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Monday, 19 January, 2015

Stretching and Twisting RNA molecules

Single molecule biophysics

Single-molecule experiments reveal surprising differences amongst the “molecular cousins” DNA and RNA when stretched and twisted.

The double-stranded structure of DNA carries our genetic information and has become an icon of molecular biology and bioengineering. In the past two decades, methods have been developed to pull on and twist individual DNA molecules and the response of double-stranded DNA to applied linear forces and torques (i.e. molecules under twist) has been mapped out with increasing precision in a series of landmark experiments.

In contrast, much less is known about the mechanical response of RNA, DNA’s molecular cousin. Chemically, RNA is very similar to DNA and like DNA, it can form a double-stranded helix. Yet in the cell, RNA carries our very different functions: RNA is a central player in translating the genetic information stored in DNA into proteins, which in turn carry out most metabolic functions in the cell. In addition, there are several more recently discovered mechanisms where RNA is involved in regulating the expression of genes, i.e. controlling the way the genetic code is executed.


Twisting and stretching RNA using single-molecule tools

A team of researchers led by Jan Lipfert, now at the LMU Munich, and Nynke H. Dekker from the TU Delft, Netherlands, have used magnetic tweezers to determine how double-stranded RNA responds to external forces and torques. In their magnetic tweezers instruments, single double-stranded RNA molecules are tethered between a functionalized glass surface and small magnetic beads. Using magnets, the researchers can apply precisely controlled forces and twists to the RNA molecules. They found that if the forces and torques are not too large, double-stranded RNA bends and twists elastically, like a rubber rod. However, when the forces and torques become too large, the molecular structure rearranges and RNA undergoes –sometimes dramatic– structural changes. From the measurements, the elastic constants of double-stranded RNA were determined. The elastic properties for bending, twisting, and stretching were found to be quite similar to DNA.


Surprising discovery

When the researchers measured a forth elastic constant, the so-called twist-stretch coupling, they made a surprising discovery: While DNA lengthens when the helix is overwound, RNA shortens, revealing a surprising difference between the chemically similar molecules. Another surprise came when the researchers used again magnetic tweezers to measure the dynamics of forming a loop, where RNA exhibited 100-times slower dynamics than DNA. Current models of DNA and RNA fail to explain these surprising findings and the current work poses an open challenge to molecular modeling approaches.

The results present for the first time a complete picture of how double-stranded RNA responds to forces and torques. They serve as a baseline to model and understand RNA in more complex biological or technological contexts and reveal unexpected properties of this key building block in molecular biology.

 

Publication:

"Double-stranded RNA under force and torque: Similarities to and striking differences from double-stranded DNA." Jan Lipfert, Gary M. Skinner, Johannes M. Keegstra, Toivo Hensgens, Tessa Jager, David Dulin, Mariana Köber, Zhongbo Yu, Serge P. Donkers, Fang-Chieh Chou, Rhiju Das, and Nynke H. Dekker. PNAS, Vol. 111, No. 43, 15408-15413. doi: 10.1073/pnas.1407197111 (Abstract)

 

Contact:

Prof. Jan Lipfert

Department of Physics
LMU Munich
Amalienstr. 54
80799 Munich
Germany

Phone: +49-89-21802005
Email: Jan.Lipfert(at)lmu.de

 

Figure:
Christoph Hohmann (NIM)
Adapted from Chemical Reviews (2015) used with permission from the American Chemical Society

 

 

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