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Drake GA, Keating LP, Huang C, Shim M. Colloidal Multi-Dot Nanorods. J Am Chem Soc 2024; 146:9074-9083. [PMID: 38517010 DOI: 10.1021/jacs.3c14115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Colloidal nanorod heterostructures consisting of multiple quantum dots within a nanorod (n-DNRs, where n is the number of quantum dots within a nanorod) are synthesized with alternating segments of CdSe "dot" and CdS "rod" via solution heteroepitaxy. The reaction temperature, time dependent ripening, and asymmetry of the wurtzite lattice and the resulting anisotropy of surface ligand steric hindrance are exploited to vary the morphology of the growing quantum dot segments. The alternating CdSe and CdS growth steps can be easily repeated to increment the dot number in unidirectional or bidirectional growth regimes. As an initial exploration of electron occupation effects on their optical properties, asymmetric 2-DNRs consisting of two dots of different lengths and diameters are synthesized and are shown to exhibit a change in color and an unusual photoluminescence quantum yield increase upon photochemical doping.
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Affiliation(s)
- Gryphon A Drake
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Logan P Keating
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Conan Huang
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Moonsub Shim
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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2
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Demers SME, Kuhne WW, Swindle AR, Dick DD, Coopersmith KJ. Quantum Dot-DNA FRET Conjugates for Direct Analysis of Methylphosphonic Acid in Complex Media. ACS OMEGA 2023; 8:23017-23023. [PMID: 37396263 PMCID: PMC10308513 DOI: 10.1021/acsomega.3c02173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023]
Abstract
Rapid detection of nerve agents from complex matrices with minimal sample preparation is essential due to their high toxicity and bioavailability. In this work, quantum dots (QDs) were functionalized with oligonucleotide aptamers that specifically targeted a nerve agent metabolite, methylphosphonic acid (MePA). These QD-DNA bioconjugates were covalently linked to quencher molecules to form Förster resonance energy transfer (FRET) donor-acceptor pairs that quantitatively measure the presence of MePA. Using the FRET biosensor, the MePA limit of detection was 743 nM in artificial urine. A decrease in the QD lifetime was measured upon DNA binding and was recovered with MePA. The biosensor's flexible design makes it a strong candidate for the rapid detection of chemical and biological agents for deployable, in-field detectors.
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3
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Wei X, Chen C, Zhao Y, Harazinska E, Bathe M, Hernandez R. Molecular Structure of Single-Stranded DNA on the ZnS Surface of Quantum Dots. ACS NANO 2022; 16:6666-6675. [PMID: 35405067 PMCID: PMC9048700 DOI: 10.1021/acsnano.2c01178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
DNA-based nanoparticle assemblies have emerged as leading candidates in the development of bioimaging materials, photonic devices, and computing materials. Here, we combine atomistic simulations and experiments to characterize the wrapping mechanism of chimeric single-stranded DNA (ssDNA) on CdSe-ZnS (core-shell) quantum dots (QDs) at different ratios of the phosphorothioate (PS) modification of the bases. We use an implicit solvent, all-atom ssDNA model to match the experimentally calculated ssDNA conformation at low salt concentrations. Through simulation, we find that 3-mercaptopropionic acid (MPA) induces electrostatic repulsion and O-(2-mercaptoethyl)-Ó-methyl-hexa (ethylene glycol) (mPEG) induces steric exclusion, and both reduce the binding affinity of ssDNA. In both simulation and experiment, we find that ssDNA is closer to the QD surface when the QD size is larger. The effect of the PS-base ratio on the conformation of ssDNA is also elaborated in this work. We found through MD simulations, and confirmed by transmission electron microscopy, that the maximum valence numbers are 1, 2, and 3 on QDs of 6, 9, and 14 nm in diameter, respectively. We conclude that the maximum ssDNA valence number is linearly related to the QD size, n ∝ R, and justify this finding through an electrostatic repulsion mechanism.
