Advancements in biophysical studies continue to elucidate the nature of DNA organization, granting improved clarity not just with protein-DNA interactions impacted by packing or expression but the increased awareness of differnt forms of DNA. This experimental information can leveraged into studies regarding the influence interactions have on free, unbound DNA. Additionally, DNA sequence in the unbound region may offer clues into the favorability of certain DNA confirmational states derived from physical models. This talk will showcase a new computational method used in the study of DNA structural bioinformatics: use of an energy minimization toolkit that generates optimized DNA configurations with respect to the elastic energy at the base-pair step level. I will discuss basic uses of this mesoscale toolkit before leading into its successful uses with experimental data from DNA looping of both lac repression looping and minichromosomal supercoiling. I will then discuss uses of the expanded base-pair step with circular DNA to observe how nearest neighbors influence the bendability of DNA. This is done using a updated elastic rest-state potential model at both the dimer and tetrameric level as we dive into a study of sequences previously explored in circular DNA.

Science Learning Center (SLC), 2.203
800 W. Campbell Road, Richardson, Texas 75080-3021

Erik Jonsson School of Engineering and Computer Science

##bioengineering #GuestLecture #Lecture

Department of Bioengineering

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