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Toader GA, Nitu FR, Ionita M. Graphene Oxide/Nitrocellulose Non-Covalent Hybrid as Solid Phase for Oligo-DNA Extraction from Complex Medium. Molecules 2023; 28:4599. [PMID: 37375154 DOI: 10.3390/molecules28124599] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/31/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
A nitrocellulose-graphene oxide hybrid that consists of a commercially nitrocellulose (NC) membrane non-covalently modified with graphene oxide (GO) microparticles was successfully prepared for oligonucleotide extraction. The modification of NC membrane was confirmed by Fourier Transform Infrared Spectroscopy (FTIR), which highlighted the principal absorption bands of both the NC membrane at 1641, 1276, and 835 cm-1 (NO2) and of GO in the range of 3450 cm-1 (CH2-OH). The SEM analysis underlined the well-dispersed and uniform coverage of NC membrane with GO, which displayed thin spider web morphology. The wettability assay indicated that the NC-GO hybrid membrane exhibited slightly lower hydrophilic behavior, with a water contact angle of 26.7°, compared to the 15° contact angle of the NC control membrane. The NC-GO hybrid membranes were used to separate oligonucleotides that had fewer than 50 nucleotides (nt) from complex solutions. The features of the NC-GO hybrid membranes were tested for extraction periods of 30, 45, and 60 min in three different complex solutions, i.e., an aqueous medium, an α-Minimum Essential Medium (αMEM), and an αMEM supplemented with fetal bovine serum (FBS). The oligonucleotides were desorbed from the surface of the NC-GO hybrid membrane using Tris-HCl buffer with a pH of 8.0. Out of the three media utilized, the best results were achieved after 60 min incubation of the NC-GO membranes in αMEM, as evidenced by the highest fluorescence emission of 294 relative fluorescence units (r.f.u.). This value corresponded to the extraction of approximately 330-370 pg (≈7%) of the total oligo-DNA. This method is an efficient and effortless way to purify short oligonucleotides from complex solutions.
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Affiliation(s)
- Georgian A Toader
- Faculty of Medical Engineering, University Politehnica of Bucharest, Gh Polizu 1-7, 011061 Bucharest, Romania
| | - Florentin R Nitu
- Faculty of Medical Engineering, University Politehnica of Bucharest, Gh Polizu 1-7, 011061 Bucharest, Romania
- Genetic Lab, Str. Milcov, nr. 5, Sector 1, 012273 Bucuresti, Romania
| | - Mariana Ionita
- Faculty of Medical Engineering, University Politehnica of Bucharest, Gh Polizu 1-7, 011061 Bucharest, Romania
- Advanced Polymer Materials Group, University Politehnica of Bucharest, Gheorghe Polizu 1-7, 011061 Bucharest, Romania
- eBio-Hub Research Centre, University Politehnica of Bucharest-Campus, Iuliu Maniu 6, 061344 Bucharest, Romania
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Petrucci S, Ramón Codina Garcia-Andrade J, Moutsiopoulou A, Broyles DB, Dikici E, Daunert S, Deo SK. A Bioluminescent Protein-Graphene Oxide Donor-Quencher Pair in DNA Hybridization Assays. Chempluschem 2022; 87:e202200372. [PMID: 36457160 DOI: 10.1002/cplu.202200372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/02/2022] [Indexed: 11/12/2022]
Abstract
Despite fluorescent quenching with graphene oxide (GO) having shown great success in various applications - bioluminescent quenching has not yet been demonstrated using GO as a quencher. To explore the ability of GO to quench bioluminescence, we used Gaussia luciferase (Gluc) as a donor and GO as a quencher and demonstrated its application in sensing of two target analytes, HIV-1 DNA and IFN-γ. We demonstrated that the incubation of Gluc conjugated HIV-1 and IFN-γ oligonucleotide probes with GO provided for monitoring of probe-target interactions based on bioluminescence measurement in a solution phase sensing system. The limits of detection obtained for IFN-γ and HIV-1 DNA detection were 17 nM and 7.59 nM, respectively. Both sensing systems showed selectivity toward the target analyte. The detection of IFN-γ in saliva matrix was demonstrated. The use of GO as a quencher provides for high sensitivity while maintaining the selectivity of designed probes to their respective targets. The use of GO as a quencher provides for an easy assay design and low cost, environmentally friendly reporter.
