Molecular determinants of optical modulation in ssDNA-carbon nanotube biosensors
Scrutinizing the underpinnings of optical modulation at the molecular level in ssDNA-functionalized SWCNT biosensors, researchers at Howard Hughes Medical Institute and University of Texas at El Paso have conducted a study. Using both experimental and computational approaches, the research team demonstrated that ligand binding alone is not enough to cause optical modulation in this class of synthetic biosensors. In contrast, the optical response following ligand binding is sensitive to the chemical properties of the ligands, akin to mechanisms seen in activity-based biosensors. Optical response is positively correlated with the amount of electron density available on the aryl motif for ligands with similar ligand binding affinities in ssDNA-SWCNT catecholamine sensors. Crucially, the researchers found that while catechol oxidation itself is not required to drive the resulting optical response of the sensor, the metal oxide must be present in close proximity to the catechol in order for the resulting electrochemical properties to correlate with sensor performance. They also explained how these findings could be used to form a basis for fine tuning performance of existing sensors and inform the design of new biosensors of this class.
Optical modulation for ssDNA-SWCNT biosensors
Photoluminescent properties of SWCNTs, arising from quantum-confined surface excitons, have been utilized for various biological applications, including fluorescence imaging, single-particle tracking, and biosensing.
In biosensing, the excitonic fluorescence of SWCNTs and their novel single-atom-thick geometry are harnessed to transduce molecular recognition events into observable optoelectronic signals. The optoelectronic characteristics of SWCNTs, and comparable shell-like nanostructures, are far more responsive to physicochemical perturbations that happen on or near the surface, allowing detection of local changes at single-molecule sensitivity. This has already been effectively demonstrated in functionalized SWCNTs.
Meticulously tailored moieties that decorate the pristine SWCNT surface are required for biosensing applications so that the resulting sensor configuration is suitable for analyte capture. Among these approaches to engineer the SWCNT-based biosensors, noncovalent functionalization with amphiphilic biopolymers, especially oligonucleotides (e.g., ssDNA), is still the dominant approach. This strategy allows differing oligonucleotide motifs that are chemically and structurally diverse to be patterned on the nanotube surface. Such an approach has allowed ssDNA-SWCNT hybrids to be successfully employed in a variety of applications ranging from nanotube-based device fabrication, chirality sorting, and SWCNT lattice remodeling. The noncovalent self-assembly of ssDNA on the surface of nanotubes creates distinct analyte binding pockets that do not exist on unmodified surfaces, allowing them to be used in biosensing applications.
Structure-activity relationship study
To illuminate the molecular basis of fluorescence modulation in ssDNA-SWCNTs, the researchers conducted structure-activity relationship analysis of a series of catechol (benzene-1,2-diol)-containing small molecule sensors. SWCNT conjugates respond with a robust fluorescence turn-on to catecholamines, with affinities reported in the nanomolar to low micromolar range. These biosensors have propelled a wealth of progress in the field of catecholamine biology, including that of dopamine (4-(2-aminoethyl)benzene-1,2-diol) in cell cultures and tissues. Nanotube vulnerary sensors based on catecholamine display high robustness, intensiometric read-out, high S/N ratio as well as fast and reversible response which are essential in biological use.
By integrating experimental and computational techniques, the researchers gained insights into how these compounds, characterized by the presence of the catechol motif, modify the fluorescence properties of SWCNT conjugates. They showed experimentally that the optical modulation in these sensors depends dominantly on particular electrochemical properties of catechols. The electron densities on the aryl motif of catechols should maximally tune the fluorescence turn-on response, with higher electron densities altering positively the turn-on response. This trend was mirrored when correlating with reduction potentials, where reduction of the more electron-rich catechols (which can be oxidized more easily) showed stronger fluorescence turn-on responses. Importantly, the correlation between the optical response and reduction potential indicated that no oxidative products were formed during molecular recognition. This indicated that the optical modulation in these sensors is due to transient perturbative phenomena rather than permanent charge transfer. The researchers used molecular dynamics (MD) simulations to explain their experimental observations. Such simulations delivered mechanistic insights for analyte-sensor interactions that, paired with experimental data, enabled the researchers to determine distinct molecular parameters that coalesce into a “perturbation cross section” for catechol-bearing ligands. The results indicate that ligand binding and the electrochemical properties of the analyte are synergistic in tuning the optical response of ssDNA-SWCNT biosensors.
Such findings could greatly influence the design of novel and more efficacious ssDNA-SWCNT biosensors. The researchers found that it was like adjusting the optical response of the ligands by changing their electron density. Such developments may find use in fabricating sensitive and specific sensors. The researchers’ work also improves understanding of how these sensors work. By using this information, new sensors could be characterized for use with a wider variety of analytes. Reference Molecular Determinants of Optical Modulation in ssDNA–Carbon Nanotube Biosensors
Andrew T. Krasley, Sayantani Chakraborty, Lela Vuković, Abraham G. Beyene https://pubs.acs.org/doi/10.1021/acsnano.4c13814 Nanotechnology World (NW)
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