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Balcioglu M, Rana M, Hizir MS, Robertson NM, Haque K, Yigit MV. Rapid Visual Screening and Programmable Subtype Classification of Ebola Virus Biomarkers. Adv Healthc Mater 2017; 6. [PMID: 27990771 DOI: 10.1002/adhm.201600739] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 10/26/2016] [Indexed: 01/27/2023]
Abstract
The massive outbreaks of the highly transmissible and lethal Ebola virus disease were caused by infection with one of the Ebolavirus species. It is vital to develop cost-effective, highly sensitive and selective multitarget biosensing platforms that allow for both the detection and phenotyping. Here, a highly programmable, cost-efficient and multianalyte sensing approach is reported that enables visual detection and differentiation of conserved oligonucleotide regions of all Ebolavirus subtypes known to infect human primates. This approach enables the detection of as little as 400 amols (24 × 106 molecules) of target sequences with the naked eye. Furthermore, the detection assay can be used to classify four virus biomarkers using a single nanoprobe template. This can be achieved by using different combinations of short single stranded initiator molecules, referred to as programming units, which also enable the simultaneous and rapid identification of the four biomarkers in 16 different combinations. The results of 16 × 5 array studies illustrate that the system is extremely selective with no false-positive or false-negative. Finally, the target strands in liquid biopsy mimics prepared from urine specimens are also able to be identified and classified.
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Affiliation(s)
- Mustafa Balcioglu
- Department of Chemistry; University at Albany; State University of New York; 1400 Washington Avenue Albany NY 12222 USA
| | - Muhit Rana
- Department of Chemistry; University at Albany; State University of New York; 1400 Washington Avenue Albany NY 12222 USA
| | - Mustafa Salih Hizir
- Department of Chemistry; University at Albany; State University of New York; 1400 Washington Avenue Albany NY 12222 USA
| | - Neil M. Robertson
- Department of Chemistry; University at Albany; State University of New York; 1400 Washington Avenue Albany NY 12222 USA
| | - Kashfia Haque
- Department of Chemistry; University at Albany; State University of New York; 1400 Washington Avenue Albany NY 12222 USA
| | - Mehmet V. Yigit
- Department of Chemistry; University at Albany; State University of New York; 1400 Washington Avenue Albany NY 12222 USA
- The RNA Institute; University at Albany; State University of New York; 1400 Washington Avenue Albany NY 12222 USA
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Rana M, Balcioglu M, Robertson NM, Hizir MS, Yumak S, Yigit MV. Low picomolar, instrument-free visual detection of mercury and silver ions using low-cost programmable nanoprobes. Chem Sci 2016; 8:1200-1208. [PMID: 28451261 PMCID: PMC5369537 DOI: 10.1039/c6sc03444f] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 09/28/2016] [Indexed: 12/13/2022] Open
Abstract
The EPA's recommended maximum allowable level of inorganic mercury in drinking water is 2 ppb (10 nM). To our knowledge, the most sensitive colorimetric mercury sensor reported to date has a limit of detection (LOD) of 800 pM. Here, we report an instrument-free and highly practical colorimetric methodology, which enables detection of as low as 2 ppt (10 pM) of mercury and/or silver ions with the naked eye using a gold nanoprobe. Synthesis of the nanoprobe costs less than $1.42, which is enough to perform 200 tests in a microplate; less than a penny for each test. We have demonstrated the detection of inorganic mercury from water, soil and urine samples. The assay takes about four hours and the color change is observed within minutes after the addition of the last required element of the assay. The nanoprobe is highly programmable which allows for the detection of mercury and/or silver ions separately or simultaneously by changing only a single parameter of the assay. This highly sensitive approach for the visual detection relies on the combination of the signal amplification features of the hybridization chain reaction with the plasmonic properties of the gold nanoparticles. Considering that heavy metal ion contamination of natural resources is a major challenge and routine environmental monitoring is needed, yet time-consuming, this colorimetric approach may be instrumental for on-site heavy metal ion detection. Since the color transition can be measured in a variety of formats including using the naked eye, a simple UV-Vis spectrophotometer, or recording using mobile phone apps for future directions, our cost-efficient assay and method have the potential to be translated into the field.
