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

Yusuke T. Maeda, Tsvi Tlusty, Albert Libchaber

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)17972-17977
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume109
Issue number44
DOIs
Publication statusPublished - Oct 30 2012
Externally publishedYes

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RNA Folding
Polymers
DNA
RNA
Catalytic RNA
Temperature
Suspensions
Hydrothermal Vents
Genome Size
Double-Stranded RNA
Oceans and Seas
Base Pairing
Lasers
Hot Temperature

All Science Journal Classification (ASJC) codes

  • General

Cite this

Effects of long DNA folding and small RNA stem-loop in thermophoresis. / Maeda, Yusuke T.; Tlusty, Tsvi; Libchaber, Albert.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 109, No. 44, 30.10.2012, p. 17972-17977.

Research output: Contribution to journalArticle

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