Publications

Advisees are indicated using a dagger symbol (†, postdoctoral scholar) or asterisk(s) (*, undergraduate; **, graduate).
Publications are listed in reverse chronological order, with the newest papers at the top.

Publications since 2017

  1. Nix, C.A.: Nottolini, I.: Caranto, J.D.; Gerasimova, Y.; Kolpashchikov D.; Saitta, E.K.H. (2022) Championing the involvement of practitioners in the Biochemistry educational research process: A phenomenological view of the early stages of collaborative action research. J. High. Educ., 11, 114.
  2. Reed, M.A.;** Gerasimova, Y.V. (2022) Single-tube isothermal label-free fluorescent sensor for pathogen detection based on their genetic signatures. Chem., 10, https://doi.org/10.3389/fchem.2022.951279
  3. Gerasimova, Y.V.; Nedorezova, D.D.;** Kolpashchikov, D.M. (2022) Split light up aptamers as a probing tool for nucleic acids. Methods, https://doi.org/10.1016/j.ymeth.2021.05.008
  4. Connelly, R.P.;** Madalozzo, P.F.;* Moderson, J.E.;* Pratt, A.D.;* Gerasimova, Y.V. (2021) Promiscuous dye binding by a light-up aptamer: Application for label-free multiwavelength biosensing. Chem. Commun., DOI: 10.1039/D1CC00594D.
    Graphical abstract: Promiscuous dye binding by a light-up aptamer: application for label-free multi-wavelength biosensing
  5. Sapia, R.J.;** Campbell, C.;* Reed, A.J.;** Tsvetkov, V.; Gerasimova, Y.V. (2021) Interaction of GelRed™ with single-stranded DNA oligonucleotides: Preferential binding to thymine-rich sequence. Dyes Pigm., 188, 109209. DOI: 10.1016/j.dyepig.2021.109209
  6. Reed, A.J.;** Sapia, R.J;** Dowis, C.;* Solarez, S.;* Gerasimova, Y.V. (2020) Interrogation of highly structured RNA with multicomponent deoxyribozyme probes at ambient temperatures. RNA, 26, 1882-1890. DOI: 10.1261/rna.074864.120
  7. Dhar, B.C.; † Reed, A.J.;** Mitra, S.; Rodriguez Sanchez, P.;* Nedorezova, D.D.; Connelly, R.P.;** Rohde, K.H.; Gerasimova, Y.V. (2020) Cascade of deoxyribozymes for the colorimetric analysis of drug resistance in Mycobacterium tuberculosis. Biosens. Bioelectron., 165, 112385. DOI: 10.1016/j.bios.2020.112385
  8. Foguel, M.V.; Balcarcel, A.M.; Reed, M.A.;** Calvo-Marzal, P.; Gerasimova, Y.V.; Kolpashchikov, D.M.; Chumbimuni-Torres, K.Y. (2020) MVF sensor enables analysis of nucleic acids with stable secondary structures. Electroanalysis, 32 (4), 835-841, DOI: 10.1002/elan.201900690
  9. Connelly, R.P.;** Verduzco, C.;* Farnell, S.;* Yishay, T.;* Gerasimova, Y.V. (2019) Toward a rational approach to design split G-quadruplex probes. ACS Chem. Biol., 14, 2701-2712, DOI: 10.1021/acschembio.9b00634
  10. Lynch, C.A.III; Foguel, M.; Reed, A.J.;** Balcarcel, A.M.; Calvo-Marzal, P.; Gerasimova, Y.V.; Chumbimuni-Torres, K.Y. (2019) Selective determination of isothermally amplified Zika virus RNA using a universal DNA-hairpin probe in less than 1 hour. Anal. Chem., 91, 13458-13464, DOI: 10.1021/acs.analchem.9b02455
  11. Kikuchi, N.; Reed, A.;** Gerasimova, Y.V.; Kolpashchikov, D.M. (2019) Split dapoxyl aptamer for sequence-selective analysis of NASBA amplicons. Anal. Chem., 91, 2667-2671, DOI: 10.1021/acs.analchem.8b03964
  12. Wood, H.N., Sidders, A.E., Brumsey, L.E., Morozkin, E.S.,† Gerasimova, Y.V., Rohde, K.H. (2019) Species typing of nontuberculous mycobacteria by use of deoxyribozyme sensors. Clin. Chem., 65, 333-341. DOI: 10.1373/clinchem.2018.295212
  13. Reed, A.J.,** Connelly, R.P.,** Williams, A.,* Tran, M.,* Shim, B.-S., Choe, H., Gerasimova, Y.V. (2019) Label-free pathogen detection by a deoxyribozyme cascade with visual signal readout. Sensors & Actuators: B. Chemical, 282, 945-951. DOI: 10.1016/j.snb.2018.11.147
  14. 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, 203-206. DOI: 10.1002/cbic.201800011. The paper was selected for a cover feature of the issue.
  15. 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. DOI: 10.1016/j.bios.2017.02.051

