Small molecule-triggered assembly of DNA nanoarchitectures

Wieland, Markus; Benz, Armin; Haar, Janina; Halder, Kangkan; Hartig, Jörg S.

doi:10.1039/b921481j

Cited by 36 publications

(25 citation statements)

References 29 publications

(37 reference statements)

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“…By taking advantage of the high versatility and designability of DNA chemistry [9][10][11][12][13][14][15][16][17][18][19] several groups have recently developed pH-triggered DNA-based probes or nanomachines [20][21][22][23][24][25][26][27][28][29][30] . Such probes typically exploit DNA secondary structures that display pH-dependence due to the presence of specific protonation sites.…”

Section: Introductionmentioning

confidence: 99%

Programmable pH-Triggered DNA Nanoswitches

2014

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ABSTRACT:Here we have rationally designed a tunable DNA-based nanoswitch whose closing/opening can be triggered over specific different pH windows. This nanoswitch forms an intramolecular triplex DNA structure through pH-sensitive parallel Hoogsteen interactions. We demonstrate that by simply changing the relative content of TAT/CGC triplets in the switch we can rationally tune its pH-dependence over more than 5 pH units. By using a combination of such nanowitches with different pH sensitivity, we also demonstrate how we can engineer a pH nanosensor that can precisely monitor pH variations over 5.5 units of pH. With their fast response time (<200 msec) and high reversibility, these pH-triggered nanoswitches appear particularly suitable for applications ranging from the real-time monitoring of pH changes in-vivo to the development of pH sensitive smart nanomaterial.Nature often employs finely pH-regulated biomolecules to modulate and tune a number of biological activities 1 ranging from enzyme catalysis 2 to protein folding 3 , membrane function 4 and apoptosis 5 . For these reasons, developing probes, switches or nanomaterials that are able to respond to specific pH changes should prove of utility for several applications in the fields of in-vivo imaging, clinical diagnostics, and drug-delivery [6][7][8] .By taking advantage of the high versatility and designability of DNA chemistry 9-19 several groups have recently developed pH-triggered DNA-based probes or nanomachines [20][21][22][23][24][25][26][27][28][29][30] . Such probes typically exploit DNA secondary structures that display pH-dependence due to the presence of specific protonation sites. These structures include I-motif [21][22][23]26,29,31 , intermolecular triplex DNA 25,28,32 , DNA tweezers 20 and, more recently, the Amotif 33 . Despite the promising and advantageous characteristics of some of these DNA-based nanomachines, which include fast response times and sustained efficiency over several cycles, a drawback inevitably affects their performances: they all respond (with an exception 33a ) over a fixed pH window that typically spans 1.5 to 2 pH units 26,34,33b . These nanomachines, therefore, cannot be adapted to provide a useful output outside these fixed pH-windows.Here we describe a method to rationally design and program pH-triggered DNA-based nanoswitches whose pH-dependence can be finely tuned and modulated over more than 5 units of pH. We created our switches by taking advantage of the wellcharacterized pH sensitivity of the parallel Hoogsteen (T,C)-motif in triplex DNA [34][35][36] . To do so we have designed a DNAbased triplex pH-triggered nanoswitch that consists in a double intramolecular hairpin stabilized with both Watson-Crick (W-C) and parallel Hoogsteen interactions (Fig. 1). More specifically, one hairpin of the triplex nanoswitch is formed by the W-C hybridization of two 10-base complementary portions separated by a 5 base loop. This duplex DNA is then able to form a triplex structure via the formation of a second hairpin through...

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Section: Introductionmentioning

confidence: 99%

Programmable pH-Triggered DNA Nanoswitches

2014

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“…DNA circuits have been integrated to form complex Boolean networks (1) and molecular neural networks (2). Such programmed circuits have begun to have applications in ordered chemical synthesis (3,4), multiplexed labeling of biomolecules for fluorescent microscopy (5,6), and detection of both nucleic acid and nonnucleic acid analytes (7)(8)(9). The combination of DNA circuitry and DNA nanotechnology (10,11) has given rise to DNA robotics (12) and assembly lines (13).…”

