New approaches in the production of error-free DNA exploit the use of self-assembly and natural error correction proteins. The enzyme is added to previously amplified PCR product, and this mixture is subjected to a second round of thermal cycling at the end of which it is put through gel electrophoresis, quantified, and cloned.
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It is, thus, most effective at removing common insertions and deletions that may occur during DNA synthesis [ 96 ]. In this case, DNA synthesis typically relies on spatial confinement of reactions to certain regions on a silica chip since this technology employs the addition of picoliters of reagents to the silica chip. Error rates can be reduced by controlling the locations on the chip where the reagents eventually end up. Another possibility could be directing reacting reagents through the use of photochemistry.
In this way, light can be used to block or restrict reactions at potential error sites. Directing redox reactions only at desirable sites in the forming DNA is another approach. All these strategies can help reduce error rates from 1 in bases to 1 in bases [ 98 ]. DNA is one for the most useful engineering materials available in nanotechnology. It has the potential for self-assembly and formation of programmable nanostructures, and it can also provide a platform for mechanical, chemical, and physical devices. While the formation of many complex nanoscale mechanisms has been perfected by nature over the course of millennia, scientists and engineers need to aggressively pursue the development of future technologies that can help expand the use of DNA in medicine, computation, material sciences, and physics.
It is imperative that nanotechnology is improved to meet the need for better detectors in the fields of biological and chemical detection and for higher sensitivity. In terms of DNA-based nanostructures, there is an urgent need to develop sophisticated architectures for diverse applications. Currently, much progress is being made in modelling DNA into various shapes through DNA origami, but the next step is to develop intelligent and refined structures that have viable physical, chemical, and biological applications.
Despite the fact that DNA computation may be in its infancy with limited forays into electronics and mathematics, future development of novel ways in which DNA would be utilized to have a much more comprehensive role in biological computation and data storage is envisaged. We are hopeful that the use of DNA molecules will eventually exceed expectations far beyond the scope of this review. His research interests are in the field of artificially designed DNA nanostructures and their applications in different fields, especially in biosensor applications, nanodevices designing and fabrication, and tissue engineering, especially in assisting burn patients.
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Biochemistry , 39 13 — Nucleic Acids Res , 26 20 — Biotechniques , 44— Methods Enzymol , — Curr Opin Chem Biol , 16 3—4 — Nat Biotechnol , 28 12 — Download references. MZ and RA gathered the research data. All authors read and approved the final manuscript. Reprints and Permissions. Search all SpringerOpen articles Search. Abstract In addition to its genetic function, DNA is one of the most distinct and smart self-assembling nanomaterials.
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The protein particles were found to predominantly exist in monomeric form, while dimeric and multimeric forms were also observed both in free solution and bound to the quadruplex structure. The formation and the dissociation events of the G-quadruplexes were well documented in real-time and the intermediate-like states were also visualized. Here, we describe the direct visualization and single-molecule analysis of the formation of a tetramolecular G-quadruplex in KCl solution. The conformational changes were carried out by incorporating two duplex DNAs, with G—G mismatch repeats in the middle, inside a DNA origami frame and monitoring the topology change of the strands.
In the absence of KCl, incorporated duplexes had no interaction and laid parallel to each other. Addition of KCl induced the formation of a G-quadruplex structure by stably binding the duplexes to each other in the middle. Such a quadruplex formation allowed the DNA synapsis without disturbing the duplex regions of the participating sequences, and resulted in an X-shaped structure that was monitored by atomic force microscopy. Further, the G-quadruplex formation in KCl solution and its disruption in KCl-free buffer were analyzed in real-time.
The orientation of the G-quadruplex is often difficult to control and investigate using traditional biochemical methods. However, our method using DNA origami could successfully control the strand orientations, topology and stoichiometry of the G-quadruplex. The B—Z DNA conformational transition requires the rotation of a double helix from a right-handed B-form to a left-handed Z-form structure. We herein designed a constrained and rotatable double-stranded DNA in which the rotational freedom was controlled by its placement into a DNA nanoscaffold. The Zab protein specifically binds to CG repeat sequences in Z-form double helices.
Related DNA Nanotechnology: From Structure to Function
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