Imaging of nucleic acids with atomic force microscopy

Abstract

Atomic force microscopy (AFM) is a key tool of nanotechnology with great importance in applications to DNA nanotechnology and to the recently emerging field of RNA nanotechnology. Advances in the methodology of AFM now enable reliable and reproducible imaging of DNA of various structures, topologies, and DNA and RNA nanostructures. These advances are reviewed here with emphasis on methods utilizing modification of mica to prepare the surfaces enabling reliable and reproducible imaging of DNA and RNA nanostructures. Since the AFM technology for DNA is more mature, AFM imaging of DNA is introduced in this review to provide experience and background for the improvement of AFM imaging of RNA. Examples of imaging different structures of RNA and DNA are discussed and illustrated. Special attention is given to the potential use of AFM to image the dynamics of nucleic acids at the nanometer scale. As such, we review recent advances with the use of time-lapse AFM.

Tuning the translational freedom of DNA for high speed AFM

“…2(b), a velocity per unit of DNA in nanometers per 100 base pairs length per second (nm·100 bp -1 ·s -1 ) was then derived as the characteristic quantity to Analyzing the motion of DNA molecules is not a novel concept. A previous study has attempted the direct superposition of sequential images aligned to immobile parts of the molecule [37] or to a reference elsewhere in the frame [38]. Deriving additional details by analysis of vectorized molecules has also been undertaken through hand-tracing methods [39] in order to examine quantities such as elastic bending energies [40] and the influence of the AFM probe [11].…”

The dynamic interactions between chemotherapy drugs and plasmid DNA investigated by atomic force microscopy

“…Mica was coated by aminopropyltriethoxy silane (APTES) [6] via the method of vapor deposition. APTES was purchased from Sigma-Aldrich (Saint Louis, MO, USA).…”

“…The advent of atomic force microscopy (AFM) provides a powerful tool for directly imaging single biological molecules in their native states with nanometer spatial resolution, such as DNAs [6], antibodies [7], and membrane proteins [8]. With AFM, we can directly observe the morphological changes of single DNAs after the treatment with drugs in aqueous environment [9].…”

Tapping Mode AFM Imaging for Functionalized Surfaces

“…One way is to reduce the size of cantilevers (9-40 µm) leading to MHz resonance frequency (Walters et al, 1996). Thanks to these cantilevers, authors obtained a sequence of images in liquid at few ms intervals (Ando et al, 2001, Lyubchenko et al, 2011. The last but not the least limiting point is the time taken by the oscillating cantilever to change amplitude (Sulchek et al, 2000).…”