People » Dmitry Kolpashchikov


Visit our research website:  http://chemistry.cos.ucf.edu/dmk-biochemlab/

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.
Click here for complete list of publications

2018

  1. 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. In addition, this article was highlighted by Chemistry World, monthly chemistry news magazine published by the Royal Society of Chemistry https://www.chemistryworld.com/news/tactile-alternative-to-colour-changes/3008395.article
  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.

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
Score (%)
Term
Total number of students in the class
Christopher Reilly
976
97.6%
Fall 2009
148
Nicole Mailloux
947
94.7%
Spring 2010
223
David Delapena
934
93.4%
Fall 2010
184
Patricia Prieto
980
98.0%
Spring 2010
240
Lauren Holliday
980
98.0%
Fall 2011
300

Congratulations, Fall 2017 Ph.D. Graduates

In a reception hosted by Dean Michael Johnson, Ph.D., the College of Sciences celebrated its new Ph.D. graduates in the Physical Sciences building. Thirteen students were recognized with family members and facu... Read more

Introducing 13 New Ph.D. Graduates

In a reception hosted by Dean Michael Johnson, Ph.D., the College of Sciences celebrated its new Ph.D. graduates in the Physical Sciences building. Thirteen students were recognized with family members and fac... Read more

COS Excellence in Academics

The UCF College of Graduate Studies recognized graduate students and faculty for excellence in research, teaching and mentoring at an awards ceremony during the 13th Annual Graduate Research Forum on April 5, 2... Read more

COS Shines at Student Research Week

Student Research Week celebrates the research and creative projects of UCF undergraduate and graduate students. From April 4 through April 7, graduate and undergraduate students attended workshops, presented r... Read more

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