nano-apertures via a hierarchical mould-based dewetting.

    abstract::Membranes with nano-apertures are versatile templates that possess a wide range of electronic, optical and biomedical applications. However, such membranes have been limited to silicon-based inorganic materials to utilize standard semiconductor processes. Here we report a new type of flexible and free-standing polymer...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms4137

    authors: Cho H,Kim J,Park H,Won Bang J,Seop Hyun M,Bae Y,Ha L,Yoon Kim D,Min Kang S,Jung Park T,Seo S,Choi M,Suh KY

    更新日期:2014-01-01 00:00:00

  • Genomic release-recapture experiment in the wild reveals within-generation polygenic selection in stickleback fish.

    abstract::How rapidly natural selection sorts genome-wide standing genetic variation during adaptation remains largely unstudied experimentally. Here, we present a genomic release-recapture experiment using paired threespine stickleback fish populations adapted to selectively different lake and stream habitats. First, we use po...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-15657-3

    authors: Laurentino TG,Moser D,Roesti M,Ammann M,Frey A,Ronco F,Kueng B,Berner D

    更新日期:2020-04-21 00:00:00

  • Decoding individual identity from brain activity elicited in imagining common experiences.

    abstract::Everyone experiences common events differently. This leads to personal memories that presumably provide neural signatures of individual identity when events are reimagined. We present initial evidence that these signatures can be read from brain activity. To do this, we progress beyond previous work that has deployed ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-19630-y

    authors: Anderson AJ,McDermott K,Rooks B,Heffner KL,Dodell-Feder D,Lin FV

    更新日期:2020-11-20 00:00:00

  • Role of T-cell reconstitution in HIV-1 antiretroviral therapy-induced bone loss.

    abstract::HIV infection causes bone loss. We previously reported that immunosuppression-mediated B-cell production of receptor activator of NF-κB ligand (RANKL) coupled with decline in osteoprotegerin correlate with decreased bone mineral density (BMD) in untreated HIV infection. Paradoxically, antiretroviral therapy (ART) wors...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms9282

    authors: Ofotokun I,Titanji K,Vikulina T,Roser-Page S,Yamaguchi M,Zayzafoon M,Williams IR,Weitzmann MN

    更新日期:2015-09-22 00:00:00

  • A freshwater predator hit twice by the effects of warming across trophic levels.

    abstract::Many ecological responses to climate change have been documented. However, due to indirect effects, some responses can be complex and difficult to predict. For example, our understanding of effects on consumers involving responses on several trophic levels is limited. Here, combining the knowledge of trophic interacti...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms6992

    authors: Jonsson T,Setzer M

    更新日期:2015-01-14 00:00:00

  • Sperm-inherited H3K27me3 impacts offspring transcription and development in C. elegans.

    abstract::Paternal epigenetic inheritance is gaining attention for its growing medical relevance. However, the form in which paternal epigenetic information is transmitted to offspring and how it influences offspring development remain poorly understood. Here we show that in C. elegans, sperm-inherited chromatin states transmit...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-09141-w

    authors: Kaneshiro KR,Rechtsteiner A,Strome S

    更新日期:2019-03-20 00:00:00

  • A light-driven three-dimensional plasmonic nanosystem that translates molecular motion into reversible chiroptical function.

    abstract::Nature has developed striking light-powered proteins such as bacteriorhodopsin, which can convert light energy into conformational changes for biological functions. Such natural machines are a great source of inspiration for creation of their synthetic analogues. However, synthetic molecular machines typically operate...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms10591

    authors: Kuzyk A,Yang Y,Duan X,Stoll S,Govorov AO,Sugiyama H,Endo M,Liu N

    更新日期:2016-02-02 00:00:00

  • Artemisinin kills malaria parasites by damaging proteins and inhibiting the proteasome.

