Abstract
Nucleic acids have been shown to be versatile molecules and engineered to produce various nanostructures. However, the poor rate of these uncatalyzed nucleic acid reactions has restricted the development and applications. Herein, we reported a novel finding that DNA self-assembly could be nonenzymatically catalyzed by artificial agents with an increasing dissociation rate constant K2. The catalytic role of several artificial agents in DNA self-assembly was verified by real-time fluorescent detection or agarose gel electrophoresis. We found that 20% PEG 200 could significantly catalyze DNA self-assembly and increase the reaction efficiency, such as linear hybridization chain reaction (HCR) and exponential hairpin assembly (EHA). Therefore, we foresee that a fast and efficient DNA self-assembly in structural DNA nanotechnology will be desirable.
Highlights
Nucleic acids have been employed as an intelligent material for engineering molecular devices[1, 2], walkers[3, 4], DNA circuits[5, 6], DNA origami[7, 8] and amplifiers[9, 10], which have attracted more and more interest among researchers
Dithiothreitol (DTT), Dimethyl sulfoxide (DMSO), Polyethylene glycol (PEG) 200, PEG 600, PEG 2000 and PEG 6000 were purchased from Aladdin Industrial Corporation (Shanghai, China). 20 × Eva Green was purchased from Bridgen (Beijing, China). 2000 bp DNA Marker and the chemicals used to prepare electrophoresis were purchased from Dalian Takara Company (China)
We conducted a systematic review of the available literature and found some substances that may accelerate DNA strand exchange and increase dissociation rate constant K218–24
Summary
Nucleic acids have been employed as an intelligent material for engineering molecular devices[1, 2], walkers[3, 4], DNA circuits[5, 6], DNA origami[7, 8] and amplifiers[9, 10], which have attracted more and more interest among researchers. The further researches showed that betaine can lower the melting template (Tm) of DNA, betaine can decrease association rate constant K1. Betaine acted as a molecular barrier to intermolecular hybridization for isothermal nucleic acid amplification, resulting in lowering the reaction efficiency[13]. Polyethylene glycol (PEG) and Cetyltrimethylammonium Bromide (CTAB) have been reported to improve the rate of DNA hybridization, so we guessed they might promote DNA self-assembly reaction[14, 15]. We inferred that those substances lowering the Tm of DNA and increasing dissociation rate constant K2 should be more beneficial to increase the dissociation degree of DNA and stimulate DNA hybridization reaction
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