To Image the “Anatomy” of a Molecule

September 10, 2009

IBM scientists have been able to image the “anatomy”—or chemical structure—inside a molecule with unprecedented resolution, using a complex technique known as noncontact atomic force microscopy (AFM).

The results push the exploration of using molecules and atoms at the smallest scale and could greatly impact the field of nanotechnology, which seeks to understand and control some of the smallest objects know to mankind.

As reported in the August 28 issue of Science magazine, IBM Research – Zurich scientists Leo Gross, Fabian Mohn, Nikolaj Moll and Gerhard Meyer, in collaboration with Peter Liljeroth of Utrecht University, used an AFM operated in an ultrahigh vacuum and at very low temperatures (–268°C or – 451°F) to image the chemical structure of individual pentacene molecules. With their AFM, the IBM scientists, for the first time ever, were able to look through the electron cloud and see the atomic backbone of an individual molecule. While not a direct technological comparison, this is reminiscent of X-rays that pass through soft tissue to enable clear images of bones.

Original publication:
Gross L, Mohn F, Moll N, Liljeroth P, and Meyer G, (2009): The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy, Science, Vol. 325, Issue 5944, pp. 1110 – 1114 (28 August 2009).

http://www.zurich.ibm.com

The delicate inner structure of a pentacene molecule imaged with an atomic force microscope. For the first time, scientists achieved a resolution that revealed the chemical structure of a molecule. The hexagonal shapes of the five carbon rings in the pentacene molecule are clearly resolved. Even the positions of the hydrogen atoms around the carbon rings can be deduced from the image. (Pixels correspond to actual data points). Source: IBM Research – Zurich

The delicate inner structure of a pentacene molecule imaged with an atomic force microscope. For the first time, scientists achieved a resolution that revealed the chemical structure of a molecule. The hexagonal shapes of the five carbon rings in the pentacene molecule are clearly resolved. Even the positions of the hydrogen atoms around the carbon rings can be deduced from the image. (Pixels correspond to actual data points). Source: IBM Research – Zurich

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Function of a Neglected Structure in Neurons Revealed

September 9, 2009
Two-photon-microscopy of neuron. Source: FMI

Two-photon-microscopy of neuron. Source: FMI

Fifty years after it was originally discovered, scientists at the Friedrich Miescher Institute for Biomedical Research have elucidated the function of a microscopic network of tubules found in neurons. This structure modulates the strength of connections between two neurons, thereby contributing to our ability to learn and to adapt to new situations.

In the current online issue of the Proceedings of the National Academy of Sciences, Oertner’s group describes how the microscopic network of tubules known as the endoplasmic reticulum (ER) modulates the strength of connections between neurons. Neural connections play an important role in our ability to learn new information and constantly adapt to new conditions. In the brain, synaptic connections between neurons are thus continually formed, strengthened or weakened.

In addition, there are connections that remain stable – for example, when we store an important memory for many years. Connections of both types coexist, and their close proximity was one of the first key findings of Thomas Oertner’s study: the two types occur side by side on the same neuron and are individually controlled.

Observations and comparisons of individual dendritic spines and synapses are anything but routine. The findings just published were only possible thanks to a new method known as two photon microscopy. In this imaging technique, a pulsed infrared laser is used to excite fluorescence in a dye molecule in a cell. It is a gentle method of investigating cells, which yields unique, high-resolution images. Thomas Oertner’s research group is one of only a few worldwide that use this technique to optically stimulate and observe individual synapses, and to measure their activity. As equipment of this type cannot simply be purchased off the shelf, these innovative microscopes are custom-built and refined by Thomas Oertner himself. 

