Prof. Yulia Gerasimova

Abstract: Nucleic acid interrogation with colorimetric and fluorescent DNA probes: Nucleic acid analysis has benefited from the development of hybridization probes that interrogate nucleic acids in a sequence-specific manner. We have efficiently utilized a split approach for the design of hybridization probes based on deoxyribozymes and aptamers as scaffolds. In split probes, analyte-recognizing fragment of the probe is divided into two parts. The two parts need to be simultaneously bound to the target for generation of either fluorescent or colorimetric signal. This approach offers such advantages as excellent selectivity, efficient interrogation of structured nucleic acid sequences, use of a universal signal reporter, and (for fluorescent probes) tolerance to inhibitors in complex mixtures (e.g. cell lysates).ÿ A promising reporter system for hybridization analysis is based on light-up aptamers, among which DNA aptamers are preferable over RNA counterparts due to greater stability and lower synthetic cost. We have studied a recently reported light-up DNA aptamer and discovered its ability to bind and increase fluorescence of otherwise non-fluorescent dyes including commercially available auramine O and crystal violet. Based on mutagenesis, spectroscopic and molecular simulation data, we proposed the structure of the aptamer and its dye-binding site. The data can be used in designing aptamer-based probes. Most recently, we discovered the preferential binding of GelRed (a commercial gel staining dye) to single-stranded oligothymidylate sequences, which suggests that poly(dT) may exhibit a regular structure, and may open a route towards designing fluorescent light up sensors. To enable in-field interrogation of nucleic acid targets, a hybridization assay would benefit for an easy-to-read signal output, such as a color change.ÿ We took advantage of a peroxidase-like activity of oligonucleotides that have a propensity to fold into a parallel guanine quadruplex structure to develop colorimetric/visual sensing systems. Such systems were used for interrogation of nucleic acid sequences to enable detection and drug-susceptibility testing of bacterial pat