What does it take to bring new chemistry to life?
Our lab answers this question by genetically engineering microbes.
We engineer them to biosynthesize chemical functional groups that are underrepresented in nature.
Here is our general approach:
Step 1: To enable the retention of many of these functional groups,
we start by eliminating entire categories of native enzymes responsible for their modification.
Step 2: To allow the cell to autonomously form these functional groups on building blocks,
we design routes to biosynthesize non-standard amino acids (nsAAs).
Step 3: To enable the formation of macromolecules that contain these functional groups for expanded function,
we couple the biosynthesis of nsAAs to modules that install nsAAs within proteins.
Step 4: To control where engineered microbes survive and to leverage evolution for improvement of steps 2 and 3,
we engineer microbes to make their survival depend on the provision or biosynthesis of nsAAs.
In summary, across our research areas, we engineer living cells to:
allow the new chemistry to happen,
produce building blocks that contain the chemistry,
introduce the chemistry within proteins,
and to rely on the chemistry.
Our technologies could help improve the sustainability of chemical manufacturing, create better vaccines and therapeutics, increase the resiliency of food crops, develop new ways to recycle or upcycle plastic and biomass wastes, and more.
Our lab answers this question by genetically engineering microbes.
We engineer them to biosynthesize chemical functional groups that are underrepresented in nature.
Here is our general approach:
Step 1: To enable the retention of many of these functional groups,
we start by eliminating entire categories of native enzymes responsible for their modification.
Step 2: To allow the cell to autonomously form these functional groups on building blocks,
we design routes to biosynthesize non-standard amino acids (nsAAs).
Step 3: To enable the formation of macromolecules that contain these functional groups for expanded function,
we couple the biosynthesis of nsAAs to modules that install nsAAs within proteins.
Step 4: To control where engineered microbes survive and to leverage evolution for improvement of steps 2 and 3,
we engineer microbes to make their survival depend on the provision or biosynthesis of nsAAs.
In summary, across our research areas, we engineer living cells to:
allow the new chemistry to happen,
produce building blocks that contain the chemistry,
introduce the chemistry within proteins,
and to rely on the chemistry.
Our technologies could help improve the sustainability of chemical manufacturing, create better vaccines and therapeutics, increase the resiliency of food crops, develop new ways to recycle or upcycle plastic and biomass wastes, and more.
VisionImagine a future where we can harness our understanding of biology to improve every facet of our lives through biomolecular engineering - from the materials we touch, to the clothes we wear, to the food we eat, to the air we breathe, and to the health we experience. Engineering microbes can help make our society more sustainable, healthier, and more equitable. Advances in synthetic biology are helping us start to realize parts of this vision, but we are limited by what molecules engineered microbes can make and where these microbes can make them.
To help address both of these limitations for the betterment of human and environmental health, our lab programs cells to create and harness building blocks that are uncommon to nature. Join our team and help us bring this future closer to reality. AffiliationsWe are connected with various departments, programs, and national institutions that provide different ways of joining our lab and engaging with the university or synthetic biology communities after joining the lab.
We are part of the Chemical & Biomolecular Engineering Department, the Chemistry-Biology Interface Program, the Microbiology Graduate Program, and the Center for Plastics Innovation at the University of Delaware. We are also affiliated with the Delaware Biotechnology Institute and the Delaware Environmental Institute. At the national level, we are members of the Engineering Biology Research Consortium and the Manufacturing Innovation Institute BioMADE . SkillsWhile every project in the Kunjapur Lab is unique, the lab has a set of core competencies that most of our graduates receive training in.
