Complex DNA Nanomachines for the Ultrasensitive Detection of Ribonucleic Acids

first_page Download PDF settings Order Article Reprints Font Type: Arial Georgia Verdana Font Size: Aa Aa Aa Line Spacing:    Column Width:    Background: Open AccessAbstract Complex DNA Nanomachines for the Ultrasensitive Detection of Ribonucleic Acids † by Margarita KuzinaMargarita Kuzina SciProfiles Scilit Preprints.org Google Scholar *, Victoria KhorolskayaVictoria Khorolskaya SciProfiles Scilit Preprints.org Google Scholar and Maria RubelMaria Rubel SciProfiles Scilit Preprints.org Google Scholar Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 197101 Saint-Petersburg, Russia * Author to whom correspondence should be addressed. † Presented at the 3rd International Electronic Conference on Biomolecules, 23–25 April 2024; Available online: https://sciforum.net/event/IECBM2024 Proceedings 2024, 103(1), 9; https://doi.org/10.3390/proceedings2024103009 Published: 12 April 2024 Download keyboard_arrow_down Download PDF Download PDF with Cover Download XML Download Epub Versions Notes Keywords: DNA nanomachines; mRNA detection; amplification free; deoxyribozyme 1. BackgroundDNA nanomachines were developed as highly accurate alternatives to costly and unreliable methods used for measuring gene expression levels. However, despite their potential, DNA nanomachines also come with several limitations. One major drawback is their tendency to interact with various biological molecules, which can compromise their functionality. Additionally, background noise often hampers their performance, leading to reduced sensitivity and less precise results. 2. GoalThe goal of our work was to create DNA nanomachines for the highly sensitive detection of RNA extracted from cell culture that can be used for assessing mRNA concentrations without amplification. 3. MethodsDNA nanomachines were partially preassembled to add more auxiliary structures. Additional quenchers were added to the structure to decrease the background noise and increase the dynamic range and limit of detection. The pre-assembly was performed with the gradual cooling of samples after a short boiling period. The resulted pre-assembled structures were confirmed via PAGE gel. Samples were incubated at 55 °C and different times of exposure were analyzed. The DNA nanomachines were characterized via limits of detection and their effectivity was assessed on total RNA extracted from cell culture. 4. ResultsThe results of the optimization experiments showed that incorporating a specific amount of DNA nanomachine with quenchers effectively reduced the background noise and non-specific fluorescence, therefore leading to more accurate evaluation of the signal. The limit of detection experiments revealed that the designed structures were capable of detecting their target at concentrations as small as picomolar. Notably, the machines equipped with quenchers exhibited even greater sensitivity, further enhancing their performance. 5. ConclusionsThe optimization experiments conducted on DNA nanomachines have unequivocally demonstrated that their sensitivity can be significantly enhanced through the incorporation of new designs and additional elements. This breakthrough paves the way for the potential utilization of these advanced constructions as highly efficient point-of-care diagnostics in the future. Author ContributionsConceptualization, M.K. and V.K.; methodology, M.R., validation, M.K., V.K. and M.R.; data curation, M.R.; writing—original draft preparation, M.K., writing—review and editing, M.R.; visualization, V.K.; supervision, M.R.; project administration, M.R. All authors have read and agreed to the published version of the manuscript.FundingThis research was funded by Russian Scientific Foundation grant number 22-24-00664.Institutional Review Board StatementNot applicable.Informed Consent StatementNot applicable.Data Availability StatementThe raw data are available upon request.Conflicts of InterestThe authors declare no conflict of interest.Disclaimer/Publisher's Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. © 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Share and Cite MDPI and ACS Style Kuzina, M.; Khorolskaya, V.; Rubel, M. Complex DNA Nanomachines for the Ultrasensitive Detection of Ribonucleic Acids. Proceedings 2024, 103, 9. https://doi.org/10.3390/proceedings2024103009 AMA Style Kuzina M, Khorolskaya V, Rubel M. Complex DNA Nanomachines for the Ultrasensitive Detection of Ribonucleic Acids. Proceedings. 2024; 103(1):9. https://doi.org/10.3390/proceedings2024103009 Chicago/Turabian Style Kuzina, Margarita, Victoria Khorolskaya, and Maria Rubel. 2024. "Complex DNA Nanomachines for the Ultrasensitive Detection of Ribonucleic Acids" Proceedings 103, no. 1: 9. https://doi.org/10.3390/proceedings2024103009 Article Metrics No No Article Access Statistics Multiple requests from the same IP address are counted as one view.