Comparative Dynamics and Sequence Dependence of DNA and RNA Binding to Single Walled Carbon Nanotubes
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Strano_EMB UNTIL May 7, 2016 Comparative dynamics.pdf
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Author(s)
Landry, Markita P.
Vuković, Lela
Kruss, Sebastian
Bisker Raviv, Gili Hana
Landry, Alexandra M.
Islam, Shahrin
Jain, Rishabh Mahendra
Schulten, Klaus
Strano, Michael S.
Date Issued
March 2015
Journal
Journal of Physical Chemistry C
Publisher
American Chemical Society (ACS)
Citation
Landry, Markita P., Lela Vuković, Sebastian Kruss, Gili Bisker, Alexandra M. Landry, Shahrin Islam, Rishabh Jain, Klaus Schulten, and Michael S. Strano. "Comparative Dynamics and Sequence Dependence of DNA and RNA Binding to Single Walled Carbon Nanotubes." Journal of Physical Chemistry C 119:18 (March 2015), pp.10048-10058.
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Author's final manuscript
Abstract
Noncovalent polymer-single walled carbon nanotube (SWCNT) conjugates have gained recent interest due to their prevalent use as electrochemical and optical sensors, SWCNT-based therapeutics, and for SWCNT separation. However, little is known about the effects of polymer-SWCNT molecular interactions on functional properties of these conjugates. In this work, we show that SWCNT complexed with related polynucleotide polymers (DNA, RNA) have dramatically different fluorescence stability. Surprisingly, we find a difference of nearly 2500-fold in fluorescence emission between the most fluorescently stable DNA-SWCNT complex, C[subscript 30] DNA-SWCNT, compared to the least fluorescently stable complex, (AT)[subscript 7]A-(GU)[subscript 7]G DNA-RNA hybrid-SWCNT. We further reveal the existence of three regimes in which SWCNT fluorescence varies nonmonotonically with SWCNT concentration. We utilize molecular dynamics simulations to elucidate the conformation and atomic details of SWCNT-corona phase interactions. Our results show that variations in polynucleotide sequence or sugar backbone can lead to large changes in the conformational stability of the polymer SWCNT corona and the SWCNT optical response. Finally, we demonstrate the effect of the coronae on the response of a recently developed dopamine nanosensor, based on (GT)[subscript 15] DNA- and (GU)[subscript 15] RNA-SWCNT complexes. Our results clarify several features of the sequence dependence of corona phases produced by polynucleotides adsorbed to single walled carbon nanotubes, and the implications for molecular recognition in such phases.
MIT Department
Massachusetts Institute of Technology. Department of Chemical Engineering
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Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
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DOI of Published Version
https://doi.org/10.1021/jp511448e
