title: Comparative Dynamics and Sequence Dependence of DNA and RNA Binding to Single Walled Carbon Nanotubes.
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, C30DNA-SWCNT, compared to the least fluorescently stable complex, (AT)7A-(GU)7G 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)15DNA- and (GU)15RNA-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.
authors.affiliation: Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.
authors.forename: Markita P
authors.initials: MP
authors.lastname: Landry
authors.affiliation: Department of Physics, University of Illinois at Urbana-Champaign, Champaign, Illinois 61820, United States ; Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Champaign, Illinois 61820, United States.
authors.forename: Lela
authors.initials: L
authors.lastname: Vuković
authors.affiliation: Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Kruss
authors.affiliation: Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.
authors.forename: Gili
authors.initials: G
authors.lastname: Bisker
authors.affiliation: Department of Chemical Engineering, University of California at Berkeley, Berkeley, California 94720, United States.
authors.forename: Alexandra M
authors.initials: AM
authors.lastname: Landry
authors.affiliation: Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.
authors.forename: Shahrin
authors.initials: S
authors.lastname: Islam
authors.affiliation: Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.
authors.forename: Rishabh
authors.initials: R
authors.lastname: Jain
authors.affiliation: Department of Physics, University of Illinois at Urbana-Champaign, Champaign, Illinois 61820, United States ; Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Champaign, Illinois 61820, United States.
authors.forename: Klaus
authors.initials: K
authors.lastname: Schulten
authors.affiliation: Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Strano