Researchers have developed a theory for calculating the force needed to separate double-stranded DNA (dsDNA) molecules. This will be useful for investigating cellular processes such as protein synthesis, which involves using proteins to unzip dsDNA1.
The DNA molecule under investigation consisted of two polynucleotide strands connected loosely by hydrogen bonds through the four base pairs — adenine always binding to thymine and guanine to cytosine. The DNA bases encode genetic messages that are essential for synthesizing cellular proteins. To read out the messages, various proteins bind to and unzip the DNA by exerting piconewton-scale forces.
Atomic force microscopy and magnetic tweezers can be used to calculate the magnitude of such forces. However, theoretical studies corroborating experimental claims at room temperature have so far remained largely unexplored. The researchers developed a first-principles theory to calculate the response of a dsDNA chain to shear stress. They considered four dsDNA molecules of lengths 17, 25, 33 and 49 base pairs exposed to forces of 40.9 pN, 47.4 pN and 60.6 pN.
Applying a shear force to a dsDNA molecule causes its two single-stranded DNA (ssDNA) strands to be pulled in opposite directions. For a molecule comprising 17 base pairs, the entire ssDNA strand moves in the direction of the applied force. For a molecule comprising 49 base pairs, nearly half of the strand moves in the direction opposite to the applied force. The study suggests that when a bond connecting bases of a pair is stretched to a distance of 2.38 Å, the bases become free.
"In addition to its biological relevance, the ability to unzip DNA has interesting applications in materials science for determining the strength of DNA and gold nanoparticle assemblies," says lead researcher Yashwant Singh.
