The innovation engine for new materials

Sebastian Arias

Sebastian Arias

Major: 

Physics

Mentor(s): 

Lourdes Velazquez

Faculty Sponsor(s): 

Deborah K Fygenson

Faculty Sponsor's Department(s): 

Physics

Project Title: 

Optimization of DNA Nunchuck Seed Design for Accurate Measurement of DNA Bend Angle

Project Description: 

DNA has been studied extensively because its base pair sequence stores information that guides living systems. However, there is more to DNA function than its sequence. There is increasing evidence that DNA bending plays a crucial role in enzymatic processes as well as information storage and retrieval. In particular, DNA bending dynamics and its effects on gene regulation remain to be fully understood.  This is due, in part, to the absence of a reliable method of measuring DNA bend angle and bend angle dynamics.  We have shown that DNA structures resembling nunchucks can be formed via tile-based DNA nanotubes whose nucleation is controlled by DNA origami seeds. We aim to use these DNA nunchucks as mechanical amplifiers with which to visualize DNA bend angle and bending dynamics. To test this approach, we have made nunchucks with intrinsically straight and intrinsically bent linkers, and measured their bend angles over time via fluorescence video microscopy.  However, the observed angles do not correlate with linker type. We hypothesize that the discrepancy is due to an unintended feature of the nunchuck design, which places a >4kb loop of single-stranded DNA protruding in the middle of each nucleating seed. We are using the asymmetric polymerase chain reaction (aPCR) to produce smaller DNA origami seeds void of any such loop.  Here we compare DNA nanotube yields in order to describe the efficiency of aPCR at producing desired DNA sequences without affecting DNA seed formation and or function.