Objectives

In vivo synthesis of functional DNA nanostructure

Our aim is to design a novel DNA nanostructure that can detect multiple miRNA targets simultaneously. We hope that our design can discriminate a single base mutation of the target miRNAs. Hence, it can be highly specific to our targets and avoid false positives. Our goal is clear - we aim to design a tool which can possibly detect a combination of biomarkers and enhance the sensitivity of detecting a particular type of cancer.
Recently, in vitro applications of DNA nanostructure have already achieved point-of-care (POC) diagnosis[11]. Therefore, we hope to move from in vitro to in vivo by developing a self-assembled DNA nanostructure that can potentially target miRNAs in vivo. Detecting serum miRNA can be challenging because of the low serum miRNA level, so methods such as quantitative polymerase chain reaction are used to amplify the target miRNAs before detecting them.[12] We hope that our DNA nanostructure, which is synthesized and assembled in vivo, can potentially eliminate the need of target amplification. In addition, our design has an advantage over the current designs of molecular beacon. Molecular beacon makes use of fluorophores and quenchers[13], which cannot be synthesized in vivo. Our design does not require the use of fluorophore and quencher and thus can work well inside cells. In addition, our DNA nanostructure can be produced at a lower cost as fluorophore and quencher are not used.

References

11. Hartman, Mark R., et al.(2013) . "Point-of-care nucleic acid detection using nanotechnology." Nanoscale 5.21 (2013): 10141-10154.
12. Wang. W.T., Chen.Y.Q. (2014). "Circulating miRNAs in cancer: from detection to therapy." Journal of Hematology & Oncology. (2014): Vol.7. 86.
13. TSOURKAS, Andrew, et al. (2003). Hybridization kinetics and thermodynamics of molecular beacons. Nucleic acids research, 2003, 31.4: 1319-1330.

Current progress

Our design is a 3-dimensional structure that can be self-assembled from oligonucleotides. Our aim is to construct a nanostructure that is able to detect multiple miRNA biomarkers such that it can reach a higher accuracy for diagnosis. For the selection of biomarkers, we are looking for a combination of miRNAs that are specific to a certain type of disease including cancers. At current stage, we are testing different designs in vitro to see if they can produce desired signals. After proving our designs can work in vitro, we will attempt to test them in vivo. Finally, we will design a mechanism such that E. coli can synthesize the required oligonucleotides to form the specified nanostructure.

Sigificances

A leap forward - in vivo synthesis of 3D functional DNA nanostructures

In the past decade, functional DNA nanostructures have been used in similar in vitro approaches to detect various cancer biomarkers.[14][15]It is noted that most of those designs were applied in vitro. Recently, 1D and 2D DNA structures were successfully expressed and assembled in vivo,[16] while several novel 3D DNA structures were synthesized to produce signals in vivo.[17],[18] Given these advancements, our ultimate goal is to enable our functional DNA nanostructure to be synthesized and self-assembled in E. coli, that can function inside the disease cells. This, if successful and with further refinement, could be a great replacement to colour coded surgery in the surgical field.[19]
Last but not least, the cost and quality of production, efficiency and accuracy of our intracellularly-synthesized 3D structure will be compared to current diagnostic methods.

References

14. Miao, P., Wang, B., Chen, X., Li, X., & Tang, Y. (2015). Tetrahedral DNA nanostructure-based microRNA biosensor coupled with catalytic recycling of the analyte. ACS applied materials & interfaces, 7(11), 6238-6243.
15. Li W. et. al. (2015). Highly selective and sensitive detection of miRNA based on toehold-mediated strand displacement reaction and DNA tetrahedron substrate. Biosensors and Bioelectronics. 71, 401-406.
16. Elbaz, J., Yin, P., & Voigt, C. A. (2016). Genetic encoding of DNA nanostructures and their self-assembly in living bacteria. Nature communications, 7.
17. Kim K. et. al. (2013). Drug delivery by self-assembled DNA tetrahedron for overcoming drug resistance in breast cancer cells. Chem. Commun. 49, 2010-2012.
18. Kim K. et. al. (2013). Sentinel lymph node imaging by a fluorescently labeled DNA tetrahedron. Biomaterials. 34, 5226-5235.
19. Nguyen, Q. T., & Tsien, R. Y. (2013). Fluorescence-guided surgery with live molecular navigation [mdash] a new cutting edge. Nature reviews cancer, 13(9), 653-662.