Recent research showcases innovative methods to stretch and fix DNA in a straight line using advanced imaging techniques and precise control of microfluidics, all while keeping thermal fluctuations to a minimum for enhanced analysis. A research team from Nagoya University explored ways to straighten a twisted DNA molecule by applying pressure to liquid flowing through a channel. The resulting shear force helped to uncoil the DNA. Their findings revealed that by adjusting the speed of the flowing liquid, they could accurately modify the shear force applied, allowing for precise control over how much the DNA was stretched.
Most microscopes can only illuminate objects down to a specific size before smaller details become indistinct. This issue, known as the diffraction limit of light, presents a challenge. However, super-resolution imaging techniques can differentiate between minute biomolecular details, particularly when thermal fluctuating movements are reduced.
This week, research published in AIP Advances by AIP Publishing details how established imaging techniques, paired with meticulous microfluidic control, can effectively stretch curly DNA into a straight line while minimizing thermal fluctuations, allowing for thorough analysis.
According to author Naoki Azuma, “By immobilizing the molecule, we essentially ‘glue’ it to a surface, which stops movements caused by thermal fluctuations.” He elaborated that super-resolution imaging often takes just seconds or minutes to capture an image, but during this interval, thermal fluctuations — the random movements from the molecule’s thermal energy — can lead to blurriness and lower lateral resolution.
In past efforts, researchers attempted to anchor one end of a DNA molecule to stretch it out, but they still faced challenges with thermal fluctuations causing movement and blurriness.
Azuma explained that “stretching DNA involves extending a single DNA strand, which naturally coils in a random manner, into a straight configuration.” Observations of the length, structure, specific base sequence, and its interactions with proteins necessitate stretching for a thorough analysis.
In their experiments, Azuma and his colleagues applied pressure to a flowing liquid in a channel to straighten the DNA molecule using the shear force generated. They discovered that by adjusting the liquid’s flow speed, they could fine-tune the shear force and accurately modify the DNA’s stretch ratio.
Precision in controlling the stretch ratio was crucial for accurate observations. Additionally, they employed a special chemical that forms bonds between the DNA and a glass surface to secure the DNA molecule in place.
Azuma pointed out, “While we cannot yet visualize individual base pairs directly, these approaches significantly enhance precision in observing structures at the molecular level.” He added, “Our goal is to refine these techniques to improve accuracy in stretching and immobilizing DNA molecules for more reliable analyses.”