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Affiliation(s)
- Muhit Rana
- Department of Chemistry , University at Albany , State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA . ; Tel: +1-518-442-3002
| | - Mustafa Balcioglu
- Department of Chemistry , University at Albany , State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA . ; Tel: +1-518-442-3002
| | - Neil M Robertson
- Department of Chemistry , University at Albany , State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA . ; Tel: +1-518-442-3002
| | - Mustafa Salih Hizir
- Department of Chemistry , University at Albany , State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA . ; Tel: +1-518-442-3002
| | - Sumeyra Yumak
- Department of Science , City University of New York , BMCC , 199 Chambers Street , New York , 10007 NY , USA
| | - Mehmet V Yigit
- Department of Chemistry , University at Albany , State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA . ; Tel: +1-518-442-3002.,The RNA Institute , University at Albany , State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA
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Robertson NM, Toscano AE, LaMantia VE, Hizir MS, Rana M, Balcioglu M, Sheng J, Yigit MV. Unlocked Nucleic Acids for miRNA detection using two dimensional nano-graphene oxide. Biosens Bioelectron 2016; 89:551-557. [PMID: 26944029 DOI: 10.1016/j.bios.2016.02.058] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 02/22/2016] [Accepted: 02/23/2016] [Indexed: 12/12/2022]
Abstract
In this study we have used Unlocked Nucleic Acids (UNAs) to discriminate a breast cancer oncomiR from two other miRNAs in the same RNA family using two-dimensional graphene oxide nanoassemblies. Fluorescently labeled single stranded probe strands and graphene oxide nanoassemblies have been used to detect miR-10b and discriminate it from miR-10a, which differs by only a single nucleotide (12th base from the 5' end), and miR-10c, which differs by only two nucleotides (12th and 16th bases from the 5' end). We have determined the discrimination efficacy and detection capacity of a DNA probe with two inserted UNA monomers (UNA2), and compared it to the DNA probe with two purposefully inserted mutations (DNAM2) and full complementary sequence (DNAfull). We have observed that UNA2 is 50 times more powerful than DNAfull in discriminating miR-10b from miR-10c while generating an equally high fluorescence signal. This fluorescence signal was then further enhanced with the use of the highly specific endonuclease dsDNase for an enzymatic amplification step. The results demonstrate that the underutilized UNAs have enormous potential for miRNA detection and offer remarkable discrimination efficacy over single and double mismatches.
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Affiliation(s)
- Neil M Robertson
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, United States
| | - Amy E Toscano
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, United States
| | - Vincent E LaMantia
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, United States
| | - Mustafa Salih Hizir
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, United States
| | - Muhit Rana
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, United States
| | - Mustafa Balcioglu
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, United States
| | - Jia Sheng
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, United States; The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, United States
| | - Mehmet V Yigit
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, United States; The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, United States.
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Hizir MS, Top M, Balcioglu M, Rana M, Robertson NM, Shen F, Sheng J, Yigit MV. Multiplexed Activity of perAuxidase: DNA-Capped AuNPs Act as Adjustable Peroxidase. Anal Chem 2015; 88:600-5. [DOI: 10.1021/acs.analchem.5b03926] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mustafa Salih Hizir
- Department
of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Meryem Top
- Department
of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Mustafa Balcioglu
- Department
of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Muhit Rana
- Department
of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Neil M. Robertson
- Department
of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Fusheng Shen
- Department
of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Jia Sheng
- Department
of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
- The
RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Mehmet V. Yigit
- Department
of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
- The
RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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Robertson NM, Hizir MS, Balcioglu M, Wang R, Yavuz MS, Yumak H, Ozturk B, Sheng J, Yigit MV. Discriminating a Single Nucleotide Difference for Enhanced miRNA Detection Using Tunable Graphene and Oligonucleotide Nanodevices. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:9943-52. [PMID: 26305398 DOI: 10.1021/acs.langmuir.5b02026] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In this study we have reported our efforts to address some of the challenges in the detection of miRNAs using water-soluble graphene oxide and DNA nanoassemblies. Purposefully inserting mismatches at specific positions in our DNA (probe) strands shows increasing specificity against our target miRNA, miR-10b, over miR-10a which varies by only a single nucleotide. This increased specificity came at a loss of signal intensity within the system, but we demonstrated that this could be addressed with the use of DNase I, an endonuclease capable of cleaving the DNA strands of the RNA/DNA heteroduplex and recycling the RNA target to hybridize to another probe strand. As we previously demonstrated, this enzymatic signal also comes with an inherent activity of the enzyme on the surface-adsorbed probe strands. To remove this activity of DNase I and the steady nonspecific increase in the fluorescence signal without compromising the recovered signal, we attached a thermoresponsive PEGMA polymer (poly(ethylene glycol) methyl ether methacrylate) to nGO. This smart polymer is able to shield the probes adsorbed on the nGO surface from the DNase I activity and is capable of tuning the detection capacity of the nGO nanoassembly with a thermoswitch at 39 °C. By utilizing probes with multiple mismatches, DNase I cleavage of the DNA probe strands, and the attachment of PEGMA polymers to graphene oxide to block undesired DNase I activity, we were able to detect miR-10b from liquid biopsy mimics and breast cancer cell lines. Overall we have reported our efforts to improve the specificity, increase the sensitivity, and eliminate the undesired enzymatic activity of DNase I on surface-adsorbed probes for miR-10b detection using water-soluble graphene nanodevices. Even though we have demonstrated only the discrimination of miR-10b from miR-10a, our approach can be extended to other short RNA molecules which differ by a single nucleotide.
