Genetic Material under a Magnifying Glass

The genetic alphabet contains four letters. Although our cells can readily decipher our genetic molecules, it isn’t so easy for us to read a DNA sequence in the laboratory. Scientists require complex, highly sophisticated analytical techniques to crack individual DNA codes.

Volker Deckert and his team at the Institute for Analytical Sciences (ISAS) in Dortmund have recently developed a method that could provide a way to directly sequence DNA. Their process is based on a combination of Raman spectroscopy and atomic force microscopy. As reported in the journal Angewandte Chemie, Deckert and Elena Bailo have successfully analyzed DNA’s closest relative, RNA.

Direct sequencing means that the letters of the genetic code are read directly, as if with a magnifying glass. A DNA or RNA strand has a diameter of only two nanometers, so the magnification must be correspondingly powerful. Deckert’s team uses an atomic force microscope to achieve this degree of magnification. Steered by the microscope, a tiny, silvered glass tip moves over the RNA strand.

A laser beam focused on the tip excites the section of the strand being examined and starts it vibrating. The spectrum of the scattered light (Raman spectrum) gives very precise information about the molecular structure of the segment. Each genetic “letter”, that is, each of the nucleic acids, vibrates differently and thus has a characteristic spectral “fingerprint”.

The direct resolution of individual bases has not been attainable, but is also not necessary. The tip only has to be moved over the RNA strand at intervals corresponding to about the base-to-base distance. Even if the measured data then consist of overlapped spectra from several neighboring bases, the information can be used to derive the sequence of the RNA.

If this method, known as tip-enhanced Raman spectroscopy (TERS), can be extended to DNA, it could revolutionize the decoding of genetic information. Previous methods for sequencing DNA are highly complex, work indirectly, and require a large sample of genetic material. In contrast, the TERS technique developed by Deckert directly “reads” the code without chemical agents or detours. It also requires only a single strand of DNA. “DNA sequencing could become very simple,” says Deckert, “like reading a barcode at the supermarket.”

Citation: Volker Deckert, Tip-Enhanced Raman Spectroscopy of Single RNA Strands: Towards a Novel Direct-Sequencing Method, Angewandte Chemie International Edition, doi: 10.1002/anie.200704054

Source: Angewandte Chemie

Related stories:

Sewing DNA thread with lasers, hooks and microbobbins
(PhysOrg.com) -- Japanese scientists have made a micro-sized sewing machine to sew long threads of DNA into shape. The work published in the Royal Society of Chemistry journal Lab on a Chip demonstrates a unique way to manipulate delicate DNA chains without breaking them.
Researchers identify new targets for RNAs that regulate genes
Tiny strands of genetic material called RNA – a chemical cousin of DNA – are emerging as major players in gene regulation, the process inside cells that drives all biology and that scientists seek to control in order to fight disease.
Refusal of suicide order: Why tumor cells become resistant
Cells with irreparable DNA damage normally induce programmed cell death, or apoptosis. However, this mechanism often fails in tumor cells so that transformed cells are able to multiply and spread throughout the body. Scientists at the German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ) have now discovered a possible cause of this failure. Tumor cells simply degrade a protein that triggers apoptosis in the case of DNA damage. Blocking this protein degradation might set apoptosis back in operation and, thus, increase the effectiveness of radiotherapy or chemotherapy. The researchers have now published their results in Nature Cell Biology.
Desert plant may hold key to surviving food shortage
The plant, Kalanchoe fedtschenkoi, is unique because, unlike normal plants, it captures most of its carbon dioxide at night when the air is cooler and more humid, making it 10 times more water-efficient than major crops such as wheat. Scientists will use the latest next-generation DNA sequencing to analyse the plant's genetic code and understand how these plants function at night.
Researchers reveal structure of protein that repairs damage to cancer cells
A team of University of Chicago scientists has shown how two proteins locate and repair damaged genetic material inside cells.
Analysis of RNA role in spreading disease advances study of damaging plant infections
Recent research that links specific pieces of RNA to an infectious organism’s duplication and spread could lead the way to the prevention of viroids, pathogens that can kill or damage food crops and other plants.
Researchers discover novel 'gene toggles' in world's top food crop
University of Delaware researchers, in collaboration with U.S. and international colleagues, have found a new type of molecule--a kind of “micro-switch”--that can turn off genes in rice, which is the primary source of food for more than half the world's population. The discovery is reported in the March 25 issue of the Proceedings of the National Academy of Sciences of the United States of America.
Scientists devise potential approach to treat spinal muscular atrophy
In the neuromuscular disease called spinal muscular atrophy, or SMA, a protein deficiency caused by a single gene mutation leads to serious damage in growing nerve cells and the muscles they control.

News discussion:

General Science news