Nanomechanics of Poly Nucleic Acids Probed with AFM Based Force Spectroscopy

Elasticity is an important property of nucleic acids. During cellular processes, DNA and RNA are subjected to various mechanical forces which greatly deform their original structure. Also, in the field of DNA nanotechnology, an understanding of how DNA will react to mechanical loading will allow for the design of novel nanostructures with different forms and functions. The elastic response of nucleic acids subjected to very high loadings on the order of 1 nN has not been previously studied.

We use AFM-based single-molecule force spectroscopy to, for the first time, compare and contrast the elasticity of different sequences of double and single stranded polynucleotides, including single stranded poly(A), poly(dA), poly(dT), poly(C), and poly(dC); and double stranded poly(dA)poly(dT), poly(dA-dT), poly(dG)poly(dC), and poly(dG-dC). We found that even up to forces as high as 800 pN poly(dA) is stiffer than the other single stranded structures. We have also observed marked differences in the behavior of double stranded poly(dA)poly(dT) and poly(dG)poly(dC) with poly(dA-dT) and poly(dG-dC), respectively. Despite their different elasticities, these double stranded polynucleotides exhibit striking features similar to those exhibited by poly(dA) when stretched.

We investigate the origin of these differences and similarities in terms of base-base and base-backbone interactions.