The DNA molecule is usually thought of as a coded sequence of instructions written out in a long string which is folded tight to save space. But as was recently shown by physicists at Leiden University, the folding itself and mechanics of the molecule are also factors that influence how DNA works. Now a team of Stanford researchers have come up with a way of measuring the orientation and movement of individual dyes labeling DNA, providing an insight into the nature of the molecule beyond its genetic sequence.
Reported in the journal Optica, the new technique utilizes single-molecule microscopy to identify the direction that fluorescent dye particles take on when attached to DNA molecules. By also noticing their motion, and combining information from thousands of molecules at the same time, a complex picture of the mechanics of DNA is produced.
The technology will certainly expand our understanding of how DNA is implemented by our bodies, and maybe lead to practical clinical applications such as identifying DNA damage that may bring on disease.
Some details from the Optical Society:
The researchers tested the enhanced DNA imaging technique by using it to analyze an intercalating dye; a type of fluorescent dye that slides into the areas between DNA bases. In a typical imaging experiment, they acquire up to 300,000 single molecule locations and 30,000 single-molecule orientation measurements in just over 13 minutes. The analysis showed that the individual dye molecules were oriented perpendicular to the DNA strand’s axis and that while the molecules tended to orient in this perpendicular direction, they also moved around within a constrained cone.
The investigators next performed a similar analysis using a different type of fluorescent dye that consists of two parts: one part that attaches to the side of the DNA and a fluorescent part that is connected via a floppy tether. The enhanced DNA imaging technique detected this floppiness, showing that the method could be useful in helping scientists understand, on a molecule by molecule basis, whether different labels attach to DNA in a mobile or fixed way.
In the paper, the researchers demonstrated a spatial resolution of around 25 nanometers and single-molecule orientation measurements with an accuracy of around 5 degrees. They also measured the rotational dynamics, or floppiness, of single-molecules with an accuracy of about 20 degrees.