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Affiliation(s)
- Neil M Robertson
- Department of Chemistry , University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Mustafa Salih Hizir
- Department of Chemistry , University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Mustafa Balcioglu
- Department of Chemistry , University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Rui Wang
- Department of Chemistry , University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Mustafa Selman Yavuz
- Department of Metallurgy and Materials Engineering, Advanced Technology Research and Application Center, Selcuk University , Konya, Turkey
| | - Hasan Yumak
- Department of Science, BMCC, City University of New York , 199 Chambers Street, New York, New York 10007, United States
| | - Birol Ozturk
- Department of Physics and Engineering Physics, Morgan State University , 1700 E. Cold Spring Lane, Baltimore, Maryland 21251, United States
| | - Jia Sheng
- Department of Chemistry , University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Mehmet V Yigit
- Department of Chemistry , University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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Balcioglu M, Buyukbekar BZ, Yavuz MS, Yigit MV. Smart-Polymer-Functionalized Graphene Nanodevices for Thermo-Switch-Controlled Biodetection. ACS Biomater Sci Eng 2014; 1:27-36. [DOI: 10.1021/ab500029h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mustafa Balcioglu
- Department
of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Burak Zafer Buyukbekar
- Department
of Metallurgy and Materials Engineering, Advanced Technology Research
and Application Center, Selcuk University, Konya, Turkey
| | - Mustafa Selman Yavuz
- Department
of Metallurgy and Materials Engineering, Advanced Technology Research
and Application Center, Selcuk University, Konya, Turkey
| | - Mehmet V. Yigit
- Department
of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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Balcioglu M, Rana M, Robertson N, Yigit MV. DNA-length-dependent quenching of fluorescently labeled iron oxide nanoparticles with gold, graphene oxide and MoS2 nanostructures. ACS APPLIED MATERIALS & INTERFACES 2014; 6:12100-12110. [PMID: 25014711 DOI: 10.1021/am503553h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We controlled the fluorescence emission of a fluorescently labeled iron oxide nanoparticle using three different nanomaterials with ultraefficient quenching capabilities. The control over the fluorescence emission was investigated via spacing introduced by the surface-functionalized single-stranded DNA molecules. DNA molecules were conjugated on different templates, either on the surface of the fluorescently labeled iron oxide nanoparticles or gold and nanographene oxide. The efficiency of the quenching was determined and compared with various fluorescently labeled iron oxide nanoparticle and nanoquencher combinations using DNA molecules with three different lengths. We have found that the template for DNA conjugation plays significant role on quenching the fluorescence emission of the fluorescently labeled iron oxide nanoparticles. We have observed that the size of the DNA controls the quenching efficiency when conjugated only on the fluorescently labeled iron oxide nanoparticles by setting a spacer between the surfaces and resulting change in the hydrodynamic size. The quenching efficiency with 12mer, 23mer and 36mer oligonucleotides decreased to 56%, 54% and 53% with gold nanoparticles, 58%, 38% and 32% with nanographene oxide, 46%, 38% and 35% with MoS2, respectively. On the other hand, the presence, not the size, of the DNA molecules on the other surfaces quenched the fluorescence significantly with different degrees. To understand the effect of the mobility of the DNA molecules on the nanoparticle surface, DNA molecules were attached to the surface with two different approaches. Covalently immobilized oligonucleotides decreased the quenching efficiency of nanographene oxide and gold nanoparticles to ∼22% and ∼21%, respectively, whereas noncovalently adsorbed oligonucleotides decreased it to ∼25% and ∼55%, respectively. As a result, we have found that each nanoquencher has a powerful quenching capability against a fluorescent nanoparticle, which can be tuned with surface functionalized DNA molecules.
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Affiliation(s)
- Mustafa Balcioglu
- Department of Chemistry and RNA Institute, University at Albany , SUNY, 1400 Washington Avenue, Albany, New York 12222, United States
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