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Albany 2019: 20th Conversation - Abstracts

category image Albany 2019
Conversation 20
June 11-15 2019
Adenine Press (2019)

Computational Design of DNA Scaffold for Optimization of CryoEM

The ability of DNA to bind proteins and other molecules makes it an ideal candidate for its use as a scaffold to which biomolecules can be attached. In this study circular DNA scaffolds of varying sizes have been designed. Curvature in the DNA ring is induced by the bacterial DNA binding protein Integration Host Factor (IHF). It is a heterodimer with an alpha helical body and two protruding beta sheet arms. These arms interact within the minor groove of DNA, and proline residues within the arms stabilize the DNA bending. Molecular dynamic simulations were run to determine the mechanics and stability of the DNA ring itself, as well as the mechanics and stability of IHF protein binding. Wet lab experiments are also being conducted to create the physical construct. Applications for this scaffold include its use in cryo-electron microscopy (CryoEM), a new molecular imaging technique that enables researchers to determine the structure of biomolecules. CryoEM requires biomolecules to be at least 200 kDa and maintain an axis of symmetry in order to obtain an accurate image of the structure. Thus, attaching biomolecules less than 200 kDa will enable them to be readily visualized by CryoEM. Additional functionality of this scaffold includes the facilitation and subsequent imaging of weak binding interactions.

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Kendar Serindag 1,2
Kelly M. Thayer 2,3,4
David L Beveridge 2,3
David R. Langley 2,3,5

1 Department of Molecular Biology and Biochemistry 2
Department of Chemistry3
Molecular Biophysics Program 4
Department of Computer Science
Wesleyan University
Middletown, CT 06459 US

5 Arvinas, New Haven, CT 06511

Email: kserindag@wesleyan.edu