Scanning probe microscopy. Probing the future

Biophysical analysis of nucleic acids

This overview unit provides a thorough overview of biophysical methods used for structure analysis, including X-ray diffraction, nuclear magnetic resonance, optical spectroscopy, theoretical and computational methods, and single-molecule methods. Advantages and disadvantages of the methods are compared.

Poly(bis-2,2,2-trifluoroethoxymethyl oxetane): enhanced surface hydrophobicity by crystallization and spontaneous asperity formation

We report a spontaneous increase in the contact angle (104 degrees --> 136 degrees +/- 4 degrees ) for a semicrystalline polyoxetane with symmetrical CF3CH2OCH2 side chains. Poly(bis-trifluoroethoxymethyl)oxetane, P(B-3FOx), Mn = 21 kDa, was prepared by a modification of conventional cationic ring opening polymerization. At ambient temperature, the polymer is between Tg (-39 degrees C) and Tm (approximately 70 degrees C). Tapping mode atomic force microscopy (TM-AFM) revealed an interesting process-dependent topology. Coatings that were melted and slow-cooled displayed increasing roughness over the course of 4-6 weeks at 25 degrees C. The result was a topology characterized by sharp micrometer-scale ridges and asperities. The heat of fusion increases from an initial value of 21.9 J/g after slow cooling (non-isothermal melt crystallization) to 28 J/g after 6 weeks (non-isothermal melt crystallization plus isothermal melt crystallization). The coating appearance changes from transparent with a slight haze to translucent. The changing topology was accompanied by a 30 degrees increase in the water contact angle, up to 140 degrees , attributed to an asperity-rich surface yielding a discontinuous three-phase contact line and to a change in the proportions of crystalline and amorphous area fractions accompanying crystallization.

Developing scanning probe–based nanodevices—stepping out of the laboratory into the clinic

This report focuses on nanotools based on the scanning force microscope (SFM) for imaging, measuring, and manipulating biological matter at the sub-micron scale. Because pathophysiological processes often occur at the (sub-) cellular scale, the SFM has opened the exciting possibility to spot diseases at a stage before they become symptomatic and cause functional impairments in the affected part of the body. Such presymptomatic detection will be key to developing effective therapies to slow or halt disease progression.

CHRONIS: an animal chromosome image database

We have constructed a database system named CHRONIS (CHROmosome and Nano-Information System) to collect images of animal chromosomes and related nanotechnological information. CHRONIS enables rapid sharing of information on chromosome research among cell biologists and researchers in other fields via the Internet. CHRONIS is also intended to serve as a liaison tool for researchers who work in different centers. The image database contains more than 3,000 color microscopic images, including karyotypic images obtained from more than 1,000 species of animals. Researchers can browse the contents of the database using a usual World Wide Web interface in the following URL: http://chromosome.med.niigata-u.ac.jp/chronis/servlet/chronisservlet. The system enables users to input new images into the database, to locate images of interest by keyword searches, and to display the images with detailed information. CHRONIS has a wide range of applications, such as searching for appropriate probes for fluorescent in situ hybridization, comparing various kinds of microscopic images of a single species, and finding researchers working in the same field of interest.

Investigations of electrospray sample deposition for polymer MALDI mass spectrometry

In the interest of a more thorough understanding of the relationship between sample deposition technique and the quality of data obtained using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry, details of the electrospray (ES) process of sample deposition are investigated using a number of techniques. Sample morphology was observed with scanning electron microscopy (SEM) and atomic force microscopy (AFM), while matrix-enhanced secondary ion mass spectrometry (MESIMS) monitored surface coverage. Electrospray deposition reduces the analyte segregation that can occur during traditional dried droplet deposition for MALDI. We attribute statistically significant improvements in the reproducibility of signal intensity and MALDI average molecular mass measurements to the ES sample deposition technique.

Surface biology of DNA by atomic force microscopy

The atomic force microscope operates on surfaces. Since surfaces occupy much of the space in living organisms, surface biology is a valid and valuable form of biology that has been difficult to investigate in the past owing to a lack of good technology. Atomic force microscopy (AFM) of DNA has been used to investigate DNA condensation for gene therapy, DNA mapping and sizing, and a few applications to cancer research and to nanotechnology. Some of the most exciting new applications for atomic force microscopy of DNA involve pulling on single DNA molecules to obtain measurements of single-molecule mechanics and thermodynamics.

Near-field scanner for moving molecules

We have fabricated using electron beam nanolithography a fixed slit near-field optical scanning device which uses near-field fluorimetry to achieve 200 nm spatial resolution of objects moving over the slits. We explore the basic physics of operating narrow slits in the waveguide cutoff mode and present data from the passage of extended double-stranded DNA molecules passing over the slits as a first example of how this device can be used to do ultrahigh spatial resolution mapping of long polymers.

Human chromosome structure studied by scanning force microscopy after an enzymatic digestion of the covering cell material

In standard preparations, metaphase human chromosomes are covered by a cell material film composed mainly of proteins and RNA. This film (approximately 30 nm thickness) hides the chromosome structure to the tip of a scanning force microscope. In this work, a mild enzymatic treatment is applied to remove the cell material film. After treatment, the individual chromatin fibers at the surface were resolved. Furthermore, the chromosome shows a thickness modulation, in which thicker/thinner regions could be associated with G/R bands. Finally, the topography of the chromosomes in solution is presented. The chromosome volume swelled about five-fold and chromatin packaging in bands and coils was observed.

Selective cleaning of the cell debris in human chromosome preparations studied by scanning force microscopy

The chromosome structure is one of most challenging biological structures to be discovered. Most evidence about the structure comes from optical microscopy. Scanning force microscopy (SFM) can achieve molecular resolution and allows imaging in liquids. However, little information about the chromosome structure has been revealed by SFM. In this work, a mild enzymatic treatment is applied to the chromosomes to remove selectively the RNA and proteins coming from the cell. The resulting SFM images indicate that a protein film with embedded RNA molecules covers chromosomes in standard cytogenetic preparations. The thickness of the protein layer is 15-35 nm and the RNA adheres preferentially to the chromosome surface. The cell material film results in a quite smooth chromosome surface without evidence of any structural detail. After treatment, the chromosome was cleaned from cell residues and individual chromatin fibers at the surface were resolved. Furthermore, insights about the higher order structure of the chromosome can be inferred.

Controlled unzipping of a bacterial surface layer with atomic force microscopy

We have combined high-resolution atomic force microscopy (AFM) imaging and force spectroscopy to gain insight into the interaction forces between the individual protomers of the hexagonally packed intermediate (HPI) layer of Deinococcus radiodurans. After imaging the HPI layer, the AFM stylus was attached to individual protomers by enforced stylus-sample contact to allow force spectroscopy experiments. Imaging of the HPI layer after recording force-extension curves allowed adhesion forces to be correlated with structural alterations. By using this approach, individual protomers of the HPI layer were found to be removed at pulling forces of approximately 300 pN. Furthermore, it was possible to sequentially unzip entire bacterial pores formed by six HPI protomers. The combination of high-resolution AFM imaging of individual proteins with the determination of their intramolecular forces is a method of studying the mechanical stability of supramolecular structures at the level of single molecules.

Atomic force microscopy and other scanning probe microscopies

The highlight of the past year is the unfolding and refolding of the muscle protein titin in the atomic force microscope. A related highlight in the intersection between experiment and theory is a recent review of the effects of molecular forces on biochemical kinetics. Other advances in scanning probe microscopy include entropic brushes, molecular sandwiches and applications of atomic force microscopy to gene therapy.