    abstract::Artemisinin and its derivatives (collectively referred to as ARTs) rapidly reduce the parasite burden in Plasmodium falciparum infections, and antimalarial control is highly dependent on ART combination therapies (ACTs). Decreased sensitivity to ARTs is emerging, making it critically important to understand the mechan...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-06221-1

    authors: Bridgford JL,Xie SC,Cobbold SA,Pasaje CFA,Herrmann S,Yang T,Gillett DL,Dick LR,Ralph SA,Dogovski C,Spillman NJ,Tilley L

    更新日期:2018-09-18 00:00:00

  • Dilution effect of the building area on energy intensity in urban residential buildings.

    abstract::Urban residential buildings make large contributions to energy consumption. Energy consumption per square meter is most widely used to measure energy efficiency in urban residential buildings. This study aims to explore whether it is an appropriate indicator. An extended STIRPAT model was used based on the survey data...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-12852-9

    authors: Gao J,Zhong X,Cai W,Ren H,Huo T,Wang X,Mi Z

    更新日期:2019-10-30 00:00:00

  • Probing biomechanical properties with a centrifugal force quartz crystal microbalance.

    abstract::Application of force on biomolecules has been instrumental in understanding biofunctional behaviour from single molecules to complex collections of cells. Current approaches, for example, those based on atomic force microscopy or magnetic or optical tweezers, are powerful but limited in their applicability as integrat...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms6284

    authors: Webster A,Vollmer F,Sato Y

    更新日期:2014-10-21 00:00:00

  • PAK proteins and YAP-1 signalling downstream of integrin beta-1 in myofibroblasts promote liver fibrosis.

    abstract::Fibrosis due to extracellular matrix (ECM) secretion from myofibroblasts complicates many chronic liver diseases causing scarring and organ failure. Integrin-dependent interaction with scar ECM promotes pro-fibrotic features. However, the pathological intracellular mechanism in liver myofibroblasts is not completely u...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12502

    authors: Martin K,Pritchett J,Llewellyn J,Mullan AF,Athwal VS,Dobie R,Harvey E,Zeef L,Farrow S,Streuli C,Henderson NC,Friedman SL,Hanley NA,Piper Hanley K

    更新日期:2016-08-18 00:00:00

  • Systemic nanoparticle delivery of CRISPR-Cas9 ribonucleoproteins for effective tissue specific genome editing.

    abstract::CRISPR-Cas9 has emerged as a powerful technology that relies on Cas9/sgRNA ribonucleoprotein complexes (RNPs) to target and edit DNA. However, many therapeutic targets cannot currently be accessed due to the lack of carriers that can deliver RNPs systemically. Here, we report a generalizable methodology that allows en...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-17029-3

    authors: Wei T,Cheng Q,Min YL,Olson EN,Siegwart DJ

    更新日期:2020-06-26 00:00:00

  • Ammonia as a case study for the spontaneous ionization of a simple hydrogen-bonded compound.

    abstract::Modern ab initio calculations predict ionic and superionic states in highly compressed water and ammonia. The prediction apparently contradicts state-of-the-art experimentally established phase diagrams overwhelmingly dominated by molecular phases. Here we present experimental evidence that the threshold pressure of ~...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms4460

    authors: Palasyuk T,Troyan I,Eremets M,Drozd V,Medvedev S,Zaleski-Ejgierd P,Magos-Palasyuk E,Wang H,Bonev SA,Dudenko D,Naumov P

    更新日期:2014-03-24 00:00:00

  • A hepatic amino acid/mTOR/S6K-dependent signalling pathway modulates systemic lipid metabolism via neuronal signals.

    abstract::Metabolism is coordinated among tissues and organs via neuronal signals. Levels of circulating amino acids (AAs), which are elevated in obesity, activate the intracellular target of rapamycin complex-1 (mTORC1)/S6kinase (S6K) pathway in the liver. Here we demonstrate that hepatic AA/mTORC1/S6K signalling modulates sys...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms8940

    authors: Uno K,Yamada T,Ishigaki Y,Imai J,Hasegawa Y,Sawada S,Kaneko K,Ono H,Asano T,Oka Y,Katagiri H

