Presentation Title

A Single-molecule Analysis to Analyze the Influence of DNA Base-Stacking Interactions in DNA Stability

Panel Name

Advances in Biomedicine and Neuroscience

Location

Lecture Centre Concourse

Start Date

3-5-2019 3:00 PM

End Date

3-5-2019 5:00 PM

Presentation Type

Poster Session

Academic Major

Biology

Abstract

DNA base stacking is thought to play a critical role in the stability of nucleic acid structures. In this project, we will investigate DNA base stacking at the single-molecule level using the Centrifuge Force Microscope (CFM). Our CFM design allows for research grade video microscopy, and a wireless transmission capability to simultaneously monitor hundreds of individually tethered microspheres as they are subjected to centrifugal force inside a conventional benchtop centrifuge. Previously, we designed DNA probes that can be anchored to microspheres and a glass surface which can hybridize to each other (through a 7-nucleotide overhang) creating a DNA tether between glass surface and microsphere. The DNA probe’s design allows for the incorporation of various degrees of spacing between the interfacial base-stacks of each strand. Our previous results from a pilot study show that strand dissociation occurred quicker as interfacial base-stacks in the DNA probe were removed. Future experimentation will focus on exposing the DNA tethers to different levels of centrifugal force to determine the half-life of the DNA tethers and the associated Koff. We will determine the base-stacking energy for the interfacing base-stacks by comparing the activation energy obtained from the off-rate of various combination of DNA probes with varying interfacial base-stacks. This information will contribute to increased understanding of the influence of DNA base stacking interactions on the overall stability of the DNA double helical structure.

Select Where This Work Originated From

Honors College Thesis

Award

Sorrell Chesin Research Award

First Faculty Advisor

Ken Halvorsen

First Advisor Email

khalvorsen@albany.edu

First Advisor Department

RNA Institute

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May 3rd, 3:00 PM May 3rd, 5:00 PM

A Single-molecule Analysis to Analyze the Influence of DNA Base-Stacking Interactions in DNA Stability

Lecture Centre Concourse

DNA base stacking is thought to play a critical role in the stability of nucleic acid structures. In this project, we will investigate DNA base stacking at the single-molecule level using the Centrifuge Force Microscope (CFM). Our CFM design allows for research grade video microscopy, and a wireless transmission capability to simultaneously monitor hundreds of individually tethered microspheres as they are subjected to centrifugal force inside a conventional benchtop centrifuge. Previously, we designed DNA probes that can be anchored to microspheres and a glass surface which can hybridize to each other (through a 7-nucleotide overhang) creating a DNA tether between glass surface and microsphere. The DNA probe’s design allows for the incorporation of various degrees of spacing between the interfacial base-stacks of each strand. Our previous results from a pilot study show that strand dissociation occurred quicker as interfacial base-stacks in the DNA probe were removed. Future experimentation will focus on exposing the DNA tethers to different levels of centrifugal force to determine the half-life of the DNA tethers and the associated Koff. We will determine the base-stacking energy for the interfacing base-stacks by comparing the activation energy obtained from the off-rate of various combination of DNA probes with varying interfacial base-stacks. This information will contribute to increased understanding of the influence of DNA base stacking interactions on the overall stability of the DNA double helical structure.