faculty

MY RESEARCH GROUP IS GENERATING INSIGHTS AND SOLUTIONS TO problems with genome engineering, specifically CRISPR/Cas systems. Over the past few years, the slow-progressing field of genome engineering has been transformed by the breakthrough of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) with astronomical applications in science, medicine, agriculture, biotechnology, and biomanufacturing. Originally derived from the bacterial immune system, the CRISPR/Cas9 technology works by introducing two components inside cells, a Cas9 nuclease that acts like molecular scissors and a guide RNA (sgRNA) that binds with Cas9 and directs the complex to the target DNA to create double-stranded cuts in the DNA. Due to its ease of use, it is becoming a standard tool for genome engineering and the toolbox is exponentially increasing with other variants of CRISPR/Cas systems with applications in DNA and RNA manipulation. The biggest challenges for CRISPR/Cas technology that are affecting the bridge between in vitro and in vivo applications are safety, efficacy, and delivery. To address these pressing concerns, the Jain lab is focused on developing a multi-scale biomolecular engineering platform using nucleic acids chemistry, protein engineering, and nanoengineering. Specific examples include:

UNDERSTANDING AND IMPROVING SPECIFICITY CRISPR/Cas9 can tolerate several mutations in the DNA resulting into undesirable off-target cleavage. What if we change the length and chemistry of the guide RNA? What if we can control the degradation of the CRISPR/Cas complex immediately after it cuts the on-target DNA? Our primary goal is to understand the molecular basis of this issue to be able to engineer CRISPR/Cas systems with improved specificity by modifying its components using nucleic acids design and protein engineering. We employ an array of bioanalytical techniques with immediate applications for the detection and treatment of genetic disorders.

TARGETED DELIVERY OF CRISPR/CAS SYSTEMS Despite the vast literature highlighting the delivery issues with CRISPR/Cas systems, it remains a major concern. How can we get large molecules like Cas9 protein and sgRNA inside the nucleus of a cell? How can we protect the components from degradation or immune response? The answer lies in developing safe and effective non-viral delivery methods. We aim to design multifunctional targeted nanoparticle systems that can protect CRISPR/Cas from degradation and target specific tissues in vivo with immediate applications for detection and treatment of cancer.

Education

Postdoc, 2013-2018, Massachusetts Institute of Technology
Ph.D., 2013, University of Missouri-Kansas City
B.Pharm., 2006, Dr. Hari Singh Gour University (Central University)

Research Areas

Bioengineering
Gene Editing
CRISPR/Cas
Nucleic acids & Protein Engineering
Nanomaterials
Responsive Systems

Awards & Distinctions

• National Academy of Inventors (NAI) Senior Member, 2025
• University of Florida Provost’s Excellence Award for Assistant Professors, 2023
• Excellence Award for Assistant Professors, Herbert Wertheim College of Engineering, 2023
• Maximizing Investigators’ Research Award (MIRA) for Early Stage Investigator (ESI), NIH-NIGMS, 2022
• Shah Rising Star Professorship, 2020

Selected Publications

• Rananaware SR, Narisetty KV, Shah R*, and Jain PK* (2026) Down to business: CRISPR-based ex vivo gene editing of donor organs, Nature Reviews Bioengineering, doi.org/10.1038/s44222-026-00462-2.
• Orosco C^§, Huang B^§, Rananaware SR^§, Bodin AP, Browning I, Fang A, Baugh MP, Lange IH, Elhabashy YB, Balaraju M, Lewis JG, Shah NH, Hanna MP, Flannery SJ, Meister KS, Karalkar V, and Jain PK* (2026) DNA-guided CRISPR/Cas12 for cellular RNA targeting, Nature Biotechnology, doi.org/10.1038/s41587-026-03129-w.
• Nguyen LT^§, Rakestraw NR^§, Pizzano BLM, Iyyappan R, Young CB, Huang Y, Beerensson KT, Fang A, Antal SG, Anamisis KV, Peggs CMD, Yan J, Jing Y, Lewis JG, Burdine RD, Adamson B, Jiang Z, Toettcher JE, Myhrvold C*, and Jain PK*  (2026) Efficient genome editing with chimeric oligonucleotide-directed editing, Nature Communications, doi.org/10.1038/s41467-026-71624-4.
• Iyyappan R, Niu Y, Hao M, Pajdzik K, Rakestraw NR, Jain PK^#, He C, Zong C, Jiang Z (2026) Single-nucleotide Resolution Epitranscriptomic Profiling Uncovers Dynamic m6A Regulation in Bovine Preimplantation Development, Cell Reports, 2026.
• Rananaware SR, Shoemaker GM, Pizzano BLM, Vesco EK, Sandoval LSW, Lewis JG, Bodin AP, Flannery SJ, Lange IH, Pedada D, Fang A, Antal SG, Aguilar D, Rakestraw NR, Karalkar VN, Meister KS, Nguyen LT, Jain PK* (2025) AsCas12a tolerates insertions in target DNA, Nucleic Acids Research, 53(17), doi.org/10.1093/nar/gkaf887.
• Xun G, Zhu Z, Singh N, Lu J, Jain PK^#, Zhao H* (2024) Harnessing noncanonical crRNA for highly efficient genome editing, Nature Communications, 15(1), 3823. doi.org/10.1038/s41467-024-48012-x.
• Nguyen LT§, Macaluso NC§, Rakestraw NR§, Carman DR, Pizzano BLM, Hautamaki RC, Rananaware SR, Roberts IE, Jain PK* (2024) Harnessing noncanonical crRNAs to improve functionality of Cas12a orthologs, Cell Reports, 43(2), 113777. doi.org/10.1016/j.celrep.2024.113777.
• Rananaware SR, Vesco EK, Shoemaker GM, Anekar SS, Sandoval LSW, Meister KS, Macaluso NC, Nguyen LT, Jain PK* (2023) Programmable RNA detection with CRISPR-Cas12a, Nature Communications, 14(1), 5409. doi.org/10.1038/s41467-023-41006-1.
• Nguyen LT, Rananaware SR, Yang LG, Macaluso NC, Ocana-Ortiz JE, Meister KS, Pizzano BLM, Sandoval LSW, Hautamaki RC, Fang ZR, Joseph SM, Shoemaker GM, Carman DR, Chang L, Rakestraw NR, Zachary JF, Guerra S, Perez A, and Jain PK* (2023) Engineering highly thermostable Cas12b via de novo structural analyses for one-pot detection of nucleic acids, Cell Reports Medicine, 4(5), 101037. doi.org/10.1016/j.xcrm.2023.101037.
• Nguyen, LT, Macaluso, NC, Pizzano BLM, Cash, M, Spacek J, Karasek J, Dinglasan RR, Salemi, M, and Jain PK* (2022) A Thermostable Cas12b from Brevibacillus Leverages One-pot Discrimination of SARS-CoV-2 Variants of Concern, eBioMedicine- The Lancet, 77, 103926. doi.org/10.1016/j.ebiom.2022.103926.