People » Yulia Gerasimova

Dr. Gerasimova’s research focuses on deoxyribozymes (Dz) – DNA molecules with catalytic properties.  Her lab is interested in isolating new catalytic DNA molecules, and applying both new and existing Dz for “green” chemistry and bioanalysis, including pathogen detection. For example, they use Dz with a peroxidase activity for sensing nucleic acids of pathogenic viruses and bacteria. In this approach, a targeted nucleic acid fragment is recognized by two sensor strands, which together fold into a G-quadruplex (G4) structure. The G4-hemin complex catalyzes oxidation of an organic indicator by H2O2 (see figure).  These sensors rely on color change as a readout, and, therefore, do not require sophisticated instrumentation and are suitable for “on-site” implementation.


  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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