Energetic Basis of Single-Wall Carbon Nanotube Enantiomer Recognition by Single-Stranded DNA

Shankar, A. N.; Zheng, Ming; Jagota, Anand

doi:10.1021/acs.jpcc.7b05168

Cited by 14 publications

(17 citation statements)

References 70 publications

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“…An alternative and a powerful way to characterize the corona phase includes computational modeling approaches, such as classical molecular dynamics (MD) simulations, which enable atomic resolution on the timescale of hundreds of nanoseconds 1,2,[29][30][31][32] . Yet, as reorganization of long polymers on SWNT surfaces occurs on a timescale of several nanoseconds, determining most probable equilibrium distributions of polymers in the corona phase necessitates enhanced sampling approaches, such as temperature replica exchange (T-REMD) MD simulations 33 .…”

Section: Introductionmentioning

confidence: 99%

Binding Affinity and Conformational Preferences Influence Kinetic Stability of Short Oligonucleotides on Carbon Nanotubes

Alizadehmojarad

Zhou

Beyene

et al. 2020

Adv Materials Inter

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DNA-wrapped single walled carbon nanotubes (SWNTs) have found a widespread use in a variety of nanotechnology applications. Yet, the relationship between structural conformation, binding affinity and kinetic stability of these polymers on SWNTs remains poorly understood. Here, we used molecular dynamics (MD) simulations and experiments to explore this relationship for short oligonucleotides adsorbed on SWNTs. First, using classical MD simulations of oligonucleotide-(9,4)-SWNT hybrid complexes, we explored the relationship between ssDNA and ssRNA surface conformation and sequence chemistry. We screened the conformation of 36 sequences of short ssDNA and ssRNA polymers on (9,4) SWNT, where the contour lengths were selected so the polymers can, to a first approximation, wrap once around the SWNT circumference. From these screens, we identified structural motifs that we broadly classified into "rings" and "non-rings." Then, several sequences were selected for detailed investigations. We used temperature replica exchange MD calculations to compute two-dimensional free energy landscapes characterizing the conformations of select sequences. "Ring" conformations seemed to be driven primarily by sequence chemistry. Specifically, strong (n,n+2) nucleotide interactions and the ability of the polymer to form compact structures, as for example, through sharp bends in the nucleotide backbone, correlated with ring-forming propensity. However, ring-formation probability was found to be uncorrelated with free energy of oligonucleotide binding to SWNTs (∆Gbind). Conformational analyses of oligonucleotides, computed free energy of binding of oligonucleotides to SWNTs, and experimentally determined kinetic stability measurements show that ∆Gbind is the primary correlate for kinetic stability. The probability of the sequence to adopt a compact, ring-like conformation is shown to play a secondary role that still contributes measurably to kinetic stability. For example, sequences that form stable compact rings (C-rich sequences) could compensate for their relatively lower ∆Gbind and exhibit kinetic stability, while sequences with strong ∆Gbind (such as (TG)3(GT)3) were found to be kinetically stable despite their low ring formation propensity. We conclude that the stability of adsorbed oligonucleotides is primarily driven by its free energy of binding and that if ring-like structural motifs form, they would contribute positively to stability.

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Section: Introductionmentioning

confidence: 99%

Binding Affinity and Conformational Preferences Influence Kinetic Stability of Short Oligonucleotides on Carbon Nanotubes

Alizadehmojarad

Zhou

Beyene

et al. 2020

Adv Materials Inter

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“…which were found to be able to displace (GT)20 DNA, a wellknown dispersant of SWCNTs, from the surface of nanotubes. Taken together, this work demonstrated the important roles of both carbohydrate ligand identity and polymer chain length of glycopolymers in stabilizing SWCNTs through the formation of helical wrapping structures on the nanotube.…”

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confidence: 99%

Carbohydrate- and Chain Length-Controlled Complexation of Carbon Nanotubes by Glycopolymers

et al. 2020

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Stable dispersions of single-wall carbon nanotubes (SWCNTs) by biopolymers in an aqueous environment facilitate their potential biological and biomedical applications. In this report, we investigated a small library of precision synthesized glycopolymers with monosaccharide and disaccharide groups for stabilizing SWCNTs via noncovalent complexation in aqueous conditions. Among the glycopolymers tested, disaccharide lactose-containing glycopolymers demonstrate effective stabilization of SWCNTs in water, which strongly depends on carbohydrate density and polymer chain length as well. The introduction of disaccharide lactose potentially makes glycopolymers less flexible as compared to those containing monosaccharide and facilitates the wrapping conformation of polymers on the surface of SWCNTs while preserving intrinsic photoluminescence of nanotubes in the near-infrared region. This work demonstrates the synergistic effects of the identity of carbohydrate pendant groups and polymer chain length of glycopolymers on stabilizing SWCNTs in water, which has not been achieved previously.

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“…This result may aid computational efforts to clarify the energetic factors controlling SWCNT enantiomer recognition by ssDNA. 18,21,22 6…”

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confidence: 99%

Enantiomers of Single-Wall Carbon Nanotubes Show Distinct Coating Displacement Kinetics

Zheng

Bachilo

Weisman

2018

J. Phys. Chem. Lett.

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It is known that specific oligomers of single-stranded DNA (ssDNA) can show remarkable selectivity when coating different structural species of single-wall carbon nanotubes (SWCNTs). We report that (ATT) ssDNA coatings strongly distinguish between the two optical isomers of (7,5) SWCNTs. This causes resolvable shifts in their fluorescence spectra and differences of 2 orders of magnitude in the room temperature rates of coating displacement, as monitored through changes in nanotube fluorescence wavelength and intensity on exposure to sodium deoxycholate. During coating displacement, the enantiomer with high affinity for the ssDNA oligomer is deduced to form an intermediate hybrid that is not observed for the low affinity enantiomer. These results reveal that enantiomeric differences in SWCNTs complexed with ssDNA are more diverse and dramatic than previously recognized.

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Energetic Basis of Single-Wall Carbon Nanotube Enantiomer Recognition by Single-Stranded DNA

Cited by 14 publications

References 70 publications

Binding Affinity and Conformational Preferences Influence Kinetic Stability of Short Oligonucleotides on Carbon Nanotubes

Binding Affinity and Conformational Preferences Influence Kinetic Stability of Short Oligonucleotides on Carbon Nanotubes

Carbohydrate- and Chain Length-Controlled Complexation of Carbon Nanotubes by Glycopolymers

Enantiomers of Single-Wall Carbon Nanotubes Show Distinct Coating Displacement Kinetics

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