CAD-assisted Drug Design Using DNA Strands

Scientists have developed a CAD drug development system that uses  synthetic DNA as a programmable molecular substrate. These strands of synthetic DNA can be constructed to have any sequence of bases. And, because complementary sequences of DNA are mutually attractive, synthetic strands can be created with sequences that cause them to align with one another and bind to form nanostructures of virtually any shape. If the DNA strands are bound to other molecular species (say, tumor-killing molecules) before self-assembly is induced, the tumor killers can be pulled into desired locations by the DNA strands during self-assembly.

In other words, LEGO for molecules.*

This is paid for partly by NSF funding, but curiously enough a private company seems to have a lock on it.  Parabon Nanolabs™ has simplified this concept down to CAD-based software for the budding mad scientist.  The Parabon inSēquio™ Sequence Design Studio graphically enters designs and then determines the DNA sequences that will self-assemble into that design.

The graphic editor lays out a nanostructure visually. Users can rotate and bend strands, define bindings between base pairs, and copy and paste sequences and structures between design documents. The cloud-based number-crunching uses a bunch of known wet-chemistry values for the binding energies and calculates the complex molecular interactions required to make the molecule desired. 

Neat, huh? This would be entirely impossible for a human to do, ever; it’s billions of calculations that need to be made and complex rules to be followed.**

Still, how they will mock up the synthesized molecules themselves should be an interesting technical feat;  I would really like to see the execution of this, rather than a neat CAD program for molecules.***

Announcement here. Parabon Nanolabs here.

 

* Some assembly required.

** Another reason not to be a chemist.

*** It’s not impossible; use synthesizers to make the short pieces, PCR copy them, keep them salty enough that they can’t self-assemble before all the other pieces are made, mix together and pray.  The devil is in these details.  Maybe we can get Rob Park to do it.