KimChi Nguyen, Biochemistry and Molecular Biology
“Determination of dsDNA Binding Site on Gene 32 Protein”
Bacteriophage T4 gene 32 protein is known to be a single-stranded binding protein which aids in the replication and repair of its own DNA within a host cell. In DNA replication, gene 32 protein helps in protecting the DNA from nuclease attack, destablization of the double-stranded helix, and guiding important protein factors to the replication site. Gene 32 protein has a high affinity for binding to single-stranded DNA; its cooperative binding abilities are due to the conserved amino acid sequence (Lys-Arg-Lys-Ser-Thr) within the binding cleft known as the Last Motif. Recent experiments suggested that gene 32 protein also contains a cluster of positive charges in a chin-like region that electrostatically interacts with double-stranded DNA. This electrostatic interaction with double-stranded DNA allows the protein to approach the replication fork and carry out its replication functions. The focus of the proposed experiment is to use DNA affinity chromatography method to obtain the binding constant for the interaction of the wild-type protein with DNA. Then we will compare the binding constant of the wild type with that of protein with a mutated chin. The result of this experiment will confirm the theory that the lysine residues are important for the protein's interaction with double-stranded DNA. This is critical because the interaction accelerates the rate at which the single- stranded binding protein gets to the single-stranded DNA in order to protect it from nucleases.
How did you find your mentor for your research project?
I have always been interested in research. In the summer of my sophomore year, I emailed Dr. Richard Karpel expressing my interest in his lab. It was a very exciting moment when Dr. Karpel emailed me back to set up a date to talk about his research. As a result, since fall 2012 I have been working in Dr. Karpel’s lab.
How did you know this was the project you wanted to do?
I started out working on projects with other undergraduates in my lab, familiarizing myself with the experiments and how to work the different instruments needed for our research. Dr. Karpel approached me one day and asked me if I wanted to work on my own project. I have always wanted the experience of independently leading a project, so I accepted. I knew I wanted to work on the project Dr. Karpel suggested because it is the same concept to which I have been exposed while working with other experienced undergraduates. However, this project will be a new learning experience for me because instead of working with ssDNA, my project will focus on dsDNA. I hope that my project will further our understanding of the interaction of dsDNA with gene 32 protein.
Is this your first independent research?
No, this is not my first independent research project. However, it is my first project that involves funding.
How much time do you put into it?
I started to work on my URA project in the spring 2012. I have been working about 10 hours a week in the summer. I plan to work 5-8 hours a week during the academic year.
How did you hear about the Undergraduate Research Award (URA) program?
Many of my undergraduate friends who work in various research labs recommended that I look into the Undergraduate Research Award. Dr. Karpel gave me a research topic, emailed me the URA application, and encouraged me to give it a try. He said to try my best and even if I was not accepted, the application process would give me experience in the future with writing proposals and asking for funding.
What academic background did you have before you applied for the URA?
I had already finished Biochemistry and was taking Biochemistry II at the time, so I felt like I was prepared for this project.
Was the URA application difficult to do?
The application was not hard to do. It was very straightforward. The process of filling out the application allowed me to expand my ideas on the topic and I was able to understand more about my project as a whole.
How much did your mentor help you with the application?
Dr. Karpel helped me proofread my application. He also gave me suggestions to improve the background information section on my application. He was very helpful and supportive.
What has been the hardest part about your research?
The hardest part of my research so far is my attempt to produce DNA cellulose because the absorbance of dsDNA was too low, so I had to repeat the process. This process requires much time because the DNA cellulose takes weeks to dry.
What else are you involved in on campus?
I have been a volunteer of Health Leads for three semesters now. Health Leads is a volunteer group that addresses the socio-economic needs of patients in impoverished areas. We help patients at St. Agnes Hospital obtain resources that can help them access employment, health insurance, adult education, and many more benefits. Starting in fall 2012, I will be a Campus Coordinator of Health Leads. In addition, I am peer mentor for Psychology 100 and President of the Vietnamese Student Association.
What is your advice to other students about getting involved in research?
Do not be afraid to approach faculty members about being a part of their research. If they see that the student is passionate and sincere about their research, then they will happily let the student in their lab. Our campus is full of research resources, you simply have to ask, and someone will guide you.