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- W3129596705 abstract "DNA-single walled carbon nanotubes (SWNT) conjugates are promising materials for optical sensing of biological molecular analytes. Here, we use molecular dynamics (MD) simulations and machine learning techniques to examine these materials by themselves and in the presence of biological analytes. First, we explore the relationship between structural conformation, binding affinity, and kinetic stability for short single-stranded oligonucleotides adsorbed on SWNTs, by using MD simulations, temperature replica exchange MD calculations, and kinetic stability experimental measurements. We screened the conformations of 36 sequences of short oligonucleotides on (9,4) SWNT, where the contour lengths were selected so the oligonucleotides can, to a first approximation, wrap once around the SWNT circumference. From these screens, we identified structural motifs that can be broadly classified into “rings” and “non-rings.” Propensity for “ring” conformations is driven primarily by sequence chemistry and the ability of the polymer to form compact structures. 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, and that if ring-like structural motifs form, they contribute positively to stability. In the second part, we explore the design of the above conjugates for sensing of small neurotransmitter molecules. Short single stranded DNA sequences are analyzed to explore patterns implicated in high-affinity binding to SWNTs and neurotransmitter serotonin." @default.
- W3129596705 created "2021-03-01" @default.
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- W3129596705 date "2021-02-01" @default.
- W3129596705 modified "2023-10-18" @default.
- W3129596705 title "Computational Modeling of DNA-Nanotube Hybrid Conjugates for Biosensor Applications" @default.
- W3129596705 doi "https://doi.org/10.1016/j.bpj.2020.11.2256" @default.
- W3129596705 hasPublicationYear "2021" @default.
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