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Affiliation(s)
- Xingfei Wei
- Department
of Chemistry, Chemical & Biomolecular Engineering and Materials Science
& Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Chi Chen
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yinong Zhao
- Department
of Chemistry, Chemical & Biomolecular Engineering and Materials Science
& Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ewa Harazinska
- Department
of Chemistry, Chemical & Biomolecular Engineering and Materials Science
& Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Mark Bathe
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rigoberto Hernandez
- Department
of Chemistry, Chemical & Biomolecular Engineering and Materials Science
& Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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4
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Gated Resonance Energy Transfer (gRET) Controlled by Programmed Death Protein Ligand 1. NANOMATERIALS 2020; 10:nano10081592. [PMID: 32823551 PMCID: PMC7466588 DOI: 10.3390/nano10081592] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/04/2020] [Accepted: 08/11/2020] [Indexed: 01/14/2023]
Abstract
The resonance energy transfer (RET) between an excited fluorescent probe molecule and a plasmonic nanoparticle (AuNP) has been investigated to evaluate the effect of protein molecules on the RET efficiency. We have found that the energy transfer to a functionalized AuNP can be modulated by a sub-monolayer film of programmed death-ligand 1 (PD-L1) protein. The interactions of PD-L1 with AuNP@Cit involve incorporation of the protein in AuNP shell and formation of a submonolayer adsorption film with voids enabling gated surface plasmon resonance energy transfer (SPRET). A model of the gated-RET system based on the protein size, estimated using Fisher-Polikarpov-Craievich density approximation, has been developed and can be utilized for other proteins, with minimum data requirement, as well. The value of the equilibrium constant KL determined for the Langmuir isotherm is high: KL = 1.27 × 108 M-1, enabling highly sensitive control of the gated-RET by PD-L1. Thus, with the gated-RET technique, one can determine PD-L1 within the dynamic range, extending from 1.2 to 50 nM. Moreover, we have found that the Gibbs free energy for PD-L1 binding to AuNP@Cit is -46.26 kJ/mol (-11.05 kcal/mol), indicating a strong adsorption with supramolecular interactions. The proposed gated-RET system, with the fluorescence intensity of the fluorophore probe molecule modulated by plasmonic quenching with AuNP and shielding of energy transfer by the adsorbed PD-L1 can be further developed for determination of PD-L1 in pharmaceutical formulations for immune checkpoint control in cancer therapy.
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Nguyen TH, Sedighi A, Krull UJ, Ren CL. Multifunctional Droplet Microfluidic Platform for Rapid Immobilization of Oligonucleotides on Semiconductor Quantum Dots. ACS Sens 2020; 5:746-753. [PMID: 32115948 DOI: 10.1021/acssensors.9b02145] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Quantum dot-DNA oligonucleotide (QD-DNA) conjugates have been used in many fields such as nucleic acid bioassays, intracellular probes, and drug delivery systems. A typical solid-phase method that achieves rapid loading of oligonucleotides on surfaces of QDs involves a two-step reaction and is performed in a batch-based approach. In contrast, droplet microfluidics offers many advantages that are unavailable when using batch processing, providing rapid and dense immobilized DNA oligonucleotides on QDs. The presented droplet microfluidic approach allows high-quality QD-DNA conjugates to be produced using one single device, which is designed to have two droplet generators, one droplet merger, and one mixer. One of the droplet generators coencapsulates QDs and magnetic beads (MBs) into nanoliter-sized droplets for the production of QD-MB conjugates and the other encapsulates oligonucleotides in nanoliter-sized droplets. These two streams of droplets then merge at a one-to-one ratio in a chamber. The merged droplets travel along the mixer, which is a serpentine microchannel with 30 turns, resulting in QD-DNA conjugation structures of high quality. This multifunctional microfluidic device provides advantages such as higher degree of control over the reaction conditions, minimized cross-contamination and impurities, and reduction of reagent consumption while eliminating any need for external vortexing and pipetting. To evaluate the quality of the QD-DNA conjugates, they were used as Forster resonance energy transfer (FRET) probes to quantify oligonucleic targets.
