Publications

Most updated list of publications

2019

1. Nedorezova D.D., Fakhardo A. F., Molden T. A., Kolpashchikov D. M. (2019)  Deoxyribozyme-based DNA Machines for Cancer Therapy. Chembiochem, doi: 10.1002/cbic.201900525.

2. Kolpashchikov D. M. (2019) Evolution of Hybridization Probes to DNA Machines and Robots. Accounts of Chemical Research. 52, 1949-1956.

3. Mills D. M., Foguel M. V., Martin C. P., Trieu T. T., Kamar O., Calvo-Marzal P., Kolpashchikov D. M., Chumbimuni-Torres K. Y. (2019) Rapid detection of different DNA analytes using a single electrochemical sensor. Sensors and Actuators B: Chemical, DOI: https://doi.org/10.1016/j.snb.2019.04.149.

4. Bakshi S. F., Guz N., Zakharchenko A., Minko S., Kolpashchikov D. M., Katz E. (2019) Towards Nanomaterials for Cancer Theranostics: A System of DNA-Modified Magnetic Nanoparticles for Detection and Suppression of RNA Marker in Cancer Cells. Magnetochemistry, 5, 24.

5. Sun S-C., Dou H-Y., Chuang M-C., Kolpashchikov D. M. (2019) Multi-Labeled Electrochemical Sensor for Cost-Efficient Detection of Single Nucleotide Substitutions in Folded Nucleic Acids. Sensors & Actuators B. Chemical, 287, 569-575.

6. Nedorezova D. D., Fakhardo A. F. Nemirich D. V. Bryushkova E. A., Kolpashchikov D. M. (2019) Towards DNA Nanomachines for Cancer Treatment: Achieving Selective and Efficient Cleavage of Folded RNA. Angew. Chem. Int. Ed. Engl., 2019, 58, 4654-4658.

7. Kikuchi N., Reed A., Gerasimova Y. V., Kolpashchikov D. M. (2019) Split Dapoxyl Aptamer for Sequence-Selective Analysis of NASBA amplicons. Analytical Chemistry, 91, 2667-2671.

8. Lyalina T. A., Goncharova E. A., Prokofeva N. Y., Voroshilina E. S., Kolpashchikov D. M. (2019) A DNA Minimachine for Selective and Sensitive Detection of DNA. Analyst, 144, 416-420.

2018

1. Lanchuk Y. V., Ulasevich S. A., Fedotova T. A, Kolpashchikov D. M., and Skorb E.V. (2018) Towards sustainable diagnostics: replacing unstable H2O2 by photoactive TiO2 in testing systems for visible and tangible diagnostics affordable by blind people. RSC Advances, 66, 37735-37739.

2. Karadeema R. J. Stancescu M., Steidl T. P. Bertot, S. C. Kolpashchikov D. M. (2018) The Owl Sensor: a ‘Fragile’ DNA Nanostructure for Analysis of Single Nucleotide Variations Nanoscale, 10, 10116-10122.

3. Evangelista B. A., Kim Y.-S., Kolpashchikov D. M. (2018) FaptaSyme: a Strategy for Converting a Monomer/Oligomer Non-Selective to Oligomer-Selective Aptameric Sensors. ChemBioChem 19, 1123 –1126.

4. Mills D. M., Martin C. P., Armas S. M., Calvo-Marzal P., Kolpashchikov D. M, Chumbimuni-Torres K. Y. (2018) A universal and label-free impedimetric biosensing platform for discrimination of single nucleotide substitutions in long nucleic acid strands. Biosensors & Bioelectronics. 109, 35-42.

5. Bakshi S. F., Guz N., Zakharchenko A., Deng H., Tumanov A., Woodworth C. D., Minko S., Kolpashchikov D. M., Katz E. (2018) Nanoreactors Based on DNAzyme-Functionalized Magnetic Nanoparticles Activated by Magnetic Field. Nanoscale, 10, 1356–1365.

2017

1. Fedotova T. A. Kolpashchikov D. M. (2017) Liquid-to-Gel Transition for Visual and Tactile Detection of Biological Analytes. Chem. Commun. (Camb.), 53, 12622 – 12625.
This paper was featured on the front cover of the journal.
This article also was highlighted by Chemistry World, monthly chemistry news magazine published by the Royal Society of Chemistry

2. Kamar O., Sun S. C., Lin C. H., Chung W. Y., Lee M. S., Liao Y. C., Kolpashchikov D. M., Chuang M. C. (2017) A mutation-resistant deoxyribozyme OR gate for highly selective detection of viral nucleic acids. Chem. Commun. (Camb.), 53, 10592-10595.