Original publication:
Holbro N et al. (2009) Differential distribution of endoplasmic reticulum controls metabotropic signaling and plasticity at hippocampal synapses. PNAS, 18 August 2009, doi: 10.1073/pnas.0905110106 -> Online publication

http://www.fmi.ch


Dynamic Microscopy meets GPCR Dimer Research 2009

September 7, 2009

From October 08 to 10, 2009 the Bio-Imaging Center at the University of Würzburg, Germany invites you to the annually Dynamic Microscopy Workshop. This year, the Workshop will be held together with the GPCR Dimer Symposium. Like in recent years, the goal of the workshop is to introduce and present some of the most modern microscopy techniques to a multi-diciplinary audience of microscopy enthusiasts from the medicinal and natural sciences and also for both the beginners and the advanced. There is no fee for the workshop or symposium. Registration is required.

www.dynamicmicroscopy.de


Imaging Surface Charges on Individual Biomolecules

September 2, 2009
Kelvin Probe Force Microscopy schematic

Kelvin Probe Force Microscopy schematic

Surface charges play a key role in determining the structure and function of proteins, DNA and larger biomolecular structures. For example, negatively charged DNA strands electrostatically interact with histone proteins, transcription factors, or polymerases thereby influencing the read-out of genetic information and the development of cancer. Similarly, the central process of protein folding and protein interaction, often governed by charges, is the major factor in protein-folding diseases such as Alzheimer’s or Parkinson’s Disease. However, thus far there have been no experimental methods to spatially resolve the electrostatic surface potential of individual biological molecules. In general, the investigation of individual molecules can shed light on their dynamic behaviour or on static heterogeneity which is masked in ensemble measurements.

A collaborative effort between researchers from the London Centre for Nanotechnology (Bart W Hoogenboom), King’s College London (Carl Leung, Patrick Mesquida) and UCL Chemistry (Stefan Howorka, Helen Kinns) has led to the first measurements of the electrostatic surface potential of individual DNA and avidin molecules with nanometre resolution using Kelvin Probe Force Microscopy (KPFM) in air.

Kelvin Probe Force Microscopy (KPFM) can measure surface charges by contactless recording of the electrostatic force between a conductive Atomic Force Microscope tip and a biomolecule on a support. To achieve this, the AFM tip is simultaneously excited at its mechanical resonance frequency and by an electrical (AC) voltage. This periodic electrical voltage on the tip leads to a force between the tip and the charges on the biomolecule, which is recorded by means of a lock-in amplifier and nullified by the Kelvin mode feedback by applying a separate DC voltage (not shown). The polarity and magnitude of this DC voltage corresponds to the local surface charge profile (in mV) which is recorded simultaneously with the topography of the biomolecule.

The investigation led at the London Centre for Nanotechnology also show, for the first time, the surface potential of buffer salts shielding DNA molecules on a surface, which would not be possible with conventional ensemble techniques. It is anticipated that the ability to visualize the electrostatic surface potentials of individual proteins and DNA at molecular resolution will be an important tool in fundamental biophysical research and in the fields of biosensing and bio-nanoelectronics.

Original Publication:

Leung C, Kinns H, Hoogenboom BW, Howorka S, Mesquida P. (2009): Imaging surface charges of individual biomolecules.  Nano Lett. 2009 Jul;9(7):2769-73.

 http://www.london-nano.com


To Study Biological Molecules and Structures

August 31, 2009

Researchers in the United States and Spain have discovered that a tool widely used in nanoscale imaging works differently in watery environments, a step toward better using the instrument to study biological molecules and structures.

The researchers demonstrated their new understanding of how the instrument – the atomic force microscope – works in water to show detailed properties of a bacterial membrane and a virus called Phi29, said Arvind Raman, a Purdue professor of mechanical engineering. An atomic force microscope uses a tiny vibrating probe to yield information about materials and surfaces on the scale of nanometers, or billionths of a meter. Because the instrument enables scientists to „see“ objects far smaller than possible using light microscopes, it could be ideal for studying molecules, cell membranes and other biological structures. The best way to study such structures is in their wet, natural environments. However, the researchers have now discovered that in some respects the vibrating probe’s tip behaves the opposite in water as it does in air, said Purdue mechanical engineering doctoral student John Melcher. The probe is caused to oscillate by a vibrating source at its base. However, the tip of the probe oscillates slightly out of synch with the oscillations at the base. This difference in oscillation is referred to as a „phase contrast,“ and the tip is said to be out of phase with the base.

Although these differences in phase contrast reveal information about the composition of the material being studied, data can’t be properly interpreted unless researchers understand precisely how the phase changes in water as well as in air, Raman said.

