People » Dmitry Kolpashchikov

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Our research interests cover all aspects of chemistry and biochemistry of nucleic acids and nucleic acids binding proteins. The following projects are in progress.

  1. Multicomponent sensors for nucleic acid analysis. This project aims at developing new hybridization probes for real-time analysis of specific DNA and RNA sequences. A multicomponent sensor produces detectable signal only when all sensor components form specific complexes with the analyzed DNA or RNA. In multicomponent sensors each constituent part can be designed to address a particular issue of target recognition. The high specialization of each component leads to the improved accuracy of genotyping for polymorphic sites, detection of folded nucleic acids and reduces the cost of multiplex assays. The sensors promise to advance molecular diagnostics of human genetic and infectious diseases.
  2. Binary reagents for DNA polymerase inactivation. . We develop two-component nucleotide reagents for highly selective irreversible inhibition of human immunodeficiency virus (HIV) reverse transcriptase (RT). The approach promises to deliver new type of efficient and side effect-free anti-AIDS drugs.
  3. DNA logic circuits. DNA-based molecular logic gates that can be used in the first DNA-based computer processor are under investigation. The main advantage of the gate design is the possibility to connect logic units in complex circuits at the molecular level.

Complete List


  1. Cox A. J., Bengtson, H. N., Rohde K. H., Kolpashchikov D. M. (2016) DNA Nanotechnology for Nucleic Acid Analysis: Multifunctional Molecular DNA Machine for RNA Detection. ChemComm, 52, 14318-14321.
  2. Stancescu M., Fedotova T. A., Hooyberghs J., Balaeff A., Kolpashchikov D. M. (2016) Non-Equilibrium Hybridization Enables Discrimination of a Point Mutation within 5-40oC. Journal of the American Chemical Society, 138, 13465–13468.
  3. 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. 21, 2038-2041. This paper was featured on the cover of 21st issue of the journal.
  4. Gerasimova Y. V., Kolpashchikov D. M. (2016) Towards a DNA Nanoprocessor: Reusable Tile-Integrated DNA Circuits. Angewandte Chemie International Edition Engl., 55, 10244-10247.
  5. Kikuchi N., Kolpashchikov D. M. (2016) Split spinach aptamer for highly selective recognition of DNA and RNA at ambient temperatures. ChemBioChem, 17, 1589-1592.
  6. Guz N., Fedotova T.A., Fratto B.E., Schlesinger O., Alfonta L., Kolpashchikov D. M., Katz E. (2016) Bioelectronic Interface Connecting Reversible Logic Gates Based on Enzyme and DNA Reactions. ChemPhysChem 17, 2247-2255.


  1. Gerasimova Y.V., Yakovchuk P., Dedkova L.M., Hecht S.M., Kolpashchikov D.M. Expedited quantification of genetically modified ribosomal RNA by binary deoxyribozyme sensors. RNA, accepted.
  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 Angewandte Chemie International Edition Engl., 54, 6562-6566. This paper was featured at Nature Nanotechnology by Ai Lin Chun ‘Molecular computing: A logical connection, doi:10.1038/nnano.2015.102.
  3. O’Steen M.R., Cornett E.M., Kolpashchikov D.M. (2015) Nuclease-Containing Media for Reversible Operation of DNA Logic Gates. ChemComm, 51, 1429–1431.
  4. Gerasimova Y.V., Kolpashchikov D.M. (2015) Divide and Control: Split Design of Multi-Input DNA Logic Gates, ChemComm, 51, 870–872.


  1. Yang K-A., Barbu M., Halim M., Pallavi P., Kim B, Kolpashchikov D.M., Pecic S., Taylor S., Worgall T.S. Stojanovic M.N. (2014) Recognition and sensing of low-epitope targets via ternary complexes with oligonucleotides and synthetic receptors. Nature Chemistry, 11, 1003-1008.
  2. Gerasimova Y.V., Kolpashchikov D.M. (2014) Enzyme-assisted target recycling (EATR) for nucleic acid detection. Chemical Society Reviews. 43, 6405-6438.
  3. Bengtson H.B., Kolpashchikov D.M. (2014) A Differential Fluorescent Receptor for Nucleic Acid Analysis ChemBioChem, 15, 228-231.