3. Bakshi S.F., Guz N., Zakharchenko A., Deng H., Tumanov A., Woodworth C. D., Minko S., Kolpashchikov D. M., Katz E. (2017) Magnetic Field-Activated Sensing of mRNA in Living Cells. Journal of the American Chemical Society, 139, 12117-12120.

4. Smith A., Kolpashchikov D. M. (2017) Divide and Control: Comparison of Split and Switch Hybridization Sensor. ChemistrySelect, 2, 5427-5431.

5. Kikuchi N., Kolpashchikov D. M. (2017) Universal Split Spinach Aptamer (USSA) Probe for Nucleic Acid Analysis and DNA/RNA Computation. Chem. Commun. (Camb.), 53, 4977-4980.

6. Campbell E. A., Peterson E., Kolpashchikov D. M. (2017) Self-Assembling Molecular Logic Gates Based on DNA Crossover Tiles. ChemPhysChem, 18, 1730-1734.

7. Bengtson H. N., Homolka S., Niemann S., Reis A. J., da Silva P. E. A, Gerasimova Y. V., Kolpashchikov D. M. Rohde K. H. (2017) Multiplex Detection of Extensively Drug Resistant Tuberculosis using Binary Deoxyribozyme Sensors. Biosensors & Bioelectronics, 94, 176-183.

8. Mills D. M. Calvo-Marzal P., Pinzon J. M., Armas S., Kolpashchikov D. M., Chumbimuni-Torres K.Y. (2017) A Single Electrochemical Probe Used for Analysis of Multiple Nucleic Acid Sequences. Electroanalysis, 29, 873–879.

9. Gamella M., Zakharchenko A., Guz N., Masi M., Minko S., Kolpashchikov D. M., Iken H., Poghossian A., Schöning, M. J. Katz E. (2017) DNA Computing Systems Activated by Electrochemically-Triggered DNA Release from a Polymer-Brush-Modified Electrode Array. Electroanalysis, 29, 398–408.

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. in press.
  2. Gerasimova Y.V., Kolpashchikov D. M. (2016) Towards a DNA Nanoprocessor: Reusable Tile-Integrated DNA Circuits. Angewandte Chemie International Edition Engl., 55, 10244-10247.
  3. Kikuchi N.K., Kolpashchikov D.M. (2016) Split spinach aptamer for highly selective recognition of DNA and RNA at ambient temperatures. ChemBioChem, 17, 1589-1592.
  4. 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.
  5. 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.
  6. 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. Chem. Commun. (Camb.), 52, 14318-14321.

2015

  1. Gerasimova Y.V., Yakovchuk P., Dedkova L.M., Hecht S.M., Kolpashchikov D.M. (2015) Expedited quantification of genetically modified ribosomal RNA by binary deoxyribozyme sensors. RNA, 10, 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 Angewandte Chemie International Edition Engl., 54, 6562-6566.
  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.

2014

  1. Gerasimova Y.V., Kolpashchikov D.M. (2014) Enzyme-assisted target recycling (EATR) for nucleic acid detection. Chemical Society Reviews, 43, 6405-6438.
  2.  Bengtson H.B., Kolpashchikov D.M. (2014) A Differential Fluorescent Receptor for Nucleic Acid Analysis ChemBioChem, 15, 228-231.

2013

  1. Cornett E.M., O’steen M.R, Kolpashchikov D.M. (2013) Operating cooperatively (OC) sensor for highly specific recognition of nucleic acids. PLOS one, PLoS ONE 8(2): e55919.
  2. Cornett E.M., Gerasimova Y.V., Kolpashchikov D.M. (2013) Two-component reagent: an approach to specific covalent inactivation of biopolymers. Bioorganic & Medicinal Chemistry, 21, 1988–1991.
  3. Gerasimova Y.V., Kolpashchikov D.M. (2013) Detection of bacterial 16S rRNA using a molecular beacon-based X sensor. Biosensors & Bioelectronics, 41, 386–390.
  4. Cornett E.M., Kolpashchikov D.M. (2013) SNP analysis using a molecular beacon-based operating cooperatively (OC) sensor. Methods in Molecular Biology, Nucleic acid detection, Humana press, 1039, 81-86.
  5.  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.
  6. 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.
  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, in press, DOI: 10.1002/cbic.201300471.
  8. 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.

 2012

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.

2011

  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.

2010

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.

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.