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

Collaboration yields discovery of 12-sided silica cages June 20th, 2018

JPK talks with Dr Frank Lafont, Director of the BioImaging Center Lille (BICeL) about the use of the NanoWizardŽ AFM together with fluorescence microscopy in the study of living cells June 19th, 2018

Powering the 21st Century with Integrated Photonics: UCSB-Led Team Selected for Demonstration of a Novel Waveguide Platform Which is Transparent Throughout the MWIR and LWIR Spectral Bands June 19th, 2018

Executives Explore Key Megatrends and Innovations in MEMS, Sensors, Imaging Tech at SEMI-MSIG European Summits: Speakers to share developments in smart automotive, smart cities, smart industrial, biomedical, consumer and IoT, September 19-21, 2018 in Grenoble, France June 19th, 2018

Nanomedicine

Collaboration yields discovery of 12-sided silica cages June 20th, 2018

JPK talks with Dr Frank Lafont, Director of the BioImaging Center Lille (BICeL) about the use of the NanoWizardŽ AFM together with fluorescence microscopy in the study of living cells June 19th, 2018

Camouflaged nanoparticles used to deliver killer protein to cancer June 17th, 2018

Graphene carpets: So neurons communicate better: Research by SISSA reveals that graphene can strengthen neuronal activity, confirming the unique properties of this nanomaterial. The study has been published on Nature Nanotechnology June 13th, 2018

Discoveries

Collaboration yields discovery of 12-sided silica cages June 20th, 2018

Carbon nanotube optics poised to provide pathway to optical-based quantum cryptography and quantum computing: Researchers are exploring enhanced potential of carbon nanotubes for unique applications June 18th, 2018

Camouflaged nanoparticles used to deliver killer protein to cancer June 17th, 2018

Squeezing light at the nanoscale: Ultra-confined light could detect harmful molecules June 17th, 2018

Announcements

Collaboration yields discovery of 12-sided silica cages June 20th, 2018

JPK talks with Dr Frank Lafont, Director of the BioImaging Center Lille (BICeL) about the use of the NanoWizardŽ AFM together with fluorescence microscopy in the study of living cells June 19th, 2018

Powering the 21st Century with Integrated Photonics: UCSB-Led Team Selected for Demonstration of a Novel Waveguide Platform Which is Transparent Throughout the MWIR and LWIR Spectral Bands June 19th, 2018

Executives Explore Key Megatrends and Innovations in MEMS, Sensors, Imaging Tech at SEMI-MSIG European Summits: Speakers to share developments in smart automotive, smart cities, smart industrial, biomedical, consumer and IoT, September 19-21, 2018 in Grenoble, France June 19th, 2018

Nanobiotechnology

Collaboration yields discovery of 12-sided silica cages June 20th, 2018

JPK talks with Dr Frank Lafont, Director of the BioImaging Center Lille (BICeL) about the use of the NanoWizardŽ AFM together with fluorescence microscopy in the study of living cells June 19th, 2018

Camouflaged nanoparticles used to deliver killer protein to cancer June 17th, 2018

Graphene carpets: So neurons communicate better: Research by SISSA reveals that graphene can strengthen neuronal activity, confirming the unique properties of this nanomaterial. The study has been published on Nature Nanotechnology June 13th, 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