Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope

Vesenka, James; Guthold, Martin; Tang, Chun; Keller, David L.; Delaine, E.; Bustamante, Carlos

doi:10.1016/0304-3991(92)90430-r

Cited by 277 publications

(194 citation statements)

References 15 publications

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“…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.…”

supporting

confidence: 84%

“…4d). This discrepancy between the theoretical 2 nm diameter of DNA and the measured height and width is probably mainly due to the huge radius of curvature of the tip in relation to that of the molecules, as already discussed [8][9][10][11][12]. DNA molécules with an apparent width of about 13 nm are obtained with Si tips operated in air (Fig.…”

mentioning

confidence: 83%

“…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].…”

mentioning

confidence: 99%

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

Delain

Fourcade

Poulin

et al. 1992

Microsc. Microanal. Microstruct.

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supporting

confidence: 84%

mentioning

confidence: 83%

mentioning

confidence: 99%

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

Delain

Fourcade

Poulin

et al. 1992

Microsc. Microanal. Microstruct.

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“…Factors that are observed to influence the "auto-orientation" process include length of polymer, drying, and tethering cation. The binding of duplex DNA to mica for atomic force microscopy (AFM) imaging in air is poor in the presence of monovalent cations, but enhanced by magnesium [12,13] and other multivalent cations [14]. AFM imaging of duplex DNA on bare mica in buffered media absolutely requires multivalent cations [8,15].…”

Section: Introductionmentioning

confidence: 99%

Auto-orientation of G-wire DNA on mica

Vesenka¹,

Bagg²,

Wolff³

et al. 2007

Colloids and Surfaces B: Biointerfaces

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Scanning probe microscopy was used to examine the orientation of Tet1.5 quadruplex DNA polymers, a.k.a. "G-wires", after adsorption onto freshly cleaved Phyllosilicate micas. The G-wires appear to have a preferential orientation at 60• intervals after thorough rinsing and slow drying. The angles the G-wires made with the fast scan direction of the SPM probe were measured and the frequency-angle information was quantitatively characterized by an empirical correlation coefficient. Careful measurements indicate the Tet1.5 G-wires orient along the b lattice vector of mica, the next nearest neighbor potassium vacancy. A model is proposed to explain this auto-orientation affect due to alignment of the G-wires' phosphate backbone through magnesium tether cations. Pairs of adjacent, parallel phosphate groups of the G-wires (0.95 nm apart) appear to align with the next nearest neighbor potassium vacancy sites of mica (0.90 nm apart). This behavior is not observed in solution. The potential for using the auto-orientation phenomena in the development of high-density biomolecular nano-electronic devices is explored.

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“…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).…”

mentioning

confidence: 99%

Atomic force microscopy of biochemically tagged DNA.

Murray

Hansma

Bezanilla

et al. 1993

Proc. Natl. Acad. Sci. U.S.A.

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Small fragments of DNA of known length were made with the polymerase chain reaction. These fragments had biotin molecules covalently attached at their ends. They were subsequently labeled with a chimeric protein fusion between streptavidin and two immunoglobulin G-binding domains of staphyloccocal protein A. This tetrameric species was expected to bind up to four DNA molecules via their attached biotin moieties. The DNA-protein complex was deposited on mica and imaged with an atomic force microscope. The images revealed the protein chimera at the expected location at the ends of the strands of DNA as well as the expected dimers, trimers, and tetramers of DNA bound to a single protein.The atomic force microscope (AFM) (1, 2) is a derivative of the better known scanning tunneling microscope (STM) (3). The AFM images by measuring and maintaining a constant load force exerted by a sharp probe as it scans over the surface. 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/(4-13).The demonstrated ability ofthe AFM to image DNA allows microscopists the opportunity to reembark on a series of experiments begun more than 30 years ago. Microscopists at that time tried to apply the newly developed ability of the transmission electron microscope (TEM) to image metalshadowed DNA with the aim of mapping and sequencing this molecule. Attempts at sequencing DNA (14-16) with the TEM involved modifying DNA bases so that they would provide different, contrasting signals. Experiments designed to map DNA with the TEM involved both the imaging of sequence-specific proteins bound to the DNA (17) as well as the identification of probes hybridized to single-stranded DNA (18).The AFM, due to its high resolution and its ability to image DNA under conditions where the native structure will be retained, offers the hope of being able to improve upon the mapping and sequencing work done by these early microscopists. 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). These results suggest that, in the future, the resolution of the STM/AFM (scanning probe) instruments may be sufficient to determine the sequence of the nucleotides of DNA (20,21).In this paper we describe the imaging of DNA fragments marked at specific locations with protein tags. These results show that the AFM has sufficient resolution to map DNA. In its simplest form, mapping involves the measurement of the physical distance between two points along the DNA. In the experiments reported here, we have demonstrated the ...

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Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope

Cited by 277 publications

References 15 publications

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

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

Auto-orientation of G-wire DNA on mica

Atomic force microscopy of biochemically tagged DNA.

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