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confidence: 99%

Stacking nonenzymatic circuits for high signal gain

Chen

Briggs

McLain

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

223

217

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Signal amplification schemes that do not rely on protein enzymes show great potential in areas as abstruse as DNA computation and as applied as point-of-care molecular diagnostics. Toeholdmediated strand displacement, a programmable form of dynamic DNA hybridization, can be used to design powerful amplification cascades that can achieve polynomial or exponential amplification of input signals. However, experimental implementation of such amplification cascades has been severely hindered by circuit leakage due to catalyst-independent side reactions. In this study, we systematically analyzed the origins, characteristics, and outcomes of circuit leakage in amplification cascades and devised unique methods to obtain high-quality DNA circuits that exhibit minimal leakage. We successfully implemented a two-layer cascade that yielded 7,000-fold signal amplification and a two-stage, four-layer cascade that yielded upward of 600,000-fold signal amplification. Implementation of these unique methods and design principles should greatly empower molecular programming in general and DNA-based molecular diagnostics in particular.amplifier | enzyme-free | DNA circuitry S ignal amplification is a ubiquitous theme in biology and engineering, and the ability to amplify signals at the molecular level in large measure determines the complexity and robustness of the molecular devices and systems that can be built. Over the past decade, DNA has been established as the ultimate "intelligent material" to build complex structures, circuits, and devices. DNA circuits have been integrated to form complex Boolean networks (1) and molecular neural networks (2). Such programmed circuits have begun to have applications in ordered chemical synthesis (3, 4), multiplexed labeling of biomolecules for fluorescent microscopy (5, 6), and detection of both nucleic acid and nonnucleic acid analytes (7-9). The combination of DNA circuitry and DNA nanotechnology (10, 11) has given rise to DNA robotics (12) and assembly lines (13).The signal amplifiers underlying many of these advances are metastable DNA substrates whose conformational transformations can be catalytically triggered by strand displacement. The first amplifier of this class was designed by Turberfield et al. (14) and was later modified by Seelig et al. by using metastable kissingloop structures (15). Since then, many hybridization-based catalytic systems have been developed, including ones based on topologically constrained interactions (16), entropy-driven strand exchange (17), and catalyzed hairpin assembly (CHA) (18). Some of these schemes allow cascading of catalysis wherein the product of one reaction serves as the catalyst of another reaction. Autocatalytic reactions (17, 19) and cross-catalytic reactions (18) may also be constructed and programmed. Such molecular amplifiers can guard against signal damping during serial signal transductions in nucleic acid circuits and are easily adapted to the integration of logical operations (20).Whereas the outcome of these amplifiers, the ampl...

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“…We have described a thermodynamically-based reaction design framework to approximate first phase output, as well as to tune the reaction acceleration in the switch-like second reaction phase. The reaction can report on a variety of analytes: specific proteins 8,[23][24][25][26] , genomic bacterial DNA 10 , viral DNA 27 , microRNA 28 , or mRNA 9 can continuously create input trigger oligonucleotides, making the biphasic DNA amplification reaction broadly applicable to a variety of target molecules. When combined with single molecule amplification, this technique has the potential to be quantitative through digital amplification and detection 42 .…”

Section: Discussionmentioning

confidence: 99%

“…Additionally, reaction design using controlled DNA association thermodynamics give some control over first phase kinetics. Proteins 8,[23][24][25][26] , genomic bacterial DNA 10 , viral DNA 27 , microRNA 28 , or mRNA 9 can be transduced into many oligonucleotide triggers, making this technique applicable to a broad range of biological sensors.…”

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confidence: 99%

First Characterization of a Biphasic, Switch-like DNA Amplification

Özay

Robertus

Negri

et al. 2017

Preprint

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We report the first DNA amplification chemistry with switch-like characteristics: the chemistry is biphasic, with an expected initial phase followed by an unprecedented high gain burst of product oligonucleotide in a second phase. The first and second phases are separated by a temporary plateau, with the second phase producing 10 to 100 times more product than the first. The reaction is initiated when an oligonucleotide binds and opens a palindromic looped DNA template with two binding domains. Upon loop opening, the oligonucleotide trigger is rapidly amplified through cyclic extension and nicking of the bound trigger. Loop opening and DNA association drive the amplification reaction, such that reaction acceleration in the second phase is correlated with DNA association thermodynamics. Without a palindromic sequence, the chemistry resembles the exponential amplification reaction (EXPAR). EXPAR terminates at the initial plateau, revealing a previously unknown phenomenon that causes early reaction cessation in this popular oligonucleotide amplification reaction. Here we present two distinct types of this biphasic reaction chemistry and propose dominant reaction pathways for each type based on thermodynamic arguments. These reactions create an endogenous switch-like output that reacts to approximately 1pM oligonucleotide trigger. The chemistry is isothermal and can be adapted to respond to a broad range of input target molecules such as proteins, genomic bacterial DNA, viral DNA, and microRNA. This rapid DNA amplification reaction could potentially impact a variety of disciplines such as synthetic biology, biosensors, DNA computing, and clinical diagnostics.

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Small molecule-triggered assembly of DNA nanoarchitectures

Abstract: The utilization of toehold-containing DNA strands allows for the assembly of complex nanostructures via kinetically driven hybridization reactions. Here, we have rendered this strategy ligand-dependent, resulting in small-molecule-inducible DNA nanoarchitectures.

Cited by 36 publications

References 29 publications

Programmable pH-Triggered DNA Nanoswitches

Programmable pH-Triggered DNA Nanoswitches

Stacking nonenzymatic circuits for high signal gain

First Characterization of a Biphasic, Switch-like DNA Amplification

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