Biophysical Society Bulletin | November 2025

Biophysicist in Profile

Alisha Jones Area of Research RNA structural biology, biophysical chemistry, and chemical biology

Institution New York University

At-a-Glance

Alisha Jones , Assistant Professor of Chemistry at New York University, has pioneered new approaches in RNA structural biology since discovering her passion for biophysics as a high school student in Toledo, Ohio. Her research focuses on developing methods to study how RNAs transition between different structured states, with the ultimate goal of creating tools that make it easier to investigate RNA conformational dynamics regardless of molecular size.

Alisha Jones

For Alisha Jones , the journey into biophysics began not in a university lecture hall, but in a high school laboratory in Toledo, Ohio. As a junior in high school, she was selected to participate in the American Chemical Society’s Project SEED Program. Jones spent a transformative summer in Ronald Viola ’s lab at the University of Toledo, learning the fundamen tals of biochemistry. Looking back at slides from her first lab presentation, she finds them “hilarious, to say the least,” but they document a passionate, ambitious 16-year-old studying aspartate semialdehyde dehydrogenase (ASADH) as a poten tial target for antimicrobial development. “I aimed to determine their structures by x-ray crystallogra phy to facilitate structure-based drug design,” Jones recalls of her initial plan to work with ASADH from six different species. She managed to generate plasmids for all six species, suc cessfully expressing and purifying only one protein, but the experience was formative. “That was a really cool summer—I returned the following year to tackle a different project and have been doing research ever since,” she shares. Born in New Haven, Connecticut, Jones moved with her family to Toledo around age 10, where she remained until leaving for college. Neither of her parents worked in science—her mother was a nurse and her father a construction worker—but they recognized early signs of scientific curiosity. “I think my parents always had a hunch that I was going to be a scientist,” Jones remembers. “I mixed a lot of things together in their bathroom.” Jones pursued her undergraduate education at Miami Univer sity, earning her bachelor’s degree in chemistry and zoology before heading to the University of Washington for her PhD in chemistry. It was during graduate school that she found her true calling in RNA structural biology, drawn by two specific interests: learning nuclear magnetic resonance (NMR) spec troscopy and developing drugs for human immunodeficiency virus (HIV). Gabriele Varani ’s lab at the University of Washing ton offered the perfect intersection of both. “The lab that I joined used NMR to determine structures of RNA to facilitate

the structure-based design of peptides that could bind those RNAs with high affinity,” she provides. Her first doctoral project focused on designing peptides that could bind to the HIV transactivation response element, to block its interaction with the HIV trans-activator protein. “Blocking this interaction prevented transcription of the viral RNA,” Jones explains. “This project highlighted the importance of RNA structure.” Jones’s subsequent work on long noncoding RNAs (lncRNAs) revealed fascinating insights about evolutionary conservation. She discovered that the Cyrano lncRNA, crucial for embryonic development, adopts a structure that is conserved across species as evolutionarily distant as zebrafish and humans; remarkably, this structural conservation was maintained despite the RNA lacking sequence conservation. Although she found the project engaging, it also exposed significant limita tions in existing methodologies. She notes, “Their large sizes complicate NMR spectroscopy. Their dynamic nature makes x-ray crystallography a nightmare.” This realization sparked a pivotal decision: going forward, she would focus on studying large RNAs and on developing biochemical and biophysical methods to make it easier to investigate them. As a postdoctoral researcher, Jones demonstrated the critical role of RNA structures across diverse cellular processes, including T cell activation, microRNA processing, X-chro mosome inactivation, and viral replication. These findings reinforced her conviction that understanding RNA structure is fundamental to understanding cellular function. Today, Jones serves as Assistant Professor of Chemistry and holds the James Weldon Johnson Assistant Professor Chair at New York University. Her laboratory focuses on developing and applying methods to investigate how RNAs transition be tween different structured states. “This is important because it establishes a fundamental model for how RNAs function but also broadens the structures one can therapeutically tar get when an RNA is implicated in a disease,” she explains. The

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