Exploring the Viability of 5-Nitroindole as a Novel Infrared Probe of DNA Local Environment

Christina working at lab bench


Engineering and Applied Sciences


Professor of Chemistry

Project Summary

This summer, as part of the Penn Undergraduate Research Mentorship program, I worked under the mentorship of principal investigator, Dr. Feng Gai; graduate student, Ismail Ahmed; and other members of the Gai lab to investigate new and exciting developments in physical chemistry and spectroscopy.

Dr. Gai’s lab recently developed a blue fluorescent unnatural amino acid that currently stands as one of the most promising fluorophores for biological spectroscopy and imaging due to its undisruptive small size, emission in the visible spectrum, and other attractive photophysical properties. The lab previously showed that it could be incorporated into antimicrobial peptides (AMPs) to monitor and analyze the mechanism by which AMPs (an essential part of all life forms’ innate immune response to microbial infection) cause cell death. However, the photophysical properties of this amino acid may change when exposed to different local environments, so my responsibility was to assist in testing whether and how these properties change when the unnatural amino acid is incorporated into dipeptides with basic, acidic, aromatic, polar, and nonpolar amino acids. Essentially, this would give us a sense of how viable the fluorophore would be in a larger range of biological studies.

This work required me to learn how to perform F-moc peptide synthesis and hand-coupling, sample purification using an HPLC, mass-verification using a MALDI-TOF mass spectrometer, absorption and emission spectra collection using a UV-Vis spectrophotometer and a fluorimeter, and quantum yield calculation.

I also took on the project of exploring the viability of novel probes for infrared spectroscopy. These probes have the potential to be incorporated into DNA and used to better understand the effects that local electric fields have on DNA molecules (for instance, on its structure and folding/conformations) by quantifying those fields. I performed vibrational solvatochromism studies on two proposed probes and learned how to construct a homemade IR cell, use a Fabry–Pérot interferometer, and curve-fit spectral data in the process.

My summer experience in Dr. Gai’s lab was incredibly enriching. First-hand experience with the spectrometers and application of principles in physical chemistry and quantum physics not only broadened my knowledge base, but strengthened my understanding of concepts I had previously only read of in my chemistry, biotechnology, and quantum courses. Over the course of the summer, I also learned how to become more proficient, responsible, and intentional with my research.

I loved working with the members of the Gai lab, and appreciate their insights into opportunities within the field of chemistry research and graduate studies, in general. Being surrounded by people who are passionate about their research has further encouraged me to strongly consider these options for my future. I am grateful for the opportunity to conduct summer research through PURM, and am thankful to Dr. Gai and the members of his lab for such an enjoyable experience.