@article {69747,
	title = {Molecular Determinants of Optical Modulation in ssDNA{\textendash}Carbon Nanotube Biosensors},
	journal = {ACS Nano},
	year = {2025},
	month = {01/2025},
	abstract = {<p>Most traditional optical biosensors operate through molecular recognition, where ligand binding causes conformational changes that lead to optical perturbations in the emitting motif. Optical sensors developed from single-stranded DNA-functionalized single-walled carbon nanotubes (ssDNA{\textendash}SWCNTs) have started to make useful contributions to biological research. However, the mechanisms underlying their function have remained poorly understood. In this study, we combine experimental and computational approaches to show that ligand binding alone is not sufficient for optical modulation in this class of synthetic biosensors. Instead, the optical response that occurs after ligand binding is highly dependent on the chemical properties of the ligands, resembling mechanisms seen in activity-based biosensors. Specifically, we show that in ssDNA{\textendash}SWCNT catecholamine sensors, the optical response correlates positively with the electron density on the aryl motif, even among ligands with similar ligand binding affinities. Importantly, despite the strong correlations with electrochemical properties, we find that catechol oxidation itself is not necessary to drive the sensor optical response. We discuss how these findings could serve as a framework for tuning the performance of existing sensors and guiding the development of new biosensors of this class.</p>
},
	doi = {10.1021/acsnano.4c13814},
	url = {https://doi.org/10.1021/acsnano.4c13814},
	author = {Krasley, Andrew T. and Chakraborty, Sayantani and Vukovi{\'c}, Lela and Beyene, Abraham G.}
}
@article {65093,
	title = {Ultralarge modulation of fluorescence by neuromodulators in carbon nanotubes functionalized with self-assembled oligonucleotide rings.},
	journal = {Nano Letters},
	volume = {18},
	year = {2018},
	month = {2018 Nov 14},
	pages = {6995-7003},
	abstract = {<p>Noncovalent interactions between single-stranded DNA (ssDNA) oligonucleotides and single wall carbon nanotubes (SWNTs) have provided a unique class of tunable chemistries for a variety of applications. However, mechanistic insight into both the photophysical and intermolecular phenomena underlying their utility is lacking, which results in obligate heuristic approaches for producing ssDNA-SWNT based technologies. In this work, we present an ultrasensitive "turn-on" nanosensor for neuromodulators dopamine and norepinephrine with strong relative change in fluorescence intensity (Δ F/ F) of up to 3500\%, a signal appropriate for in vivo neuroimaging, and uncover the photophysical principles and intermolecular interactions that govern the molecular recognition and fluorescence modulation of this nanosensor synthesized from the spontaneous self-assembly of (GT) ssDNA rings on SWNTs. The fluorescence modulation of the ssDNA-SWNT conjugate is shown to exhibit remarkable sensitivity to the ssDNA sequence chemistry, length, and surface density, providing a set of parameters with which to tune nanosensor dynamic range, analyte selectivity\&nbsp;and strength of fluorescence turn-on. We employ classical and quantum mechanical molecular dynamics simulations to rationalize our experimental findings. Calculations show that (GT) ssDNA form ordered rings around (9,4)\&nbsp;SWNTs, inducing periodic surface potentials that modulate exciton recombination lifetimes. Further evidence is presented to elucidate how dopamine analyte binding modulates SWNT fluorescence. We discuss the implications of our findings for SWNT-based molecular imaging applications.</p>
},
	keywords = {Biosensing Techniques, DNA, Single-Stranded, Dopamine, Fluorescence, Nanotubes, Carbon, Neurotransmitter Agents, Norepinephrine, Oligonucleotides},
	issn = {1530-6992},
	doi = {10.1021/acs.nanolett.8b02937},
	author = {Beyene, Abraham G and Alizadehmojarad, Ali A and Dorlhiac, Gabriel and Goh, Natalie and Streets, Aaron M and Kr{\'a}l, Petr and Vukovi{\'c}, Lela and Landry, Markita P}
}
