Our group’s research focuses on various aspects of functional engineered DNA molecules – deoxyribozymes and aptamers – from their selection and characterization to their application for bioanalysis. Deoxyribozymes are DNA molecules exhibiting catalytic properties for a number of chemical transformations, from phosphodiester bond cleavage to Diels Alder reactions. They have a potential to serve as “green” catalysts, RNA cleaving anti-cancer agents, or for detection of ions and biomolecules. Aptamers can be viewed as receptors or antibodies made of DNA. Their ability to tightly and selectively bind a ligand (small molecule, protein, cell, etc.) is explored in designing chemical sensors and/or constructs with gene expression control capabilities. We use both types of functional DNA as a scaffold to design multicomponent probes that self-assemble in response to a specific nucleic acid target and report the target’s presence. The probes exhibit advantages of cost-efficient and straightforward design, which makes them easily optimizable and fined-tunable, high selectivity of nucleic acid recognition, ability to interrogate even highly structured nucleic acids, and a variety of signal readouts including a color change. Our goal is to employ the probes to advance “on-site” (point-of-care) diagnostics of bacterial and viral pathogens.
- Connelly, R.P, Morozkin E.S., Gerasimova, Y.V.* (2018) Alphanumerical visual display made of DNA logic gates for drug susceptibility testing of pathogens. Chembiochem 19, DOI: 10.1002/cbic.201800011. The paper was selected for a cover feature of the issue.
- Bengtson H.N., Homolka S., Niemann S., Reis A.J., da Silva P.E., Gerasimova Y.V., Kolpashchikov D.M., Rohde K.H.* (2017) Multiplex detection of extensively drug resistant tuberculosis using binary deoxyribozyme sensors. Biosens. Bioelectron. 94, 176-183.
- Cox A.J., Bengtson H.N., Gerasimova Y.V., Rohde K.H., Kolpashchikov D.M.* (2016) DNA antenna tile-associated deoxyribozyme sensor with improved sensitivity. Chembiochem 17, 2038-2041. This paper was featured on the cover of the issue.
- Gerasimova Y.V, Kolpashchikov D.M.* (2016) Towards a DNA nanoprocessor: reusable tile-integrated DNA circuits. Angew. Chem. Int. Ed. Engl. 55, 10244-10247.
- Gentry R.C., Childs J.J., Gevorkyan J., Gerasimova Y.V., Koculi E.* (2016) Time course of large ribosomal subunit assembly in E. coli cells overexpressing a helicase inactive DbpA protein. RNA, 22, 1055-1064. doi:10.1261/rna.055137.115
- Gerasimova Y.V.*, Yakovchuk P., Dedkova L.M., Hecht S.M., Kolpashchikov D.M. (2015) Expedited quantification of mutant ribosomal RNA by binary deoxyribozyme (BiDz) sensors. RNA, 21, 1834-1843.
- Mailloux S., Gerasimova Y.V., Guz N., Kolpashchikov D.M.*, Katz E.* (2015) Bridging the two worlds: a universal interface between enzymatic and DNA computing systems. Angew. Chem. Int. Ed. Engl. 54, 6562-6566. This paper was featured at Nature Nanotech. 2015, 10(5).
- Gerasimova Y.V., Kolpashchikov D.M.* (2015) Divide and control: split design of multi-input DNA logic gates. Chem. Commun., 51, 870-872.
- Gerasimova Y.V., Cornett E.M., Edwards E., Su X., Rohde K.H.*, Kolpashchikov D.M.* (2013) Deoxyribozyme cascade for visual detection of bacterial RNA. Chembiochem 14, 2087-2090.
- Gerasimova Y.V.,* Kolpashchikov D.M.* (2013) Folding of 16S rRNA in a signal-producing structure for the detection of bacteria. Angew. Chem. Int. Ed. Engl. 52, 10586-10588. This paper was featured on the back cover of the issue.
- Cornett E.M., Gerasimova Y.V., Kolpashchikov D.M.* (2013) Two-component covalent inhibitor. Bioorg. Med. Chem. 21, 1988-1991.
- Gerasimova Y.V.,* Kolpashchikov D.M.* (2013) Detection of bacterial 16S rRNA using a molecular beacon-based X sensor. Biosens. Bioelectron., 41, 386–390, DOI: 10.1016/j.bios.2012.08.058.
- Gerasimova Y.V., Kolpashchikov D.M.* (2012) Connectable DNA logic gates: OR and XOR logics. Chem. Asian J., 7, 534-540.
- Kolpashchikov D.M.*, Gerasimova Y.V., Khan M.S. (2011) DNA Nanotechnology for nucleic acid analysis: DX motif-based sensor. Chembiochem, 12, 2564-2567.
- Nguyen C., Grimes J., Gerasimova Y.V., Kolpashchikov D.M.* (2011) Molecular beacon-based tricomponent probe for SNP analysis in folded nucleic acids, Chemistry, 17, 13052-13058.
- Gerasimova Y.V.*, Peck S., Kolpashchikov D.M. (2010) Enzyme-assisted binary probe for sensitive detection of RNA and DNA. Chem. Commun., 46, 8761-8763.
- Grimes J., Gerasimova Y.V., Kolpashchikov D.M.* (2010) Real-time SNP analysis in secondary structure-folded nucleic acids. Angew. Chem. Int. Ed. Engl., 49, 8950-8953. This paper was highlighted by Faculty 1000.
- Gerasimova Y.V., Hayson A.,Ballantyne J., Kolpashchikov D.M.* (2010) A single molecular beacon probe is sufficient for the analysis of multiple nucleic acid sequences. Chembiochem, 11, 1762-1768.
- Gerasimova Y.V., Cornett E., Kolpashchikov D.M.* (2010) RNA cleaving deoxyribozyme sensor for nucleic acid analysis: the limit of detection. ChemBioChem, 11, 811-817. This paper was featured on the cover of April 2010 issue of the journal.
University of Central Florida scientists, including three Department of Chemistry faculty members, received a total of nearly $1.3 million in state funds Wednesday to research the Zika virus with the goal of ... Read more
The College of Sciences at the University of Central Florida welcomes 50 new faculty members this fall. In conjunction with the new faculty hiring campaign, approximatley 200 new faculty will begin at the... Read more