A fluorescence assay for microRNA let-7a by a double-stranded DNA modified gold nanoparticle nanoprobe combined with graphene oxide
https://pubs.rsc.org/en/content/articlelanding/2020/an/c9an02274k/unauth#!divAbstract
The authors used a cascaded toehold-mediated strand displacement reaction as a biosensor for miRNA. This required both a fuel strand and a target strand and the target strand was recycled as part of the reaction, to amplify the signal for detection.
Orthogonal regulation of DNA nanostructure self-assembly and disassembly using antibodies
https://www.nature.com/articles/s41467-019-13104-6
Despite tremendous developments in DNA nanotechnology and antibody research, there have been very few examples of designing a DNA-based network specifically responsive to a particular biomarker. Here the researchers demonstrate the design of an antigen-conjugated split-input invader strand which increases the rate of a TMSD reaction when it binds a specific antibody. Different antibody-controlled reactions can be triggered orthogonally in a solution with several reaction components without any crosstalk. The output strands of these reactions can be specifically tuned to trigger a dynamic self-assembly of DNA tiles into a nanostructure or the disassembly of it into individual building blocks.
Availability-Driven Design of Hairpin Fuels and Small Interfering Strands for Leakage Reduction in Autocatalytic Networks
https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.0c01229
Enzymes are hard to use in detection and amplification circuits for eg. diagnostics. Nucleic acids provide an alternative, but are subject to unintended leaks in the absence of input. In this article, the authors seek to avoid leak reactions by sequestering nucleotides that are predicted - based on simple thermodynamic models - to trigger these leaks. However, success is limited because sequestering these nucleotides, if effective, also interferes with the intended reactions in the presence of a trigger.
Nicking-Assisted Reactant Recycle To Implement Entropy-Driven DNA Circuit
https://pubs.acs.org/doi/10.1021/jacs.9b07521
Molecular circuits implemented using nucleic acid nanotechnology typically produce double-stranded waste complexes when they run. In this work, the authors propose that these waste complexes can be reconverted into active reaction-ready multi-stranded "gates" through the action of a nicking enzyme that cleaves the backbone of one of the fuel strands. This approach means that, in the simplest of settings, only a supply of single-stranded molecules (rather than harder-to-produce gate complexes) is required to sustain circuit function.
Although impressive, these circuits show a fairly high level of unwanted leak reactions. Moreover, the recycling of waste does not occur indefinitely, and complex cascaded circuits cannot be produced due to sequence constraints. The article really emphasizes the need for in situ production of nucleic acid complexes.
ATP-Triggered, Allosteric Self-Assembly of DNA Nanostructures
https://pubs.acs.org/doi/10.1021/jacs.9b10272
Trigger-responsive DNA self-assembly is commonly observed in several biological processes and have potential application in sensing and smart biomaterials. In this article, the authors show the design of a double stranded DNA which, upon binding with ATP, can form T-junctions among themselves to make larger self-assembled structures. In the absence of ATP, such structures are not formed. It also demonstrated that the ATP-binding and subsequent change in the overall conformation of the DNA is the crucial part of stimulus-responsiveness.
Fluorogenic probe for fast 3D whole-cell DNA-PAINT
https://www.biorxiv.org/content/10.1101/2020.04.29.066886v1
DNA-PAINT is a super-resolution microscopy method that uses fluorophore-modified DNA labels to image some target DNA strands. However, DNA-PAINT requires a high concentration of labels, resulting in high levels of background fluorescence during the imaging. In addition, the binding speed of the labels can hinder DNA-PAINT by reducing its imaging speed. This research introduces a new type of label for DNA-PAINT. The new labels reduce its fluorescence emission in solution by attaching a dedicated quencher. Since no hairpin in the label is needed for quenching the fluorescence, the binding rate to the target is increased. The unbinding rate is increased as well by adding mismatches between target and label. The new label design results in a higher imaging speed while still producing a low background fluorescence.
Information Coding in Reconfigurable DNA Origami Domino Array
https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.202003823
DNA origami domino arrays, whose building blocks adopts two different conformations, were used to encrypt information in their 2D pattern. Additionally, strand-displacement was used to reveal overhangs with specific sequence that encodes information.
Non-enzymatic primer extension with strand displacement
https://doi.org/10.7554/eLife.51888
Non-enzymatic template copying reactions are the precursor to biological self-replication. Separating the duplex that forms between parent and daughter strands after templated copying is key to ensuring independent function of the daughter and cyclical copying of the template. Cycling environmental conditions (hydration/pH/temperature) have been posed as solutions to the duplex separation problem. However, here an RNA template is copied by primer extension and simultaneously the previous daughter (blocker) is displaced from the template by a strand invasion reaction, enabling further extension.
Here a template RNA is occupied by a partially complete primer strand and a blocker strand (equivalent to an earlier daughter) with a large free toehold. The blocker strand prevents extension of the primer by binding to the next extension site thereby occluding the template. An invader strand is introduced that binds the blocker toehold and then invades the blocker-template bond at the extension site. The strand invasion interaction opens the template which triggers the extension of the primer. Increase in primer length is confirmed by PAGE.
Artificial molecular motors
https://pubs.rsc.org/en/content/articlelanding/2017/cs/c7cs00245a#!divAbstract
Living cells use a plethora of molecular motors to carry out key biological processes. Muscle contraction, production of ATP from ADP, DNA transcription are all examples of molecular motors at different scales. Development of synthetic motors is a contemporary field of research in nanoscience with one application being drug delivery to cancer cells. Molecular switches and motors are 2 different types of molecular machines. In both these machines, a change in relative position of components with respect to each other occurs; the cycle of a motor, however, can perform work. Present research explains the physics of these molecular machines utilizing the chemistry (steric interactions, effect of pH, acidity) of chemical compounds.
This review focuses on molecular devices constructed using organic chemistry, rather than biomolecules. Research groups have been developing nanocars and are actively working on making them unidirectional. Unidirectionality in the presence of light has been shown at microscale (rotation of an alkene doped glass rod) and macroscale (droplet along a photo-responsive surface). Molecular motors have evolved from elegant proof-of-principles to advanced designs, the main question remains is how to convert this motion into useful functionality?
Encoding multiple digital DNA signals in a single analog channel https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa303/5825621
DNA strand displacement systems' output readouts are normally limited by the different amount of fluorophores that can be implemented and read in the fluorescent reporter systems. This limitation usually results in systems with a very limited number of outputs: one possible output per fluorescent channel. In the present work the authors propose method to overcome this limitation based on representing multiple discrete bits of information in a single analog fluorescent signal. With this method, optimizing the toehold and sequence design they are able to encode reliably a 4-bit signal in a single fluorescent signal - they could detect the presence of 4 different genes with a single fluorophore - as well as applying the methodology to two channels simultaneously, thus increasing remarkably the number of possible readable outputs of a circuit.
A Coculture Based Tyrosine-Tyrosinase Electrochemical Gene Circuit for Connecting Cellular Communication with Electronic Networks
https://pubs.acs.org/doi/abs/10.1021/acssynbio.9b00469
In this paper, authors reported a cell-based synthetic biology−electrochemical device. The system builds on the tyrosinase-mediated conversion of tyrosine to L-DOPA and L-DOPA quinone which are both redox active and can be detected by a gold electrode. The use of cell consortia allows for divisions of labor to lower any particular metabolic burden in the production of tyrosine and tyrosinase. To induce the expression of these molecules, they use quorum sensing signalling molecules and pyocyanin that are secreted by Pseudomonas aeruginosa.
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