Press release 50:  Copyright:

Date: June 30, 2016, No. 50

SFB 716 researchers at University of Stuttgart investigate new type of DNA sequencing

Gold and diamonds provide glamour – and have the potential to read-out the genome

Researchers of the Collaborative Research Center 716 (SFB 716) of the University of Stuttgart in collaboration with scientists in Sweden and Brazil have proposed a way to analyze genetic material faster, easier and more cost-effective – by using gold and diamonds, materials that usually make the hearts of jewelry lovers beat faster. 

Sequencing the human genome has been a goal for many years. It was finally realized in 2003 at a very high cost and involving numerous groups. This made it necessary to investigate other types of sequencing techniques – the way of involving nanopores has been found. These are nanometer-sized pores drilled in a material. DNA molecules can be pulled through the nanopores and identified – by embedding electrodes in the nanopore which are capable of measuring the electronic signals, such as current, arising from the genetic code in DNA. The nanopores can, thus, be thought of as a “scanner” for reading-out the genetic information.

Graduate Student Ganesh Sivaraman and Junior Professor Dr. Maria Fyta (Institute of Computational Physics, University of Stuttgart) together with their collaborators Prof. Ralph Scheicher (Sweden) and Prof. Rodrigo Amorim (Brazil) have shown in their computational studies, that a specific chemical modification of the gold electrodes in a nanopore greatly strengthens the effectiveness of sequencing DNA. Specifically, attaching tiny diamond-like particles on the electrodes significantly increases the electronic signals coming from the DNA and reduces the errors in sequencing. “The genetic code is saved in the four different units within DNA, known as the four nucleobases”, Jun. Prof. Fyta explained. “The study has shown that the use of the diamond-like particles for coating the gold electrodes results in a distinguishable electronic current for each nucleobase. Accordingly, the genetic code could be identified and sequenced.”

The study has been carried out using quantum-mechanical computer simulations and has proposed the use of diamond-like coated gold electrodes as a key ingredient for making DNA sequencing devices. A next step to be resolved is the identification of other factors proven essential for the use of gold/diamond-like devices. It also remains to be shown in the lab, whether such devices can be easily produced and used commercially.

The study was recently published in RSC Nanoscale.

Sivaraman, Ganesh; Amorim, Rodrigo G.; Scheicher, Ralph H.; Fyta, Maria: Diamondoid-functionalized gold nanogaps as sensors for natural, mutated, and epigenetically modified DNA nucleotides.

In: Nanoscale (2016), http://pubs.rsc.org/en/Content/ArticleLanding/2016/NR/C6NR00500D

About the collaborative research center 716 (SFB 716) “Dynamic simulation of systems with large particle numbers”

With the help of numerical simulations, questions about material properties, biochemistry processes and chemical engineering can be answered. Due to complex and comprehensive data their use is only possible by means of efficient algorithms, coarsening and acceleration mechanisms, improved hardware and special visualization techniques. Focus of the collaborative research center (SFB 716) is the development of dynamic simulation methods for systems with large particle numbers for use in industrial research and further development in future.

Further information:

JP Dr. Maria Fyta, University of Stuttgart, Institute for Computational Physics, Phone: +49(0)711/685-63935, Mail mfyta@icp.uni-stuttgart.de

Links:

http://www.sfb716.uni-stuttgart.de

http://www.icp.uni-stuttgart.de

 
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A touch of diamond – Nanopores with golden electrodes and diamond tips could potentially read the genetic code. Picture: SFB 716