People » Yulia Gerasimova

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.


  1. 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.


  1. 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.


  1. 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.
  2. Gerasimova Y.V, Kolpashchikov D.M.* (2016) Towards a DNA nanoprocessor: reusable tile-integrated DNA circuits. Angew. Chem. Int. Ed. Engl. 55, 10244-10247.
  3. 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


  1. 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.
  2. 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).
  3. Gerasimova Y.V., Kolpashchikov D.M.* (2015) Divide and control: split design of multi-input DNA logic gates. Chem. Commun., 51, 870-872.


  1. 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.
  2. 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.
  3. Cornett E.M., Gerasimova Y.V., Kolpashchikov D.M.* (2013) Two-component covalent inhibitor. Bioorg. Med. Chem. 21, 1988-1991.
  4. 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.


  1. Gerasimova Y.V., Kolpashchikov D.M.* (2012) Connectable DNA logic gates: OR and XOR logics. Chem. Asian J., 7, 534-540.


  1. Kolpashchikov D.M.*, Gerasimova Y.V., Khan M.S. (2011) DNA Nanotechnology for nucleic acid analysis: DX motif-based sensor. Chembiochem, 12, 2564-2567.
  2. 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.


  1. 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.
  2. 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.
  3. 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.
  4. 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.

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