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Affiliation(s)
- Sabrina Petrucci
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.,Dr. John T. MacDonald Foundation Biomedical Nanotechnology Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Josep Ramón Codina Garcia-Andrade
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.,Dr. John T. MacDonald Foundation Biomedical Nanotechnology Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Angeliki Moutsiopoulou
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.,Dr. John T. MacDonald Foundation Biomedical Nanotechnology Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - David B Broyles
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.,Dr. John T. MacDonald Foundation Biomedical Nanotechnology Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Emre Dikici
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.,Dr. John T. MacDonald Foundation Biomedical Nanotechnology Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.,Dr. John T. MacDonald Foundation Biomedical Nanotechnology Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.,Clinical and Translational Science Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Sapna K Deo
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.,Dr. John T. MacDonald Foundation Biomedical Nanotechnology Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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Function of Graphene Oxide as the “Nanoquencher” for Hg2+ Detection Using an Exonuclease I-Assisted Biosensor. Int J Mol Sci 2022; 23:ijms23116326. [PMID: 35683005 PMCID: PMC9180964 DOI: 10.3390/ijms23116326] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 02/04/2023] Open
Abstract
Graphene oxide is well known for its excellent fluorescence quenching ability. In this study, positively charged graphene oxide (pGO25000) was developed as a fluorescence quencher that is water-soluble and synthesized by grafting polyetherimide onto graphene oxide nanosheets by a carbodiimide reaction. Compared to graphene oxide, the fluorescence quenching ability of pGO25000 is significantly improved by the increase in the affinity between pGO25000 and the DNA strand, which is introduced by the additional electrostatic interaction. The FAM-labeled single-stranded DNA probe can be almost completely quenched at concentrations of pGO25000 as low as 0.1 μg/mL. A simple and novel FAM-labeled single-stranded DNA sensor was designed for Hg2+ detection to take advantage of exonuclease I-triggered single-stranded DNA hydrolysis, and pGO25000 acted as a fluorescence quencher. The FAM-labeled single-stranded DNA probe is present as a hairpin structure by the formation of T–Hg2+–T when Hg2+ is present, and no fluorescence is observed. It is digested by exonuclease I without Hg2+, and fluorescence is recovered. The fluorescence intensity of the proposed biosensor was positively correlated with the Hg2+ concentration in the range of 0–250 nM (R2 = 0.9955), with a seasonable limit of detection (3σ) cal. 3.93 nM. It was successfully applied to real samples of pond water for Hg2+ detection, obtaining a recovery rate from 99.6% to 101.1%.
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Label-Free Homogeneous microRNA Detection in Cell Culture Medium Based on Graphene Oxide and Specific Fluorescence Quenching. NANOMATERIALS 2021; 11:nano11020368. [PMID: 33540562 PMCID: PMC7912907 DOI: 10.3390/nano11020368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/19/2021] [Accepted: 01/28/2021] [Indexed: 02/07/2023]
Abstract
Label-free homogeneous optical detection of low concentration of oligonucleotides using graphene oxide in complex solutions containing proteins remains difficult. We used a colloidal graphene oxide (GO) as a fluorescent probe quencher to detect microRNA-21 spiked-in cell culture medium, overcoming previously reported problematic aspects of protein interference with graphene oxide. We used a "turn off" assay for specific quenching-based detection of oligo DNA-microRNA hybridization in solution. A fluorescein conjugated 30-mer single-stranded DNA (ssDNA) probe was combined with a complementary synthetic microRNA (18 nucleotides) target. The probe-target hybridization was detected by specific quenching due to photoinduced electron transfer (PET). On the next step, GO captures and quenches the unhybridized probe by fluorescence resonance energy transfer (FRET) in the presence of cell culture medium supplemented with platelet lysate, 0.1% sodium dodecyl sulfate (SDS), 0.1% Triton X-100 and 50% formamide. This resulted in sensitive measurement of the specific probe-target complexes remaining in solution. The detection is linear in the range of 1 nM and 8 nM in a single 100 μL total volume assay sample containing 25% cell culture medium supplemented with platelet lysate. We highlight a general approach that may be adopted for microRNA target detection within complex physiological media.
