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Öğe Discriminating a Single Nucleotide Difference for Enhanced miRNA Detection Using Tunable Graphene and Oligonucleotide Nanodevices(AMER CHEMICAL SOC, 2015) Robertson, Neil M.; Hizir, Mustafa Salih; Balcioglu, Mustafa; Wang, Rui; Yavuz, Mustafa Selman; Yumak, Hasan; Ozturk, BirolIn 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 degrees 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 Ion 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.Öğe Smart polymer functionalized graphene nano-devices for thermo-switch controlled biodetection(TAYLOR & FRANCIS INC, 2015) Balcioglu, Mustafa; Buyukbekar, Burak Zafer; Yavuz, Mustafa Selman; Yigit, Mehmet V.[Abstract not Available]Öğe Smart-Polymer-Functionalized Graphene Nanodevices for Thermo-Switch-Controlled Biodetection(AMER CHEMICAL SOC, 2015) Balcioglu, Mustafa; Buyukbekar, Burak Zafer; Yavuz, Mustafa Selman; Yigit, Mehmet V.In this work, we have developed a general methodology for constructing an activatable biosensor utilizing a thermoresponsive polymer and two-dimensional nanosheet. We have demonstrated the detection of four different types of biological compounds using the smart PEGMA (poly(ethylene glycol) methyl ether methacrylate), oligonucleotides, and graphene oxide nanoassembly. The activity of the functional nanodevice is controlled with a thermo-switch at 39 degrees C. In this design, the nanosized graphene oxide serves as a template for fluorophore labeled probe oligonucleotides while quenching the fluorescence intensities dramatically. On the other hand, the PEGMA polymer serves as an activatable protecting layer covering the graphene oxide and entrapping the probe oligonucleotides on the surface. The PEGMA polymers are hydrophobic above their lower critical solution temperature (LCST) and therefore interact strongly with the hydrophobic surface of graphene oxide, creating a closed configuration (OFF state) of the nanodevice. However, once the temperature decreases below the LCST, the polymer undergoes conformational change and becomes hydrophilic. This opens up the surface of the graphene oxide (open configuration, ON state), freeing the encapsulated payload on the surface. We have tuned the activity of the nanodevice for the detection of a sequence-specific DNA, miR-10b, thrombin, and adenosine. The activity of our functional system can be decreased by 80% with a thermo-switch at 39 C. Our approach can be extended to other antisense oligonucleotide, aptamer, or DNAzyme based sensing strategies.Öğe Stimulus-responsive water-soluble graphene nanodevices for tunable biomarker detection(AMER CHEMICAL SOC, 2015) Balcioglu, Mustafa; Buyukbekar, Burak Zafer; Yavuz, Mustafa; Yigit, Mehmet[Abstract not Available]Öğe Tuning the detection capacity and specificity of polymer protected graphene nanoassemblies using endonucleases(AMER CHEMICAL SOC, 2015) Robertson, Neil; Hizir, Mustafa; Rana, Muhit; Balcioglu, Mustafa; Yavuz, Mustafa; Yigit, Mehmet[Abstract not Available]