  1. Labib M., Ghobadloo S.M., Khan N., Kolpashchikov D.M., Berezovski M.V. (2013) Four-Way Junction Formation Promoting Ultrasensitive Electrochemical Detection of MicroRNA. Anal. Chem. 85, 9422-9427.
  2. Gerasimova Y.V., Kolpashchikov D.M. (2013) Folding 16S RNA in a signal-producing structure for detection of bacteria, Angewandte Chemie International Edition Engl. 52, 10586-10588. This paper was  featured on the cover of a September 2013 issue of the journal.
  3. 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, in press, DOI: 10.1002/cbic.201300471.
  4. Cornett E.M., O’steen M.R, Kolpashchikov D.M. (2013) Operating cooperatively (OC) sensor for highly specific recognition of nucleic acids. PLOS one 8, e55919.
  5. Cornett E.M., Gerasimova Y.V., Kolpashchikov D.M. (2013) Two-component covalent inhibitor: Bioorganic & Medicinal Chemistry, 21, 1988–1991.
  6. Gerasimova Y.V., Kolpashchikov D.M. (2013) Detection of bacterial 16S rRNA using a molecular beacon-based X sensor. Biosensors & Bioelectronics, 41, 386–390.
  7. Cornett E.M., Kolpashchikov D.M.* SNP analysis using a molecular beacon-based operating cooperatively (OC) sensor. Methods in Molecular Biology, Nucleic acid detection, Humana press, 2013. 1039, 81-86.
  8. Gerasimova Y.V.,* Ballantyne J., Kolpashchikov D.M. Detection of SNP-Containing human DNA sequences using a split sensor with universal molecular beacon reporter. Methods in Molecular Biology, Nucleic acid detection, Humana press, 2013. 1039, 69-80.


  1. Gerasimova Y.V., Kolpashchikov D.M. (2012) Connectable DNA Logic Gates: OR and XOR logics. Chemistry-An Asian Journal, 7, 534-540.
  2. Cornett E.M., Campbell E.A., Gulenay G., Peterson E, Bhaskar N, Kolpashchikov D.M. (2012) Molecular logic gates for DNA analysis: detection of rifampin resistance in M.tuberculosis DNA. Angew Chem Int Ed Engl. 51, 9075-9077
  3. Kolpashchikov D.M. (2012) An Elegant Biosensor Molecular Beacon Probe: Challenges and Recent Solutions, Scientifica, 2012, ID 928783.


  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: A European J. 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. and Kolpashchikov D.M. (2010) Real-Time SNP Analysis in Secondary Structure-Folded Nucleic Acids, Angew Chem Int Ed Engl. 49: 8950-8953. This article was rated by Faculty of 1000 (Uttamchandani M, Yao S: 2010.
  3. Kolpashchikov D.M. (2010) Binary Probes for Nucleic Acid Analysis, Chem. Rev. 110, 4709-4723.
  4. 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.
  5. Lake A., Shang S., Kolpashchikov D.M. (2010) Molecular Logic Gates Connected via DNA Four Way Junctions, Angew. Chemie Int. Ed. Engl., 49, 4459-4462.
  6. 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 6th issue of ChemBioChem journal.
  7. Gerasimova Y.V., Kolpashchikov D.M. (2010) Nucleic acid detection using MNAzymes. Chemistry & Biology, 17, 104-106.


  1. Kolpashchikov D.M. (2009) Triple-stem DNA probe: a new conformationally constrained probe for SNP typing. ChemBioChem, 10, 1443-1445.

Motivated, open-minded students are welcome in our lab. Students will be involved in all aspects of scientific research including literature search, experiment design, data collection and analysis, poster and oral presentations, publishing in scientific journals. Techniques that students will be exposed in our lab include gel electrophoresis, UV/vis and fluorescent spectroscopy, SELEX, bioorganic synthesis (including DNA synthesis), chromatography (including HPLC), photochemistry and others.


Teaching: Biochemistry I course (BCH4053)

The course is focused on chemical structure and functions of the four major classes of biological molecules in the following order: carbohydrates, nucleic acids, proteins and lipids. The course builds on students’ prior knowledge of physical and organic chemistry to understand architecture of biological molecules and how this architecture makes biomolecules functionally active. The complex molecular interplay is illustrated by protein-nucleic acid interactions, membrane transport and biological signaling. ‘Introduction to metabolism’ prepares students for Biochemistry II course.

Each student in the class receives an individual score by the end of semester. Students who collected the highest scores during previous terms are listed below.

Student Name
Score (%)
Total number of students in the class
Christopher Reilly
Fall 2009
Nicole Mailloux
Spring 2010
David Delapena
Fall 2010
Patricia Prieto
Spring 2010
Lauren Holliday
Fall 2011

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