Nesterova, I. V.; Briscoe, J. R.; Nesterov, E. E. Rational Control of Folding Cooperativity in DNA Quadruplexes. J. Am. Chem. Soc. 2015; 137(35), 11234–7.
Nesterova, I. V.; Elsiddieg, S. O.; Nesterov, E. E. A Dual Input DNA‐based Molecular Switch. Mol. BioSyst. 2014; 10(11), 2810–4.
Nesterova, I. V.; Nesterov, E. E. Rational Design of Highly Responsive pH Sensors Based on DNA i‐Motif. J. Am. Chem. Soc. 2014; 136(25), 8843–6.
Nesterova, I. V.; Elsiddieg, S. O.; Nesterov, E. E. Design and Evaluation of an i‐Motif‐Based Allosteric Control Mechanism in DNA–Hairpin Molecular Devices. J. Phys. Chem. B. 2013; 117(35), 10115–21.
Nesterova, I. V.; Hupert, M. L.; Witek, M. A.; Soper, S. A. Hydrodynamic Shearing of DNA in a Polymeric Microfluidic Device. Lab Chip. 2012; 12(6), 1044–7.
Nesterova, I. V.; Bennett, C. A.; Erdem, S. S.; Hammer, R. P.; Deininger, P. L.; Soper, S. A. Near‐IR single fluorophore quenching system based on phthalocyanine (Pc) aggregation and its application for monitoring inhibitor/activator action on a therapeutic target: L1‐EN. Analyst. 2011; 136(6), 1103–5.
Nesterova, I. V.; Erdem, S. S.; Pakhomov, S.; Hammer, R. P.; Soper, S. A. Phthalocyanine Dimerization‐Based Molecular Beacons Using Near‐IR Fluorescence. J. Am. Chem. Soc. 2009; 131(7), 2432–3.
Nesterova, I. V.; Verdree, V. T.; Pakhomov, S.; Strickler, K. L.; Allen, M. W.; Hammer, R. P.; Soper, S. A. Metallo‐phthalocyanine near‐IR fluorophores: Oligonucleotide conjugates and their applications in PCR assays. Bioconjugate Chem. 2007, 18(6), 2159–2168.
Research in our group evolves around the development of new platforms for analysis of biologically relevant targets. Students working in my lab will become proficient in the variety of contemporary analytical techniques and will develop a solid vision and understanding of the modern field of biological analysis. My ultimate goal is to train the students to become successful in their research field. Therefore, upon graduation, they will be well equipped to pursue their professional dreams and will be competitive in the modern analytical chemistry job market.
Figure 1. From a chemist's point of
view, DNA is a polymeric material
composed of four monomers.
In one of the projects, we focus on the development of sensing materials based on DNA backbone. DNA is a well‐known genetic material that is present in humans and in almost all other living systems as a carrier of genetic information. Billions of years of evolution resulted in DNA to be very stable, programmable, compatible with biological systems, and nontoxic. No wonder, it is very attractive for us, chemists, to look at DNA beyond its pure biological role and to try to take advantage of its refined by the Nature properties in order to design practically useful molecular devices.
One of the ways we can take advantage of DNA versatility is to use it to develop molecular sensors compatible with biological applications. In order to develop such molecular devices, we design short synthetic DNA strands specifically designed to bind a particular target. DNA in living system exists as double helix with two complementary strands held together via hydrogen bonding between either G–C or A–T base pairs. However, it is well established that DNA strands can get involved into noncanonical binding (different from classic base pairing, Figure 2). For analytical chemists, the fact that noncanonical structures can bind various non‐oligonucleotide targets significantly extends utility of the DNA‐based sensing systems.
For example, currently we are working on the development of molecular sensors capable to quantify very small changes in H+ concentration. The devices promise to find utility in various applications: either for accurate measurements of differences in pH inside cells and living systems or as detectors of very small amounts of protons released as result of biochemical processes (many of those proceed with protons participating). The sensors are based on a noncanonical DNA i‐motif, a single‐stranded DNA that binds protons and changes its conformation into quadruplex upon the binding event. The transition proceed with high cooperativity. Cooperativity is one of the mechanisms the Nature developed to generate sharp responses. Deliberate incorporation of the mechanism in molecular sensing systems allows achieving detection sensitivities unparalleled with conventional sensors.
In order to improve the device's performance and to maximize its sensitivity we are developing of set of structural and kinetic tools to control its folding mechanism. For example, we deliberately modify the devices and include special guiding elements to control folding mechanism kinetically. The guiding elements minimize number of stable intermediate structures yielding ultimately higher response sensitivity (Figure 3).
Other sensing systems are also being developed. Please, do not hesitate to stop by and talk about ongoing projects in my group!
Figure 3. Mechanism of i‐motif folding (above) can be controlled via deliberate incorporation of kinetic control element (hairpin, green, below) resulting in minimized formation of misfolded structures. The modification ultimately yields sharper response sensitivities.
PostDoc, Louisiana State University, 2006–2012
Ph.D. (Chemistry), Moscow State University, 1997
B.S., M.S. (Chemistry), Moscow State University, 1992
Development of sensing systems for biological analysis; methodology of bioanalysis; biocompatible signal transduction platforms; monitoring of biochemical events inside cells; and in vitro.
Figure 2. Examples of noncanonical DNA structures.
Some of the structures not only exist in living systems
but also have biological significance.