Towards self-assembly of viruses using DNA

Seth Fraden, Brandeis University, DMR 0907428

Intellectual Merit:

The rod-like viruses fd, Y21M and M13 are 1 m in length and 7 nm in diameter. They self-assemble into a variety of liquid crystalline and other ordered structures, or form gels depending on processing conditions.

In a step forward in the use of biomaterials, we attqach oligomers of DNA to the virus to control the self-assembly. We attach the virus to surfaces, oriented either parallel, or perpendicular to to the surface. Then we add complementary DNA linkers to produce attractions between the virus to control the phase behavior and assembly kinetics.

This year we have developed protocols to attach the virus to surfaces, attach oligos of ssDNA to the virus, and to link the viruses together. We have applied characterization techniques to validate our process, as demonstrated in the figure.

A significant validation of the DNA directed assembly process was the observation of hybridization between the strand of DNA attached to the virus and a DNA strand containing a fluorescent molecule.

Fd

Fd+DNA

Y21M

B

A) Electron micrograph of fd virus B) Normalized Absorption spectrum of the Olido DNA (pink), the Fd virus (Blue) and the Fd with the attached DNA (green). A quantitative analysis of the spectra reveals the number of DNA molecules per virus. C) Gel electrophoresis of Fd virus, Y21M virus, and Virus with attached DNA. D) Sequence of melting and annealing of complementary DNA segment into the DNA attached to the virus.T=10C T=22C T=32C T=17C T=5C D

A

C

Towards self-assembly of viruses using DNA

Seth Fraden, Brandeis University, DMR 0907428

Broader Impacts:

•As part of his career development, Brandeis graduate student Rafael A. Cabanas learned how to coordinate a team of three students and organized the tasks needed to complete this project. Rafael will travel to the University of Cambridge in Spring to continue our collaboration with Dr. Erika Eiser of the Cavendish where he will conduct DNA-colloid experiments and impart his knowledge about virus biomaterials. This year he supervised:

• Katherine Elfer, an REU from Louisiana Tech University, spent the summer at Brandeis learning soft matter and bio-physics techniques. She developed methods to link the virus-DNA to each other and to surfaces.

• Camille Girabawe arrived from Rwanda in summer 2011 as a first year graduate student. Rafael taught him LabView and microfluidics and Camille is developing a “drop on demand” microfluidic device for measuring the phase diagram of biopolymers using samples of 1 nl volume.

• Taiki Nayagishima, a graduate student from the University of Cambridge Cavendish Laboratory, visited for three weeks where Rafael trained him in the production and characterization of filamentous virus.

A: Katherine Elfer during her poster presentation at the end of the Summer.

B: Camille Girabawe (right) in an evening visit to Cambridge, MA

A: Taiki Nayagishima (right) (Cambridge, UK) and Rafael A. Cabanas after a long day in the lab.