Effects of long DNA folding and small RNA stem–loop in thermophoresis

In thermophoresis, with the fluid at rest, suspensions move along a gradient of temperature. In an aqueous solution, a PEG polymer suspension is depleted from the hot region and builds a concentration gradient. In this gradient, DNA polymers of different sizes can be separated. In this work the effe...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2012-10, Vol.109 (44), p.17972-17977
Main Authors: Maeda, Yusuke T, Tlusty, Tsvi, Libchaber, Albert
Format: Article
Language:English
Subjects:
Aqueous solutions
Bacteriophage T4 - genetics
Biological Sciences
Condensation
Deoxyribonucleic acid
DNA
DNA, Viral - chemistry
Material concentration
Molecules
Nucleic Acid Conformation
Perceptual localization
Phase transitions
Physical Sciences
Polyethylene glycol
Polyethylene Glycols - chemistry
Polymers
Ribonucleic acid
RNA
RNA - chemistry
Soret coefficient
stems
Temperature
Temperature gradients
temperature profiles
Thermophoresis
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Summary:In thermophoresis, with the fluid at rest, suspensions move along a gradient of temperature. In an aqueous solution, a PEG polymer suspension is depleted from the hot region and builds a concentration gradient. In this gradient, DNA polymers of different sizes can be separated. In this work the effect of the polymer structure for genomic DNA and small RNA is studied. For genome-size DNA, individual single T4 DNA is visualized and tracked in a PEG solution under a temperature gradient built by infrared laser focusing. We find that T4 DNA follows steps of depletion, ring-like localization, and accumulation patterns as the PEG volume fraction is increased. Furthermore, a coil–globule transition for DNA is observed for a large enough PEG volume fraction. This drastically affects the localization position of T4 DNA. In a similar experiment, with small RNA such as ribozymes we find that the stem–loop folding of such polymers has important consequences. The RNA polymers having a long and rigid stem accumulate, whereas a polymer with stem length less than 4 base pairs shows depletion. Such measurements emphasize the crucial contribution of the double-stranded parts of RNA for thermal separation and selection under a temperature gradient. Because huge temperature gradients are present around hydrothermal vents in the deep ocean seafloor, this process might be relevant, at the origin of life, in an RNA world hypothesis. Ribozymes could be selected from a pool of random sequences depending on the length of their stems.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.1215764109