If the instrument is operating in air, the tip’s phase lags slightly when interacting with a viscous material and advances slightly when scanning over a hard surface. Now researchers have learned the tip operates in the opposite manner when used in water: it lags while passing over a hard object and advances when scanning the gelatinous surface of a biological membrane.

Researchers deposited the membrane and viruses on a sheet of mica. Tests showed the differing properties of the inner and outer sides of the membrane and details about the latticelike protein structure of the membrane. Findings also showed the different properties of the balloonlike head, stiff collar and hollow tail of the Phi29 virus, called a bacteriophage because it infects bacteria.

Original Publication:

Melcher J, Carrasco C, Xu X, Carrascosa JL, Gómez-Herrero J, José de Pablo P, Raman A. (2009): Origins of phase contrast in the atomic force microscope in liquids. Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13655-60. Epub 2009 Aug 5.

Researchers in the United States and Spain have discovered that an atomic force microscope - a tool widely used in nanoscale imaging - works differently in watery environments, a step toward better using the instrument to study biological molecules and structures. The researchers demonstrated their new understanding of how the instrument works in water to show details of the mechanical properties of a virus called Phi29. The images in "a" and "c" show the topography, and the image in "b" shows the different stiffness properties of the balloonlike head, stiff collar and hollow tail of the Phi29 virus, called a bacteriophage because it infects bacteria. (C. Carrasco-Pulido, P. J. de Pablo, J. Gomez-Herrero, Universidad Autonoma de Madrid, Spain)

Researchers in the United States and Spain have discovered that an atomic force microscope - a tool widely used in nanoscale imaging - works differently in watery environments, a step toward better using the instrument to study biological molecules and structures. The researchers demonstrated their new understanding of how the instrument works in water to show details of the mechanical properties of a virus called Phi29. The images in "a" and "c" show the topography, and the image in "b" shows the different stiffness properties of the balloonlike head, stiff collar and hollow tail of the Phi29 virus, called a bacteriophage because it infects bacteria. (C. Carrasco-Pulido, P. J. de Pablo, J. Gomez-Herrero, Universidad Autonoma de Madrid, Spain)

http://news.uns.purdue.edu


Real-Time Observation of Nanocrystal Growth

August 21, 2009

Interim Berkeley Lab Director Paul Alivisatos and Ulrich Dahmen, director of Berkeley Lab’s National Center for Electron Microscopy (NCEM), led a team of experts in nanocrystal growth and electron microscopy who combined their skills to observe the dynamic growth of colloidal platinum nanocrystals in solution with subnanometer resolution. Their results showed that while some crystals in solution grow steadily in size via classical nucleation and aggregation – meaning molecules collide and join together – others grow in fits and spurts, driven by “coalescence events,” in which small crystals randomly collide and fuse together into larger crystals. Despite their distinctly different growth trajectories, these two processes ultimately yield a nearly monodisperse distribution of nanocrystals, meaning the crystals are all approximately the same size and shape.

A new technique known as “liquid cell in situ transmission electron microscopy,” in which the powerful resolution capabilities of a transmission electron microscope (TEM) are brought to bear on a liquid cell that allows liquids to be observed inside a vacuum, enables the visualization of single nanoparticles in solution. The Berkeley researchers deployed this technique on NCEM’s JEOL 3010 In-Situ microscope. Utilizing an electron beam operating at 300 kilovolts of energy, the JEOL 3010 provides outstanding specimen penetration and spatial resolution of about 8 angstroms through the thick liquid cell sample.

Original publication:

Zheng H, Smith RK, Jun YW, Kisielowski C, Dahmen U, Alivisatos AP (2009): Observation of Single Colloidal Platinum Nanocrystal Growth Trajectories. Science Jun 5;324(5932):1309-12.

http://newscenter.lbl.gov


Grant from NIH to Develop AFM Probes

August 19, 2009

Carbon Design Innovations has announced that it has grant in the amount of $390,000 from the National Institutes of Health (NIH) Small Business Innovation Research (SBIR) Program. The grant will fund the development and commercialization of Carbon Nanotube (CNT) Atomic Force Microscope (AFM) probes for bioimaging and investigations in cellular biology. Carbon Design Innovations will collaborate with the University of California at Davis, US on the development of the probes.
www.carbondesigninnovations.com