    更新日期:2015-08-13 00:00:00

  • A synthetic microbial biosensor for high-throughput screening of lactam biocatalysts.

    abstract::Biocatalytic cyclization is highly desirable for efficient synthesis of biologically derived chemical substances, such as the commodity chemicals ε-caprolactam and δ-valerolactam. To identify biocatalysts in lactam biosynthesis, we develop a caprolactam-detecting genetic enzyme screening system (CL-GESS). The Alcalige...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-07488-0

    authors: Yeom SJ,Kim M,Kwon KK,Fu Y,Rha E,Park SH,Lee H,Kim H,Lee DH,Kim DM,Lee SG

    更新日期:2018-11-29 00:00:00

  • Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy.

    abstract::Theory, simulations and experimental results have suggested an important role of internal friction in the kinetics of protein folding. Recent experiments on spectrin domains provided the first evidence for a pronounced contribution of internal friction in proteins that fold on the millisecond timescale. However, it ha...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2204

    authors: Borgia A,Wensley BG,Soranno A,Nettels D,Borgia MB,Hoffmann A,Pfeil SH,Lipman EA,Clarke J,Schuler B

    更新日期:2012-01-01 00:00:00

  • The landscape of chromothripsis across adult cancer types.

    abstract::Chromothripsis is a recently identified mutational phenomenon, by which a presumably single catastrophic event generates extensive genomic rearrangements of one or a few chromosome(s). Considered as an early event in tumour development, this form of genome instability plays a prominent role in tumour onset. Chromothri...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-16134-7

    authors: Voronina N,Wong JKL,Hübschmann D,Hlevnjak M,Uhrig S,Heilig CE,Horak P,Kreutzfeldt S,Mock A,Stenzinger A,Hutter B,Fröhlich M,Brors B,Jahn A,Klink B,Gieldon L,Sieverling L,Feuerbach L,Chudasama P,Beck K,Kroiss M,H

    更新日期:2020-05-08 00:00:00

  • An electrostatic mechanism for Ca(2+)-mediated regulation of gap junction channels.

    abstract::Gap junction channels mediate intercellular signalling that is crucial in tissue development, homeostasis and pathologic states such as cardiac arrhythmias, cancer and trauma. To explore the mechanism by which Ca(2+) blocks intercellular communication during tissue injury, we determined the X-ray crystal structures of...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms9770

    authors: Bennett BC,Purdy MD,Baker KA,Acharya C,McIntire WE,Stevens RC,Zhang Q,Harris AL,Abagyan R,Yeager M

    更新日期:2016-01-12 00:00:00

  • Osteoclast-derived exosomal miR-214-3p inhibits osteoblastic bone formation.

    abstract::Emerging evidence indicates that osteoclasts direct osteoblastic bone formation. MicroRNAs (miRNAs) have a crucial role in regulating osteoclast and osteoblast function. However, whether miRNAs mediate osteoclast-directed osteoblastic bone formation is mostly unknown. Here, we show that increased osteoclastic miR-214-...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms10872

    authors: Li D,Liu J,Guo B,Liang C,Dang L,Lu C,He X,Cheung HY,Xu L,Lu C,He B,Liu B,Shaikh AB,Li F,Wang L,Yang Z,Au DW,Peng S,Zhang Z,Zhang BT,Pan X,Qian A,Shang P,Xiao L,Jiang B,Wong CK,Xu J,Bian Z,Liang Z,

    更新日期:2016-03-07 00:00:00

  • Prevailing oxic environments in the Pacific Ocean during the mid-Cretaceous Oceanic anoxic event 2.

    abstract::The occurrence of Oceanic Anoxic Event 2 (OAE2) 94 million years ago is considered to be one of the largest carbon cycle perturbations in the Earth's history. The marked increase in the spatial extent of the anoxic conditions in the world's oceans associated with OAE2 resulted in the mass accumulation of organic-rich ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms1233

    authors: Takashima R,Nishi H,Yamanaka T,Tomosugi T,Fernando AG,Tanabe K,Moriya K,Kawabe F,Hayashi K