From a discipline perspective, we guide graduates towards a Systems and Synthetic Biology framework that consists of familiarity with the different "-omes" (genome, transcriptome, metabolome, proteome) that cells have and how to manipulate them. For example, this often involves genome engineering (to stabilize new chemistries), metabolic engineering (to biosynthesize new chemistries), and protein engineering (to introduce new chemistries within proteins). From a skills perspective, we emphasize training in the ABCs: Analytical: liquid chromatography, high-resolution mass spectrometry, intact or digested protein mass spectrometry, flow cytometry Biological: molecular cloning, recombineering, genetic circuit design, genetic code expansion, library design, protein purification, biochemical characterization Computational: sequence similarity network construction, protein structure prediction, protein-substrate docking, next-generation sequencing analysis, machine learning guided enzyme engineering soft skills: writing, speaking, plotting, and illustrating to expert and lay audiences Organisms: Most projects feature E. coli to more rapidly demonstrate proofs-of-concept, though an increasing number include work with a second organism such as mammalian cells or Bacillus subtilis. Many projects explore and compare the use of cell-based and cell-free chemical transformations. |
Recent Lab NewsFall 2025:
Aditya was honored to receive the Department of Energy's Early Career Researcher Award. Aditya enjoyed being on sabbatical in Denmark as an Otto Mønsted Visiting Professor at Denmark Technical University. Congrats to Dr. Neil Butler and Nitro Biosciences for receiving an NSF STTR grant! Congratulations to Roman, Mandy, Shelby, and Madan for successfully defending their doctoral theses! Summer 2025: Congratulations to Austin for successfully defending his master's thesis! Aditya was honored to receive some recognitions from the University of Delaware, including the Roberta Colman Innovation Award (along with John Koh and Shelby Anderson in recognition of the CBI Bootcamp initiative), the Gerard J. Mangone Young Scholar Award from the Francis Alison Society, and promotion to Associate Professor with tenure. Spring 2025: Mandy's paper on demonstrating an exclusive reliance between one engineered organism and another was accepted for publication in Nature Microbiology. Congrats, Mandy! Congratulations to Dr. Sunny Sen on successfully defending his doctoral thesis! Jan 2025: Aditya organized two special events this month: 1) The 2025 Mid-Atlantic Synthetic Biology Network Symposium - held at U. Delaware and with free registration thanks to several event sponsors. Registration is full with >220 registrants. 2) A pilot edition of a Chemical Biology Bootcamp for the Chemistry Biology Interface program fellows Fall 2024: A company spun out of the lab and led by Dr. Neil Butler, Nitro Biosciences, has secured an Early Stage Growth Grant from the Delaware Innovation Space, a 2024 Delaware EDGE Grant, and a BARDA Vital Dev award. Nitro has secured independent lab space and will be looking to hire soon. Aditya is now the Thomas Willing Early Career Assistant Professor of Chemical & Biomolecular Engineering and is grateful to the Willing family for their support. Aditya was honored to be awarded the 2024 B&B Daniel I.C. Wang Award with an accompanying lecture at the 2025 ACS BIOT meeting. Michaela was recognized as a Rising Star in Chemical Engineering by MIT and attended the ChemE Rising Stars Workshop. She will soon start as a post-doc at MIT. Congrats, Michaela! Shelby's paper on constructing a one-pot biocatalytic cascade to synthesize L-phenylalanine derivatives from aryl aldehydes or carboxylic acids was accepted for publication in ChemCatChem. Congrats, Shelby! Summer 2024: Welcome to the lab, undergraduates Lekha Antala and Justin Swing, Master's student Niteesha Adapala, and Ph.D. student James VanAntwerp. Congratulations to Dr. Michaela Jones for defending her doctoral thesis! Aditya was elated to receive the College of Engineering Early Career Faculty award. Congratulations to Dr. Neil Butler for receiving the Allan P. Colburn Prize for Outstanding Dissertation in the Mathematical Sciences and Engineering! Apr 2024: Congratulations to Michaela on receiving the 2024 Saurabh A. Palkar Graduate Award for Mentoring! Congratulations to Shelby on receiving the 2024 Richard Wool Award for Women in Green Engineering! Aditya was honored to receive the Grand Prize for the 2024 BioInnovation Institute & Science Prize for Innovation. The prize included an opportunity to have an essay about our entrepreneurial directions published in Science and a chance to chat with folks from the journal. Aditya was also honored to receive the Outstanding Faculty Award from the Delaware Valley Section of the AIChE. Our biocatalysis team published a couple of interesting review articles. Check out Madan's review on using biocatalysts for selective functionalization towards polymer upcycling applications, and check out the team's review, led by Roman, on flavor and fragrance biosynthesis. Jan 2024: Welcome to the lab, Ph.D. student Monona Khare and Lab Coordinator Dana Arnold! |
