Nanotechnology Now

Our NanoNews Digest Sponsors

Heifer International

Wikipedia Affiliate Button

Home > Press > Backing out of the nanotunnel: New method for nucleic acid analysis

Abstract:
Nanopores provide a versatile tool for probing molecular structures. A new study shows that one can obtain more detailed information about the dynamic behavior of nucleic acids during passage through nanopores by directing them to asymmetric pores for the return journey.

Backing out of the nanotunnel: New method for nucleic acid analysis

Germany | Posted on January 10th, 2012

In the world of biomolecules such as proteins and the hereditary nucleic acids DNA and RNA, three-dimensional structure determines function. Analysis of the passage of such molecules through nanopores offers a relatively new, but highly promising, technique for obtaining information about their spatial conformations. However, interactions between the test molecules and the proteins used as pores have so far hindered quantitative analysis of the behavior of even simply structured molecules within nanopores. This problem must be solved before the technique can be routinely used for structure determination. In a project carried out under the auspices of the Cluster of Excellence "Nanosystems Initiative Munich" (NIM), researchers led by LMU physicist Professor Ulrich Gerland and Professor Friedrich Simmel (Technical University of Munich) have developed a new method that depends on the analysis of reverse translocation through asymmetric pores, which minimizes the interference caused by interactions with the pore material itself. This approach has enabled the team to construct a theoretical model that allows them to predict the translocation dynamics of nucleic acids that differ in their nucleotide sequences.

The nucleic acids RNA and DNA both belong to the class of molecules known chemically as polynucleotides. Both are made up of strings of four basic types of building blocks called nucleotides, which fall into two complementary pairs. In their single-stranded forms, DNA and RNA can fold into what are called secondary structures, as complementary nucleotides in the sequence pair up, forcing the intervening segments to form loops. If the single-stranded loop is very short, the secondary structure is referred to as a hairpin. As in the case of proteins, the secondary structures of nucleic acids influence their biochemical functions. The elucidation of the secondary structure of nucleic acid sequences is therefore of great interest. "Nanopores are increasingly being employed to investigate the secondary structures of RNA and DNA," Gerland points out. "Passage through narrow nanopores causes the sequence to unfold, and the dynamics of translocation provide insights into the structural features of the molecules, without the need to modify them by adding a fluorescent label. The technique is relatively new, and its potential has not yet been fully explored." In the new study, he and his collaborators used a new experimental procedure, which allowed them to quantitatively describe the passage of simply structured polynucleotide sequences through nanopores, and develop a theoretical model that accounts for their findings. This level of understanding has not been achieved previously, because complicating factors such as interactions between the protein nanopore and the polynucleotide have had a significant influence on the measurements and made it difficult to predict the behavior of the test molecules. Thanks to a clever change in experimental design, the impact of these factors has now been minimized. The trick is to perform the measurements on molecules as they translocate through the pore in reverse. First, the polynucleotide of interest is forced through the conical orifice from one side under the influence of an electrical potential. This causes its secondary structure to unfold and, as it emerges, the molecule refolds. An anchor at the end of the polynucleotide chain prevents it from passing completely through the pore onto the other side. For the return journey the potential is reversed, so that the process of unfolding now begins at the narrow end of the pore, and at this point the analysis is initiated. "In contrast to the situation during forward translocation, no significant interactions appear to take place during the reverse trip," says Simmel. On the basis of their experimental measurements, the researchers went on to construct a theoretical model that enabled them to predict the translocation dynamics of various hairpin structures with the aid of thermodynamic calculations of so-called "free-energy landscapes". "This model could in the future provide the foundation of a procedure for the elucidation of the secondary structures of complex polynucleotides," says Gerland. (göd)

Publication:
"Quantitative Analysis of the Nanopore Translocation Dynamics of Simple Structured Polynucleotides"
S. Schink, S. Renner, K. Alim, V. Arnaut, F.C. Simmel, U. Gerland
Biophysical Journal Vol. 102, January 2012, pp 1-11
doi: 10.1016/j.bpj.2011.11.4011

####

For more information, please click here

Contacts:
Dr. Katrhin Bilgeri

49-892-180-6938

Prof. Dr. Ulrich Gerland
Biological Physics and Quantitative Biology
Arnold Sommerfeld Center for Theoretical Physics, LMU
Phone: +49 89 2180 4514
Email:

Copyright © Ludwig-Maximilians-Universität München

If you have a comment, please Contact us.

Issuers of news releases, not 7th Wave, Inc. or Nanotechnology Now, are solely responsible for the accuracy of the content.

Bookmark:
Delicious Digg Newsvine Google Yahoo Reddit Magnoliacom Furl Facebook

Related Links

Website:

Related News Press

News and information

Halas wins American Chemical Society Award in Colloid Chemistry: Rice University nanophotonics pioneer honored for colloid research September 18th, 2018

Leti & EFI Aim to Dramatically Improve Reliability & Speed of Low-Cost Electronic Devices for Autos: Project Will Extend Model Predictive Control Technique to Microcontrollers, Digital Signal Processors and Other Devices that Lack Powerful Computation Capabilities September 18th, 2018

Researchers managed to prevent the disappearing of quantum information September 14th, 2018

Tiny camera lens may help link quantum computers to network September 14th, 2018

Nanomedicine

Halas wins American Chemical Society Award in Colloid Chemistry: Rice University nanophotonics pioneer honored for colloid research September 18th, 2018

A Comprehensive Guide: The Future of Nanotechnology September 13th, 2018

Carbon nanodots do an ultrafine job with in vitro lung tissue: New experiments highlight the role of charge and size when it comes to carbon nanodots that mimic the effect of nanoscale pollution particles on the human lung. September 12th, 2018

Rice U. lab probes molecular limit of plasmonics: Optical effect detailed in organic molecules with fewer than 50 atoms September 5th, 2018

Discoveries

Researchers managed to prevent the disappearing of quantum information September 14th, 2018

Tiny camera lens may help link quantum computers to network September 14th, 2018

New devices based on rust could reduce excess heat in computers: Physicists explore long-distance information transmission in antiferromagnetic iron oxide September 14th, 2018

New photonic chip promises more robust quantum computers September 14th, 2018

Announcements

Halas wins American Chemical Society Award in Colloid Chemistry: Rice University nanophotonics pioneer honored for colloid research September 18th, 2018

Leti & EFI Aim to Dramatically Improve Reliability & Speed of Low-Cost Electronic Devices for Autos: Project Will Extend Model Predictive Control Technique to Microcontrollers, Digital Signal Processors and Other Devices that Lack Powerful Computation Capabilities September 18th, 2018

New devices based on rust could reduce excess heat in computers: Physicists explore long-distance information transmission in antiferromagnetic iron oxide September 14th, 2018

New photonic chip promises more robust quantum computers September 14th, 2018

Nanobiotechnology

Halas wins American Chemical Society Award in Colloid Chemistry: Rice University nanophotonics pioneer honored for colloid research September 18th, 2018

Neutrophil nanosponges soak up proteins that promote rheumatoid arthritis September 3rd, 2018

Arrowhead Pharmaceuticals to Present at Upcoming September 2018 Conferences August 31st, 2018

A human enzyme can biodegrade graphene August 28th, 2018

NanoNews-Digest
The latest news from around the world, FREE



  Premium Products
NanoNews-Custom
Only the news you want to read!
 Learn More
NanoStrategies
Full-service, expert consulting
 Learn More











ASP
Nanotechnology Now Featured Books




NNN

The Hunger Project