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Ngamdee T, Yin LS, Vongpunsawad S, Poovorawan Y, Surareungchai W, Lertanantawong B. Target Induced-DNA strand displacement reaction using gold nanoparticle labeling for hepatitis E virus detection. Anal Chim Acta 2020; 1134:10-17. [PMID: 33059855 DOI: 10.1016/j.aca.2020.08.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/08/2020] [Accepted: 08/11/2020] [Indexed: 12/19/2022]
Abstract
DNA strand displacement is an attractive, enzyme-free target hybridization strategy for nano-biosensing. The target DNA induces a strand displacement reaction by replacing the pre-hybridized strand that is labeled with gold nanoparticles (AuNPs). Thus, the amount of displaced-AuNP-labeled strand is proportional to the amount of target DNA in the sample. The use of a magnetogenosensing technique to isolate the target DNA allows for a simple, one-pot detection approach, which minimizes possible carry-over contamination and pipetting errors. We sought a proof-of-concept for this technology in its ability to detect DNA-equivalent of hepatitis E virus (HEV), which causes acute viral hepatitis for which rapid and simple diagnostic methods remain limited. Signal detection was done via visual observation, spectrophotometry, and electrochemistry. The sensor demonstrated good sensitivity with detection limits of 10 pM (visual), 10 pM (spectrophotometry) and 1 fM (electrochemical). This sensor also exhibited high specificity for real target amplicons and could discriminate between perfect and mismatched sequences. Lyophilized biosensor reagents stored at 4 °C, 25 °C, and outdoor ambient temperature, were stable for up to 90, 50, and 40 days, respectively. The integration of magnetic separation and target DNA-induced strand displacement reaction in a dry reagent form makes the sensing platform easy-to-use and suitable for field settings.
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Affiliation(s)
- Tatchanun Ngamdee
- Department of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Lee Su Yin
- Faculty of Applied Sciences, AIMST University, Bedong, Kedah, 08100, Malaysia
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Werasak Surareungchai
- Department of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand; Nanoscience and Nanotechnology Program, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10140, Thailand
| | - Benchaporn Lertanantawong
- Nanoscience and Nanotechnology Program, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10140, Thailand; Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand.
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Variable Angle Spectroscopic Ellipsometry Characterization of Reduced Graphene Oxide Stabilized with Poly(Sodium 4-Styrenesulfonate). COATINGS 2020. [DOI: 10.3390/coatings10080743] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Lately, the optical properties of Graphene Oxide (GO) and Reduced Graphene Oxide (RGO) films have been studied in the ultraviolet and visible spectral range. However, the accurate optical properties in the extended near-infrared and mid-infrared range have not been published yet. In this work, we report a Variable Angle Spectroscopic Ellipsometry (VASE) characterization of GO thin films dip-coated on SiO2/Si substrates and thermally reduced GO films in the 0.38–4.1 eV photon energy range. Moreover, the optical properties of RGO stabilized with poly(sodium 4-styrenesulfonate) (PSS) films dip-coated on SiO2/Si substrates are studied in the same range for the first time. The Lorentz optical models fit well with the experimental data. In addition, the morphological properties of the samples were investigated by Scanning Electron Microscopy (SEM) analysis.
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