Systematic Investigation of Two-Dimensional DNA Nanoassemblies for Construction of a Nonspecific Sensor Array

Abstract

We have performed a systematic study to analyze the effect of ssDNA length, nucleobase composition, and the type of two-dimensional nanoparticles (2D-nps) on the desorption response of 36 two-dimensional nanoassemblies (2D-NAs) against several proteins. The studies were performed using fluorescently labeled polyA, polyC, and polyT with 23, 18, 12, and 7 nucleotide-long sequences. The results suggest that the ssDNAs with polyC and longer sequences are more resistant to desorption, compared to their counterparts. In addition, 2D-NAs assembled using WS were least susceptible to desorption by the proteins tested, whereas nGO 2D-NAs were the most susceptible nanoassemblies. Later, the results of these systematic studies were used to construct a sensor array for discrimination of seven model proteins (BSA, lipase, alkaline phosphatase, acid phosphatase, protease, β-galactosidase, and Cytochrome c). Neither the ssDNAs nor the 2D-nps have any specific interaction with the proteins tested. Only the displacement of the ssDNAs from the 2D-np surface was measured upon the disruption of the existing forces within 2D-NAs. A customized sensor array with five 2D-NAs was developed as a result of a careful screening/filtering process. The sensor array was tested against 200 nM of protein targets, and each protein was discriminated successfully. The results suggest that the systematic studies performed using various ssDNAs and 2D-nps enabled the construction of a sensor array without a bind-and-release sensing mechanism. The studies also demonstrate the significance of systematic investigations in the construction of two-dimensional DNA nanoassemblies for functional studies.

Array-Based Discriminative Optical Biosensors for Identifying Multiple Proteins in Aqueous Solution and Biofluids

“…By altering the surface functionality, the two-element array (dopamine-Fe 3 O 4 NPs and trimethylammonium-Fe 3 O 4 NPs) was able to identify 10 proteins, and differentiate unknown samples with an accuracy of 95%. Nandu et al ( 2018 ) reported a five-element sensor array containing two-dimensional nanoparticles (2D-nps, including MoS 2 , WS 2 , and nGO) and fluorescently labeled ssDNA after a careful screening/filtering process. The displacement of ssDNA from the surface of 2D-nps made the array able to discriminate seven proteins.…”

Machine-Learning Single-Stranded DNA Nanoparticles for Bacterial Analysis

“…We have used a single statistical analysis method to identify individual pure target molecules in the past. 8,9,22 Herein, we have adapted a number of ML tools to identify and discriminate complex matrixes reproducibly using four bacterial species.…”

“…8,9,26 Upon displacement of the fluorescently labeled ssDNAs, the quenched fluorescence recovers. 20,8,9 Each ssDNA interacts differently with each 2Dnp, depending on their nucleobase composition and length, as observed in our previous studies. 9 As a result, the degree of displacement of ssDNAs from each 2D-np surface is observed to be different, creating fingerprint fluorescent patterns.…”

“…Over the years, the versatility of nanoparticles has been utilized for building functional nanodevices, − drug-delivery vectors, , bioimaging agents, , sensors, − and more. Many of the synthesized or discovered nanoparticles display a selective affinity for single-stranded oligonucleotides and quench fluorescently labeled oligomers.…”

“…Using the nanosensor array, the differences in the cellular content of each sample are discerned and translated into a fluorescence recovery dataset that can be processed by ML algorithms. We have used a single statistical analysis method to identify individual pure target molecules in the past. ,, Herein, we have adapted a number of ML tools to identify and discriminate complex matrixes reproducibly using four bacterial species.…”