    更新日期:2011-01-01 00:00:00

  • A mouse model of adult-onset anaemia due to erythropoietin deficiency.

    abstract::Erythropoietin regulates erythropoiesis in a hypoxia-inducible manner. Here we generate inherited super-anaemic mice (ISAM) as a mouse model of adult-onset anaemia caused by erythropoietin deficiency. ISAM express erythropoietin in the liver but lack erythropoietin production in the kidney. Around weaning age, when th...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2950

    authors: Yamazaki S,Souma T,Hirano I,Pan X,Minegishi N,Suzuki N,Yamamoto M

    更新日期:2013-01-01 00:00:00

  • Terahertz spectroscopy on Faraday and Kerr rotations in a quantum anomalous Hall state.

    abstract::Electrodynamic responses from three-dimensional topological insulators are characterized by the universal magnetoelectric term constituent of the Lagrangian formalism. The quantized magnetoelectric coupling, which is generally referred to as topological magnetoelectric effect, has been predicted to induce exotic pheno...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12245

    authors: Okada KN,Takahashi Y,Mogi M,Yoshimi R,Tsukazaki A,Takahashi KS,Ogawa N,Kawasaki M,Tokura Y

    更新日期:2016-07-20 00:00:00

  • Photocathode functionalized with a molecular cobalt catalyst for selective carbon dioxide reduction in water.

    abstract::Artificial photosynthesis is a vibrant field of research aiming at converting abundant, low energy molecules such as water, nitrogen or carbon dioxide into fuels or useful chemicals by means of solar energy input. Photo-electrochemical reduction of carbon dioxide is an appealing strategy, aiming at reducing the greenh...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-17125-4

    authors: Pati PB,Wang R,Boutin E,Diring S,Jobic S,Barreau N,Odobel F,Robert M

    更新日期:2020-07-13 00:00:00

  • Semaphorin 4C Plexin-B2 signaling in peripheral sensory neurons is pronociceptive in a model of inflammatory pain.

    abstract::Semaphorins and their transmembrane receptors, Plexins, are key regulators of axon guidance and development of neuronal connectivity. B-type Plexins respond to Class IV semaphorins and mediate a variety of developmental functions. Here we report that the expression of Plexin-B2 and its high-affinity ligand, Sema4C, pe...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00341-w

    authors: Paldy E,Simonetti M,Worzfeld T,Bali KK,Vicuña L,Offermanns S,Kuner R

    更新日期:2017-08-02 00:00:00

  • MreB polymers and curvature localization are enhanced by RodZ and predict E. coli's cylindrical uniformity.

    abstract::The actin-like protein MreB has been proposed to coordinate the synthesis of the cell wall to determine cell shape in bacteria. MreB is preferentially localized to areas of the cell with specific curved geometries, avoiding the cell poles. It remains unclear whether MreB's curvature preference is regulated by addition...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-05186-5

    authors: Bratton BP,Shaevitz JW,Gitai Z,Morgenstein RM

    更新日期:2018-07-18 00:00:00

  • Evolutionary signals of selection on cognition from the great tit genome and methylome.

    abstract::For over 50 years, the great tit (Parus major) has been a model species for research in evolutionary, ecological and behavioural research; in particular, learning and cognition have been intensively studied. Here, to provide further insight into the molecular mechanisms behind these important traits, we de novo assemb...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms10474

    authors: Laine VN,Gossmann TI,Schachtschneider KM,Garroway CJ,Madsen O,Verhoeven KJ,de Jager V,Megens HJ,Warren WC,Minx P,Crooijmans RP,Corcoran P,Great Tit HapMap Consortium.,Sheldon BC,Slate J,Zeng K,van Oers K,Visser ME,Gro

    更新日期:2016-01-25 00:00:00