title: Discriminating a Single Nucleotide Difference for Enhanced miRNA Detection Using Tunable Graphene and Oligonucleotide Nanodevices.
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.
authors: Department of Chemistry , University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
authors: Neil M
authors: NM
authors: Robertson
authors: Department of Chemistry , University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
authors: Mustafa Salih
authors: MS
authors: Hizir
authors: Department of Chemistry , University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
authors: Mustafa
authors: M
authors: Balcioglu
authors: 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
authors: Rui
authors: R
authors: Wang
authors: Department of Metallurgy and Materials Engineering, Advanced Technology Research and Application Center, Selcuk University , Konya, Turkey.
authors: Mustafa Selman
authors: MS
authors: Yavuz
authors: Department of Science, BMCC, City University of New York , 199 Chambers Street, New York, New York 10007, United States.
authors: Hasan
authors: H
authors: Yumak
authors: Department of Physics and Engineering Physics, Morgan State University , 1700 E. Cold Spring Lane, Baltimore, Maryland 21251, United States.
authors: Birol
authors: B
authors: Ozturk
authors: 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
authors: Jia
authors: J
authors: Sheng
authors: 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
authors: Mehmet V
authors: MV
authors: Yigit
mesh_terms: D006108:Graphite / Q000737:chemistry*; D035683:MicroRNAs / Q000235:genetics*; D036103:Nanotechnology; D009841:Oligonucleotides / Q000737:chemistry*; D020641:Polymorphism, Single Nucleotide; D013050:Spectrometry, Fluorescence
chemical_list: D035683:MicroRNAs; D009841:Oligonucleotides; D006108:Graphite