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Affiliation(s)
- Thu H. Nguyen
- Department of Mechanical and Mechatronics Engineering, University of Waterloo, 200 University Avenue West, Waterloo N2L3G1, Ontario Canada
| | - Abootaleb Sedighi
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga L5L1C6, Ontario, Canada
| | - Ulrich J. Krull
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga L5L1C6, Ontario, Canada
| | - Carolyn L. Ren
- Department of Mechanical and Mechatronics Engineering, University of Waterloo, 200 University Avenue West, Waterloo N2L3G1, Ontario Canada
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Chern M, Kays JC, Bhuckory S, Dennis AM. Sensing with photoluminescent semiconductor quantum dots. Methods Appl Fluoresc 2019; 7:012005. [PMID: 30530939 PMCID: PMC7233465 DOI: 10.1088/2050-6120/aaf6f8] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Fluorescent sensors benefit from high signal-to-noise and multiple measurement modalities, enabling a multitude of applications and flexibility of design. Semiconductor nanocrystal quantum dots (QDs) are excellent fluorophores for sensors because of their extraordinary optical properties. They have high thermal and photochemical stability compared to organic dyes or fluorescent proteins and are extremely bright due to their large molar cross-sections. In contrast to organic dyes, QD emission profiles are symmetric, with relatively narrow bandwidths. In addition, the size tunability of their emission color, which is a result of quantum confinement, make QDs exceptional emitters with high color purity from the ultra-violet to near infrared wavelength range. The role of QDs in sensors ranges from simple fluorescent tags, as used in immunoassays, to intrinsic sensors that utilize the inherent photophysical response of QDs to fluctuations in temperature, electric field, or ion concentration. In more complex configurations, QDs and biomolecular recognition moieties like antibodies are combined with a third component to modulate the optical signal via energy transfer. QDs can act as donors, acceptors, or both in energy transfer-based sensors using Förster resonance energy transfer (FRET), nanometal surface energy transfer (NSET), or charge or electron transfer. The changes in both spectral response and photoluminescent lifetimes have been successfully harnessed to produce sensitive sensors and multiplexed devices. While technical challenges related to biofunctionalization and the high cost of laboratory-grade fluorimeters have thus far prevented broad implementation of QD-based sensing in clinical or commercial settings, improvements in bioconjugation methods and detection schemes, including using simple consumer devices like cell phone cameras, are lowering the barrier to broad use of more sensitive QD-based devices.
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Affiliation(s)
- Margaret Chern
- Department of Materials Science and Engineering, Boston University, Boston, United States of America
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Kumari S, Solanki A, Mandal S, Subramanyam D, Das P. Creation of Linear Carbon Dot Array with Improved Optical Properties through Controlled Covalent Conjugation with DNA. Bioconjug Chem 2018; 29:1500-1504. [PMID: 29634254 DOI: 10.1021/acs.bioconjchem.8b00173] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Controlled conjugation of fluorescent carbon dots (CDs) with DNA and subsequent fabrication of the CDs into an array through hybridization mediated self-assembly in the solution phase is reported. Covalent conjugation of CD with DNA and the subsequent array formation change the mobility of the CD-DNA array in gel electrophoresis and HPLC significantly. Interspatial distance in the CD-DNA array is tuned by the DNA sequence length and maintained at ∼8 ± 0.3 nm as revealed by electron microscopy studies. An increase in fluorescence lifetime by ∼2 ns was observed for the CD-DNA array compared to a solitary CD, vis-á-vis better imaging prospects of HEK293 cells by the former. Thus, the array displays improved fluorescence and unhindered cell penetration.
