DNA

Nucleic acids, DNA, RNA and various proteins are the most common biomacromolecules examined with AFM. Visualization of conformations of individual DNA strands, DNA-protein complexes and other single macromolecules brings unique information that is hardly accessible by other methods.

Fig. 1. AFM images of double stranded DNA on mica (a) and hexagonal DNA self-assembly obtained with series 14 probes. Scans courtesy of S.Magonov (Agilent). Sample courtesy of A. Koyfman (UCSB).

An example of an AFM image of DNA is given in Fig 1a. Supercoiling is one of the most interesting DNA-related phenomenon, which is the focus of many studies with emphasis on high-resolution imaging with ultra sharp AFM probes. High-resolution visualization of DNA is also the subject of studies addressing the formation of DNA-protein complexes and the results of enzyme cleavage. Other properties that have been successfully investigated with AFM are DNA stiffness and elasticity and the segmental dynamics of DNA. In the past five years, there has been intense research into the construction of 2D and 3D architectures using self-assembly of single stranded DNA macromolecules. AFM has become the most useful technique for the characterization of these arrays. One such example is the hexagonal DNA array is seen in Fig. 1b.

An example of AFM images of another biomacromolecule is given below.

Fig. 2. AFM images of fibrinogen molecules (a) and single fibrin strands (b). The image in (a) was obtained with a regular probe of the 14 series and image in (b) with a Hi'Res-C probe. The color contrast (red-to-white) covers a 0 - 3.5 nm height scale. Images courtesy of L. Chtcheglova.

Two AFM images of plasma protein fibrinogen and its assemblies known as fibrin are presented in Fig. 2a-b. These images demonstrate that Hi'Res-C probes provide higher resolution in images of the fibrin, making fine features of the aggregate visible.

Topography image of individual fibrin molecules obtained using a General Purpose probe is shown in Fig. 3.

Fig. 3. Tapping mode topography image of single molecules of fibrinogen on mica (Agilent 5500 AFM, General Purpose probe). Scan size 350 x 350 nm. Scan height 1.5 nm. Image courtesy of S. Magonov, Agilent Technologies.

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contact mode


Ambient conditions

HQ:CSC probes for contact mode
HQ:CSC17/Al BS


Aqueous conditions
Probes with stable reflective coating
HQ:NSC18/Cr-Au BS


In aggressive liquid media
Probes with chemically stable coating
HQ:CSC17/Cr-Au



tapping mode

Ambient conditions
HQ:NSC probes with medium spring constant
HQ:NSC14/Al BS


High resolution imaging
Hi'Res-C probes with medium spring constant
Hi'Res-C14/Cr-Au

Aqueous conditions
HQ:NSC probes with stable reflective coating
HQ:NSC18/Cr-Au BS


Agressive liquid environment
Probes with chemically stable coating
HQ:NSC18/Cr-Au


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