High-throughput evolution of near-infrared serotonin nanosensors

Jeong, Sanghwa; Yang, Darwin; Beyene, Abraham G.; Bonis-O’Donnell, Jackson Travis Del; Gest, Anneliese; Navarro, Nicole; Sun, Xiaoqi; Landry, Markita P.

doi:10.1126/sciadv.aay3771

Cited by 79 publications

(137 citation statements)

References 64 publications

(91 reference statements)

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“…The most valuable asset of single-wall carbon nanotubes (SWCNTs) for photonics applications is their structure-dependent optical transitions, which can be optically or electrically stimulated to emit light in the near-infrared (IR) wavelength range ( 1 – 3 ). This, together with the compatibility of SWCNTs with a range of biological ( 4 ), chemical ( 5 ), and complementary metal-oxide semiconductor processing methods ( 6 , 7 ), makes SWCNTs highly attractive for application as fluorescence markers in photoluminescence (PL) microscopy or as nanoscale emitters for on-chip data transmission with light ( 8 – 10 ). In particular, the sp 3 functionalization of SWCNTs enables not only tuning of their photon emission into telecom wavelengths but also great enhancement of their photon emission efficiency ( 5 , 11 ).…”

Section: Introductionmentioning

confidence: 99%

Submilligram-scale separation of near-zigzag single-chirality carbon nanotubes by temperature controlling a binary surfactant system

Yang

Wei

et al. 2021

Sci. Adv.

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Mass production of zigzag and near-zigzag single-wall carbon nanotubes (SWCNTs), whether by growth or separation, remains a challenge, which hinders the disclosure of their previously unknown property and practical applications. Here, we report a method to separate SWCNTs by chiral angle through temperature control of a binary surfactant system of sodium cholate (SC) and SDS in gel chromatography. Eleven types of single-chirality SWCNT species with chiral angle less than 20° were efficiently separated including multiple zigzag and near-zigzag species. Among them, (7, 3), (8, 3), (8, 4), (9, 1), (9, 2), (10, 2), and (11, 1), were produced on the submilligram scale. The spectral detection results indicate that lowering the temperature induced selective adsorption and reorganization of the SC/SDS cosurfactants on SWCNTs with different chiral angles, amplifying their interaction difference with gel. We believe that this work is an important step toward industrial separation of single-chirality zigzag and near-zigzag SWCNTs.

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Section: Introductionmentioning

confidence: 99%

Submilligram-scale separation of near-zigzag single-chirality carbon nanotubes by temperature controlling a binary surfactant system

Yang

Wei

et al. 2021

Sci. Adv.

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“…Generating extended sets of data from systematically sampled atomistic resolution simulations could open attractive routes for developing predictive frameworks for corona phase design, which could overcome the present severe limits of ab initio predictions of polymers with specific functions, such as SWNT or analyte recognition. Several recent experimental studies already address the lack of big data in the polymerfunctionalized SWNT field in general, utilizing high throughput approaches to discover polymers (nucleic acid sequences) which can recognize specific chiralities of SWNTs or sense particular analytes, such as serotonin 35,36 . In the present paper, we select an extended set of related nucleic acid polymers, which vary in sequence but have similar short lengths, and combine extended atomistic-resolution computational screening (MD, T-REMD simulations) with lower-resolution experimental screening (kinetic stability surfactant displacement experiments) to relate and generalize the relationships between structural conformation, binding affinity and kinetic stability of short oligonucleotides adsorbed on SWNTs.…”

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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“…Microdialysis and fast-scan cyclic voltammetry have been widely used to follow 5-HT dynamics, but are limited in temporal resolution, spatial precision, and/or chemical selectivity. 4,5 Recent studies have reported several synthetic fluorescent sensors, 6,7 but the need for long-term, cell-specific, and minimally invasive imaging of 5-HT in vivo has not yet been addressed. In this context, there is a great interest to develop genetically encoded 5-HT biosensors.…”

Section: Figmentioning

confidence: 99%

A Fast High-Affinity Fluorescent Serotonin Biosensor Engineered from a Tick Lipocalin

Zhang

Drobizhev

et al. 2020

Preprint

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Serotonin (5-HT) is an important signaling monoamine in and beyond the central nervous system (CNS). We report structure-guided engineering of a green fluorescent, genetically encoded serotonin sensor (G-GESS) from a 5-HT-binding lipocalin in the soft tick. G-GESS shows fast response kinetics and high affinity, specificity, brightness, and photostability. We used G-GESS to image 5-HT dynamics in vitro and in behaving mice, demonstrating the broad utility of this novel biosensor.

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High-throughput evolution of near-infrared serotonin nanosensors

Cited by 79 publications

References 64 publications

Submilligram-scale separation of near-zigzag single-chirality carbon nanotubes by temperature controlling a binary surfactant system

Submilligram-scale separation of near-zigzag single-chirality carbon nanotubes by temperature controlling a binary surfactant system

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

A Fast High-Affinity Fluorescent Serotonin Biosensor Engineered from a Tick Lipocalin

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