A scientist has devised a standard protocol for measuring distances in biomolecules. Architects cannot build a house without the proper dimensions of the foundation. Likewise, scientists cannot develop targeted drug therapies without first measuring the surfaces of biomolecules such as proteins, RNA or DNA. The study was published in Nature Methods.

Biomolecule

The best practice for gathering these measurements is hotly contested in the fields of biophysics and structural biology because scientists prefer different, personalized methods that often yield a variety of results for one given biomolecule.

In a race to the finish, a team of 27 labs across the world including Hugo Sanabria's "Single Molecule Biophysics" lab at Clemson University -set out to address this discrepancy. Their findings, they have developed a standardized protocol for Förster resonance energy transfer (FRET), arguably one of the most precise methods of measuring distances within biomolecules.

In FRET, two chromophores, or light-sensitive chemical compounds, are attached to a biomolecule at two different positions. When the chromophores fall in proximity to one another and are positioned in just the right orientation, an energy transfer occurs from one chromophore in the excited state a donor to the other chromophore an acceptor.

After incorporating Förster's theory, which describes the energy transfer process between the two chromophores, the distance between them can be captured under a microscope. One way is when you fix your sample on a microscope cover glass, and you look at that one molecule for a standard period. These are immobilization studies.

The other method is when the molecules are moving around, so they're free to diffuse, and you sample many individual molecules over many short periods of time.  The idea to bring together the two methodologies came in 2012 at a conference in Germany, where researchers in the single molecule community put in motion a worldwide benchmark study for determining FRET efficiencies.

In the study, the participating researchers each were sent two sets of double-stranded DNA molecules that were tagged with FRET chromophores at differing positions. Some researchers measured the molecules using the immobilization method and others with the diffusion method. 

Structural Biology

With this study comes an expanded set of capabilities in structural biology for measuring molecules of different shapes and sizes and producing newfound structural models of those molecules. And FRET, Sanabria says, is the only method that can overcome size and stability limitations that the "golden standards of structural biology."

As pioneers of the FRET methodology, Sanabria and his colleagues in the single molecule community are working to deposit the structural models of biomolecules uncovered by FRET into a publicly available database so that interested researchers can further their studies into structural biology.