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

Abstract

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.

Rapid SARS-CoV-2 Spike Protein Detection by Carbon Nanotube-Based Near-Infrared Nanosensors

“…We further assessed the stability of the ACE2-SWCNT interface with a surfactant displacement assay, which confirmed strong and stable adsorption of ACE2 to the SWCNT (Figure S6). , Taken together, these results suggest that ACE2 adsorbs to the SWCNT surface, displaces ssDNA originally on the SWCNT surface, and forms a stable ACE2-SWCNT conjugate that can be tested for its utility as a CoV-2 nanosensor.…”

Dye Quenching of Carbon Nanotube Fluorescence Reveals Structure-Selective Coating Coverage

“…Replica exchange MD (REMD) was performed to compare the energy landscapes of (ATT) 4 on the two (7,5) enantiomers. Previous reports suggest that REMD is a robust method to investigate DNA–SWCNT interactions. − Each system was solvated in a 3.61 × 3.61 × 4.40 nm 3 box with a sodium chloride concentration of 0.1 M for consistency with experimental conditions. In addition to sodium counterions, there were 1728 water molecules and 20 Na + and Cl – ions in the box.…”

The molecular origin of the electrostatic gating of single-molecule field-effect biosensors investigated by molecular dynamics simulations

“…Our result on single-stranded DNA (ssDNA)-nanotube interactions are in line with previous MD simulations. [51][52][53][54][55][56] More precisely, ssDNA samples a variety of structures -extended, loop and partial wrapping, but not complete wrapping nor ring -stabilized by aromatic interactions with the nanotube and by intramolecular H-bonds and contacts (Table 2). As in these previous simulations, ssDNA binds quickly on the surface of the nanotube and does not detach from it.…”

“…55 Recently, the structural ensemble of 36 sequences of 10, 11 and 12 nt ssDNA on SWCNT has been investigated using REMD simulations showing that these adopt ring and helix-like configurations, the precise balance depending on the sequence. 56 Protein-SWCNT interactions have also been investigated, revealing that these interactions can be sufficient to perturb their functional regions. 57,58 Yet, a thorough sampling at the molecular level of the interactions between SWCNT-biomolecules (proteins, ssDNA and dsDNA) in the context of the SWCNT-bioFET device remains to be done because the biomolecule is covalently grafted or non covalently anchored to the SWCNT and because few simulations were performed on the interactions of large protein or dsDNA with SWCNT.…”