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Affiliation(s)
- Sonam Kumari
- Department of Chemistry , IIT Patna, Bihta , Patna 801103 , India
| | - Apurv Solanki
- National Centre for Cell Science , Pune 411007 , Maharashtra , India
| | - Saptarshi Mandal
- Department of Chemistry , IIT Patna, Bihta , Patna 801103 , India
| | - Deepa Subramanyam
- National Centre for Cell Science , Pune 411007 , Maharashtra , India
| | - Prolay Das
- Department of Chemistry , IIT Patna, Bihta , Patna 801103 , India
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ZHANG M, HAI H, ZHOU FY, ZHONG JC, LI JP. Electrochemical Luminescent DNA Sensor Based on Polymerase-assisted Signal Amplification. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/s1872-2040(17)61067-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Zhou FY, Hai H, Yuan YL, Li JP. Ultrasensitive Electrochemiluminescence Biosensor for mRNA Based on Polymerase Assisted Signal Amplification. ELECTROANAL 2016. [DOI: 10.1002/elan.201600590] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- F. Y. Zhou
- Guangxi Key laboratory of Electrochemical and Magnetochemical Function Materials, College of Chemistry and Bioengineering; Guilin University of Technology; Guilin 541004 P. R. China
| | - H. Hai
- Guangxi Key laboratory of Electrochemical and Magnetochemical Function Materials, College of Chemistry and Bioengineering; Guilin University of Technology; Guilin 541004 P. R. China
| | - Y. L. Yuan
- Guangxi Key laboratory of Electrochemical and Magnetochemical Function Materials, College of Chemistry and Bioengineering; Guilin University of Technology; Guilin 541004 P. R. China
| | - J. P. Li
- Guangxi Key laboratory of Electrochemical and Magnetochemical Function Materials, College of Chemistry and Bioengineering; Guilin University of Technology; Guilin 541004 P. R. China
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10
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Oligonucleotide-based recognition in colloidal systems - opportunities and challenges. Curr Opin Colloid Interface Sci 2016. [DOI: 10.1016/j.cocis.2016.09.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Alam R, Karam LM, Doane TL, Coopersmith K, Fontaine DM, Branchini BR, Maye MM. Probing Bioluminescence Resonance Energy Transfer in Quantum Rod-Luciferase Nanoconjugates. ACS NANO 2016; 10:1969-77. [PMID: 26760436 DOI: 10.1021/acsnano.5b05966] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We describe the necessary design criteria to create highly efficient energy transfer conjugates containing luciferase enzymes derived from Photinus pyralis (Ppy) and semiconductor quantum rods (QRs) with rod-in-rod (r/r) microstructure. By fine-tuning the synthetic conditions, CdSe/CdS r/r-QRs were prepared with two different emission colors and three different aspect ratios (l/w) each. These were hybridized with blue, green, and red emitting Ppy, leading to a number of new BRET nanoconjugates. Measurements of the emission BRET ratio (BR) indicate that the resulting energy transfer is highly dependent on QR energy accepting properties, which include absorption, quantum yield, and optical anisotropy, as well as its morphological and topological properties, such as aspect ratio and defect concentration. The highest BR was found using r/r-QRs with lower l/w that were conjugated with red Ppy, which may be activating one of the anisotropic CdSe core energy levels. The role QR surface defects play on Ppy binding, and energy transfer was studied by growth of gold nanoparticles at the defects, which indicated that each QR set has different sites. The Ppy binding at those sites is suggested by the observed BRET red-shift as a function of Ppy-to-QR loading (L), where the lowest L results in highest efficiency and furthest shift.
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Affiliation(s)
- Rabeka Alam
- Department of Chemistry, Syracuse University , Syracuse, New York 13244, United States
| | - Liliana M Karam
- Department of Chemistry, Syracuse University , Syracuse, New York 13244, United States
| | - Tennyson L Doane
- Department of Chemistry, Syracuse University , Syracuse, New York 13244, United States
| | - Kaitlin Coopersmith
- Department of Chemistry, Syracuse University , Syracuse, New York 13244, United States
| | - Danielle M Fontaine
- Department of Chemistry, Connecticut College , New London, Connecticut 06320, United States
| | - Bruce R Branchini
- Department of Chemistry, Connecticut College , New London, Connecticut 06320, United States
| | - Mathew M Maye
- Department of Chemistry, Syracuse University , Syracuse, New York 13244, United States
- Syracuse Biomaterials Institute, Syracuse University , Syracuse, New York 13244, United States
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