Publications from 1998-2016

  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
  4. 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.
  5. 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).
  6. Gerasimova Y.V., Kolpashchikov D.M. (2015) Divide and control: split design of multiinput DNA logic gates. Chem. Commun., 51, 870-872.
  7. 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.
  8. 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.
  9. Cornett E.M., Gerasimova Y.V., Kolpashchikov D.M. (2013) Two-component covalent inhibitor. Bioorg. Med. Chem. 21, 1988-1991.
  10. 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.
  11. Gerasimova Y.V., Kolpashchikov D.M. (2012) Connectable DNA logic gates: OR and XOR logics. Chem. Asian J., 7, 534-540.
  12. Kolpashchikov D.M., Gerasimova Y.V., Khan M.S. (2011) DNA Nanotechnology for nucleic acid analysis: DX motif-based sensor. Chembiochem, 12, 2564-2567.
  13. Nguyen C., Grimes J., Gerasimova Y.V., Kolpashchikov D.M. (2011) Molecular beaconbased tricomponent probe for SNP analysis in folded nucleic acids, Chem. Eur. J., 17, 13052-13058.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. Gerasimova Y.V., Bobik T.V., Ponomarenko N.A., Shakirov M.M., Zenkova M.A., Tamkovich, N.V., Popova T.V., Knorre D.G., Godovikova T.S. (2010) RNA-hydrolyzing activity of human serum albumin and its recombinant analogue. Bioorg. Med. Chem. Lett., 20, 1427-1431.
  19. Shundrina I.K., Vaganova T.A., Kusov S.Z., Rodionov V.I., Karpova E.V., Koval V.V., Gerasimova Y.V., Malykhin E.V. (2009) Synthesis and characterization of polyimides based on novel isomeric perfluorinated naphthylenediamines. J. Fluorine Chem., 130, 733-741.
  20. Khranenko S.P., Plusnin N.E., Sheludyakova L.A., Gerasimova Y.V., Korol’kov I.V., Korenev S.V. (2009) Study of the complexation reaction between crystallized trans-[Pd(H2O)2(NO3)2] and acetyl acetone. Russ. J. Coord. Chem., 35, 1-7.
  21. Nechepurenko I.V., Komarova N.I., Gerasimova Y.V., Koval V.V., Polovinka M.P., Korchagina D.V., Salakhutdinov N.F. (2009) Structure of oligomeric proanthocyanidines from Hedysarum thienum roots studied by thiolysis and MALDI-TOF MS. Chem. Nat. Comp., 45, 32-39.
  22. Gerasimova Y.V., Knorre D.G., Shakirov M.M., Godovikova T.S. (2008) Human serum albumin as a catalyst of RNA cleavage: N-homocysteinylation and N-phosphorylation by oligonucleotide affinity reagent alter the reactivity of the protein. Bioorg. Med. Chem. Lett., 18, 5396-5398.
  23. Gerasimova Y.V., Erchenko I.A., Shakirov M.M., Godovikova T.S. (2008) Interaction of human serum albumin and its clinically relevant modification with oligoribonucleotides. Bioorg. Med. Chem. Lett., 18, 4511-4514.
  24. Gerasimova Y.V., Alekseyeva I.V., Bogdanova T.G., Erchenko I.A., Kudryashova N.V., Chelobanov B.P., Laktionov P.P., Alekseyev P.V., Godovikova T.S. (2006) Affinity separation of polyribonucleotide-binding human blood protein. Bioorg. Med. Chem. Lett., 16, 5526-5529.
  25. Savinkova L.K., Sokolenko A.A., Rau V.A., Arshinova T.V., Gerasimova Y.V., Kudryashova N.V., Godovikova T.S. (2000) Affinity labeling of RNA-polymerase II in the transcriptionally active complex by a phosphorylating analog of the initiation substrate. Biochemistry (Moscow) 65, 1129-1134.
  26. Knorre D.G., Alekseyev P.V., Gerassimova Yu.V., Silnikov V.N., Maksakova G.A., Godovikova T.S. (1998) Intraduplex photocross-linking of p-azidoaniline residue and amino acid side chains linked to the complementary oligonucleotides via a new phosphorylating intermediate formed in the Mukaiyama System. Nucleosides&Nucleotides, 17, 397-410.