Atomic force microscopy of single-and double-stranded DNA

Abstract

A method has been developed for imaging single-stranded DNA with the atomic force microscope (AFM). phi X174 single-stranded DNA in formaldehyde on mica can be imaged in the AFM under propanol or butanol or in air. Measured lengths of most molecules are on the order of 1 mu, although occasionally more extended molecules with lengths of 1.7 to 1.9 mu are seen. Single-stranded DNA in the AFM generally appears lumpier than double-stranded DNA, even when extended. Images of double-stranded lambda DNA in the AFM show more sharp kinks and bends than are typically observed in the electron microscope. Dense, aggregated fields of double-stranded plasmids can be converted by gentle rinsing with hot water to well spread fields.

Comparative observations of biological specimens, especially DNA and filamentous actin molecules in atomic force, tunnelling and electron microscopes

“…We were able to measure the length of plasmid DNA with very reproducible results, in contrast to some reports [8,11,16]. Similar faithful length measurements were also reported for RNA adsorbed onto APTES-treated mica [18]: the results were comparable to those obtained by traditional electron microscopy.…”

“…The Atomic Force Microscope (AFM), for which no conductivity is needed, is often used to observe organic or biological molecules deposited on the surface of mica [reviews in [5][6][7]. Recently, an increasing number of papers have shown images of non ambiguous double-stranded DNA [8][9][10][11][12][13][14][15][16][17], RNA [18] and even single-stranded DNA [16,17] [20][21][22][23] or a 2D arrangement [24][25][26].…”

Immobilizing DNA on gold via thiol modification for atomic force microscopy imaging in buffer solutions

“…In propanol (which is known to dehydrate DNA) images with better resolution and a width better corresponding to the actual diameter of DNA can be obtained [30]. The DNA in Fig.…”

Atomic force microscopy of biochemically tagged DNA.

“…This characteristic of the AFM makes it ideally suited for imaging nonconducting samples like biological molecules. Several groups have previously used the AFM to image both single-and double-stranded DNA/ (4)(5)(6)(7)(8)(9)(10)(11)(12)(13).…”

“…To sequence DNA, the AFM must be able to differentiate between the four types of nucleotide base pairs. Present images of single-stranded DNA (9) do not offer sufficient resolution to observe the functional groups that distinguish one nucleotide base from another. However, other researchers have reported the ability to distinguish between pyrimidines and purines (nucleotide bases with one and two rings) in two-dimensional surface layers with the STM (19).…”