Logic-Based Dual-Functional DNA Tweezers with Protein and Small Molecule as Mechanical Activators

Li, Xuemei; Li, Wei; Ge, Anqing; Chen, Hong‐Yuan

doi:10.1021/jp106174h

Cited by 15 publications

(13 citation statements)

References 34 publications

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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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“…Sensitive and selective simultaneous detection of ATP and lysozyme are very important in biomedical research and clinical diagnosis. Aptamer-based sensors have been made on multiplexed detection of ATP and lysozyme and their analogues, including electrochemistry 4 10 29 30 31 32 33 34 fluorescence 35 36 37 and surface-enhanced Raman scattering (SERS) 38 . For example, Xiang et al developed an electrochemical aptamer-based sensing platform for one-spot simultaneous determination of lysozyme and adenosine 31 .…”

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confidence: 99%

“…However, such labeling has disadvantages that the labeling process makes the experiments relatively complex and expensive and also affects the binding affinity between the targets and their aptamers to a certain degree. Chen et al developed a fluorescent probe for the detection ATP and thrombin by monitoring the fluorescent intensities with the corresponding Cy5 and TAMRA 35 . In their report, six DNA strands were designed and hybridized to form a closed state, and the aptamers were respectively immobilized on magnetic beads, however, multiple DNA strands makes the experiments complex and expensive.…”

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confidence: 99%

“Click on the bidirectional switch”: the aptasensor for simultaneous detection of lysozyme and ATP with high sensitivity and high selectivity

Chen

Cai

Chen

et al. 2016

Sci Rep

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A bifunctional and simple aptasensor was designed to one-spot simultaneously detect two analytes, lysozyme and ATP. The aptasensor was obtained by the electronic interaction between methyl violet (MV) and dsDNA. The dsDNA was obtained by hybridization of ATP aptamer and lysozyme aptamer. And we used the resonance light scattering (RLS) technique to detect the concentration of lysozyme and ATP. During the procedure of detection, the aptasensor works like a bidirectional switch, the corresponding side of the dsDNA will open when the target (lysozyme or ATP) “click” the aptamer, which results in corresponding RLS signal change. By the combination of the RLS technique, it is found that the changed RLS intensity was proportional to the concentration of lysozyme and ATP. The mixtures of ATP and lysozyme also met two binary function relations. The results indicated that the aptasensor could achieve simultaneous detection of ATP and lysozyme, the detection limits of ATP and lysozyme could reach 10−11 M and 10−12 M, respectively. The aptasensor shows potential application for small molecule and protein detection by RLS, it could extend the application of RLS technique.

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“…[8][9][10][11][12][13][14][15][16][17][18] Most DNA tweezers translate molecular recognition (typically another DNA strand) into short-range mechanical motion, resulting in a signal or function. 13,[19][20][21][22][23][24][25][26][27] Extended DNA tweezers with arms containing multiple binding sites along their lengths would be able to translate multiple guest binding events into large-scale mechanical motion, reminiscent of octopus or squid tentacles around prey. This large-scale motion may find applications in molecular robotics, biosensing schemes with amplification, and cellular probes that interrogate and influence large sections of the cell membrane.…”

Section: Introductionmentioning

confidence: 99%