DNA Functionalized Nanoparticles in Nanobiosensor and Sensor Array Development for Molecular Diagnostics and in Vitro Identification of Biomolecule

Nucleic acid technology along with vast variety of nanomaterials has demonstrated a great potential in many applications from biosensing studies to molecular diagnostics, from biomedical and bioanalytical research to environmental analysis. Especially short single stranded (ss) DNA molecules, called oligonucleotides, are extraordinary biopolymers featuring diverse functionality on the nanoparticles thanks to their high degree of programmability, target-specific binding or cleavage, molecular recognition ability, structure-switching capability, and unique interactions at the bio-nano interfaces. Among those, there have been many biosensing applications utilizing ss DNAs and numerous nanomaterials through various detection techniques such as fluorometric, colorimetric or electrochemical methods. Although many groundbreaking applications have been carried out, some challenges arising from sensitivity or selectivity issues remain to be addressed, especially for molecular diagnostics. Functional sensory systems with cost-effective, rapid, and easy-to-operate layouts, which are crucial for point-of-care diagnostics, are still an unmet need for certain fields to target disease-related critical biomarkers such as proteins, cells, circulating DNAs or miRNAs.;Here, we aim to address the current challenges of biosensor and sensor array development for biosensing applications. By utilizing various nanomaterials integrated with nucleic acid technology, we discuss recent improvements from materials aspect. Our main focus here is two-dimensional (2D) nanoparticles functionalized by oligonucleotides to resolve sensitivity and specificity issues in biosensing implementations to a certain degree. Here, 2D nanoparticle-based sensing platforms are coupled with fluorometric detection techniques which have great promise for highly sensitive measurements, which could end up with successful practical applications for clinical studies. Also, we study colloidal gold nanoparticles (AuNPs) for their intrinsic enzyme-like properties and the use of this property for potential aptasensor designs coupled with colorimetric methods.;Here, we report mainly 2D biosensing platforms composed of 2D nanoparticles and fluorescently labeled ss DNAs as sensory components, and functionalized by smart polymers and/or enzyme-coupled amplification strategies. Both individual 2D sensor platforms and multi-component sensor arrays employ target-specific sensing models while the arrays can also be programmed for unbiased non-specific sensory approaches for universal applications. As aforementioned, fluorometric techniques are coupled with 2D biosensor or sensor array devices through fluorescently labeled ss DNAs as sensing probes. That enables one to achieve a highly sensitive detection of targets of interest in pure systems by monitoring the target-induced changes on the sensing platform almost regardless of how subtle they are. Using these sensor designs, a broad range of biomolecules or biomarkers can be targeted, detected, and discriminated both in buffer and in biological matrices such as liquid biopsies or cancer cell lines regardless of the homology among them.;We demonstrate that DNA-functionalized nanomaterials can be employed to develop powerful biosensors and sensor arrays as alternative diagnostic strategies to identify and differentiate biosystems such as novel disease biomarkers, important macromolecules, and living cancer cells both in buffered solutions and biological environments such as liquid biopsies (blood serum, saliva, or urine).;Nanozymes that are inorganic nanoparticles carrying enzyme-like properties are advantageous alternatives over their biological counterparts. These artificial enzymes provide more stable working conditions and the ease of preparation along with tunable activity properties. As a peroxidase-mimic, citrate-capped AuNPs can be adjusted in activity using ss DNA molecules. Different amounts, base compositions or lengths of DNAs could alter the intrinsic enzymatic activity of the material, which gives one the control over the activity to deploy the material into functional aptasensor designs. The on-hand DNA-induced enhancement in the peroxidase-like activity can be utilized by using specific aptamers to detect proteins. Pre-incubation of a protein with its aptamer before aptamer-AuNP interaction results in reduced enhancement due to the occupied aptamer molecules which is proportional to the amount of the incubated protein. Using this indirect aptasensor strategy, numerous DNA-binding molecules can be detected through the artificial enzyme property of nanomaterials (nanozymes).