23 December 2009

DNA sequencing using nanopores: even faster and cheaper

A fast and cheap method of DNA analysis has been developedChemPort
Experts from the University of Boston have developed a method for preparing a DNA sample for genome sequencing, which is faster and more accurate than existing ones.

In addition, the new method makes it possible to significantly reduce the amount of DNA required for analysis and get rid of the expensive and lengthy stage of DNA amplification.

Amit Meller's research group reports on a revolutionary work on the detection of DNA molecules passing through nanopores in silicon. To push long strands of DNA through the pores (whose width is about 4 nm), researchers use an electric field. Measurements make it possible to record the passage of a single nucleic acid molecule through the nanopore.

Moeller notes that the results of the study demonstrate the possibility of determining and analyzing smaller amounts of DNA than has been possible up to now. He adds that sequencing or profiling the genome using nanopores will reduce the amount of DNA needed for analysis.

Currently, before DNA sequencing, it is necessary to perform nucleic acid amplification to obtain billions of copies necessary for the procedure of decoding the sequence of nitrogenous base pairs. In addition to the fact that amplification requires additional time and resources, the amplification process can lead to distortion of the structure of the nucleic acid copying products.

In Meller's group, it was decided to use electric fields localized near the "outgoing holes" of nanopores to affect long negatively charged DNA strands and drag them through the nanopores, after passing through which the DNA molecule can be studied in more detail. This approach allows you to use fewer copies of DNA for further analysis.

To develop a new method, the researchers studied electrophysical phenomena occurring at the nanoscale, at which it is impossible to fully use the principles of macroscopic physics. In the course of the study, it was unexpectedly discovered that DNA strands with a longer length pass through the pores at a higher speed. This circumstance suggests that a system of nanopores can be optimized for detecting long strands of DNA consisting of tens of thousands or even more pairs of nitrogenous bases. This circumstance can lead to a significant acceleration of the genome analysis procedure, allowing you to directly analyze long DNA chains, instead of cutting them and reconstructing their structure from fragments of short segments.

Moeller adds that existing DNA amplification technologies limit the size of the analyzed DNA to a thousand base pairs. Since the new method allows you to get rid of the amplification procedure, it not only reduces the cost, time and error rate characteristic of DNA analysis by previous methods, but also allows you to study DNA strands that are much longer than possible due to the limitations characteristic of existing methods.

The researchers did not stop there, continuing to modify the developed methodology. To change the parameters of the electric field near the pores, they applied salt concentration gradients, which allowed to accelerate the time of capture of DNA molecules by the field, thus contributing to their faster passage through nanopores and reducing the amount of DNA needed for accurate measurements.

Source: Meni Wanunu et al., Electrostatic focusing of unlabelled DNA into nanoscale pores using a salt gradient, Nature Nanotechnology, 2009, published online 20 December 2009.

Portal "Eternal youth" http://vechnayamolodost.ru23.12.2009

Found a typo? Select it and press ctrl + enter Print version