Biophysical Applications of a Combined Atomic Force/Fluorescence Microscope Part 1: Blood clotting and NanoSelection® drug discovery

In my first talk, I will describe two of the more mature research projects in my lab; in both we utilize a combined Atomic Force/Optical Microscope to study biophysical problems.

1. The major structural component of a blood clot is a mesh of fibrin fibers (diameter ~ 100 nm), and these fibers have the mechanical task of stemming the flow of blood. Over the last few years we have studied the mechanical properties of single fibrin fibers (see figure), with the goal of developing a deeper understanding of blood clot mechanical behavior. We found that fibrin fibers are extraordinarily extensible and elastic. They can be stretched to over three times their length before breaking and about twice their length before incurring permanent damage. This large elasticity is especially surprising in light of the semi-crystalline internal structure of fibrin fibers, and it implies that the individual fibrin monomers must be elastically extensible. We also determined the Young’s modulus (~ 4 MPa) and numerous other mechanical properties such as relaxation, and energy loss and energy storage.
Our future goal is develop a mechanical model of a blood clot, to relate the mechanical properties to diseases, and to device better methods for blood clot dissolution (as need in heart attacks and strokes).

2. In collaboration with a start-up company we are developing a novel drug discovery method to screen oligonucleotides and oligonucleotide-encoded molecules, such as the DNA-encoded macrocycles created by Dr. Liu (Harvard University). In this method, termed Lab-on-Bead™ NanoSelection®, nanobeads functionalized with potential drug candidates are flowed over a target area, for example, a surface functionalized with Scr kinase – a molecule implicated in some cancers. Binding of nanobeads is observed via optical microscopy, and target bound beads are extracted via a nanoManipulator. The DNA on the extracted bead is PCR amplified and sequenced, which allows positive identification of the encoded macrocycle.