Molecular recognition using corona phase complexes made of synthetic polymers adsorbed on carbon nanotubes

Zhang, Jingqing; Landry, Markita P.; Barone, Paul W.; Kim, Jong Ho; Lin, Shangchao; Ulissi, Zachary W.; Lin, Dahua; Mu, Bin; Boghossian, Ardemis A.; Hilmer, Andrew J.; Rwei, Alina Y.; Hinckley, Allison C.; Kruss, Sebastian; Shandell, Mia A.; Nair, Nitish; Blake, Steven; Şen, Fatih; Şen, Selda; Cray, Robert G.; Li, Deyu; Yum, Kyungsuk; Ahn, Jin Ho; Hong, Jin; Heller, Daniel A.; Essigmann, John M.; Blankschtein, Daniel; Strano, Michael S.

doi:10.1109/nebec.2014.6972997

Cited by 62 publications

(123 citation statements)

References 50 publications

(61 reference statements)

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“…However, as shown in Fig. 2, the sequences (TAT) 4 and (ATTT) 3 did exhibit chirality dependent responses that appear to correlate well with their reported chirality specificities of (6,5) and (8,4) respectively. Although the (8,4) chirality was not included in the deconvolution algorithm, the (9,4) and (7,6) chiralities, which emit at roughly the same wavelength as (8,4) SWNT, are nearly unresponsive to the addition of dopamine and other catecholamines ( Supplementary Figs.…”

Section: Resultssupporting

confidence: 55%

“…The 24 ssDNA wrappings were screened against nine different analytes (Fig. 1b), several of which were previously shown to induce strong sensor responses for DNA-wrapped nanotubes [5,17]. Glucose and sucrose were added to the sensors at a concentration of 10 mM, which resembles the glucose concentration in human blood.…”

Section: Resultsmentioning

confidence: 99%

“…[5]). Normalized fluorescence responses were calculated for each chirality upon the addition of each analyte using the peak areas output by the deconvolution code.…”

Section: Spectrum Deconvolutionmentioning

confidence: 99%

“…The polymer corona phase of individually-dispersed singlewalled carbon nanotubes (SWNTs) forms the basis of many active areas of investigation including SWNT separation technologies [1,2], targeted biomolecule delivery [3,4], molecular detection [5], materials development and energy applications [6]. The inherent fluorescence of semiconducting single-walled carbon nanotubes has prompted their widespread use as signal transducers for optical sensing applications [7][8][9].…”

Section: Introductionmentioning

confidence: 99%

“…These properties, along with the capability of single molecule detection [16], have made SWNT nanosensors valuable tools to study physical, chemical and biological processes at short length and time scales otherwise not obtainable from other detection platforms. As a result, considerable effort has been devoted to the design and development of SWNT-based optical sensors for a variety of target analytes including neurotransmitters [17], proteins [18][19][20], carbohydrates [21][22][23] and assorted small molecules [5,16,24].…”

Section: Introductionmentioning

confidence: 99%

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Chirality dependent corona phase molecular recognition of DNA-wrapped carbon nanotubes

Salem

Landry

Bisker

et al. 2016

Carbon

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a b s t r a c tCorona phase molecular recognition (CoPhMoRe) is a phenomenon whereby a polymer or surfactant corona phase wrapped around a nanoparticle selectively recognizes a particular molecule. The method can potentially generate non-biological, synthetic molecular recognition sites, analogous to antibodies, for a broad range of biomedical applications, including new types of sensors, laboratory and clinical assays, as well as inhibitors and targeted therapeutics. In this work, we utilize near infrared fluorescent single-walled carbon nanotubes (SWNTs) wrapped with specific single stranded DNA sequences to explore the (n,m) chirality dependence of CoPhMoRe. Specific DNA oligonucleotide sequences are known to recognize and interact uniquely with certain (n,m) SWNTs enabling their enrichment in ion exchange chromatography. We explore the CoPhMoRe effect using corona phases constructed from a library of 24 such sequences, screening against a biomolecule panel that includes common neurotransmitters, amino acids, saccharides and riboflavin. Example sequences include (ATT) 4 , (TAT) 4 and (ATTT) 3 which recognize (7,5), (6,5) and (8,4) SWNTs, respectively. We find that these recognition sequences indeed form CoPhMoRe phases that are distinct among SWNT chiralities, and appear to pack more densely as to exclude analyte adsorption on the chirality they recognize. These results have encouraging implications for the controlled design of CoPhMoRe phases for biomedical applications.

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Section: Resultssupporting

confidence: 55%

Section: Resultsmentioning

confidence: 99%

“…[5]). Normalized fluorescence responses were calculated for each chirality upon the addition of each analyte using the peak areas output by the deconvolution code.…”

Section: Spectrum Deconvolutionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Chirality dependent corona phase molecular recognition of DNA-wrapped carbon nanotubes

Salem

Landry

Bisker

et al. 2016

Carbon

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General Synthesis Methods of Inorganic Materials for Supercapacitors

Çalımlı

Karahan

Khan

et al. 2021

Handbook of Supercapacitor Materials

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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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Molecular recognition using corona phase complexes made of synthetic polymers adsorbed on carbon nanotubes

Cited by 62 publications

References 50 publications

Chirality dependent corona phase molecular recognition of DNA-wrapped carbon nanotubes

Chirality dependent corona phase molecular recognition of DNA-wrapped carbon nanotubes

General Synthesis Methods of Inorganic Materials for Supercapacitors

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

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