A Multichannel Pattern-Recognition-Based Protein Sensor with a Fluorophore-Conjugated Single-Stranded DNA Set.

Mari Okada,Ryoji Kurita,Hiroka Sugai,Shunsuke Tomita

doi:10.3390/s20185110

Abstract

Recently, pattern-recognition-based protein sensing has received considerable attention because it offers unique opportunities that complement more conventional antibody-based detection methods. Here, we report a multichannel pattern-recognition-based sensor using a set of fluorophore-conjugated single-stranded DNAs (ssDNAs), which can detect various proteins. Three different fluorophore-conjugated ssDNAs were placed into a single microplate well together with a target protein, and the generated optical response pattern that corresponds to each environment-sensitive fluorophore was read via multiple detection channels. Multivariate analysis of the resulting optical response patterns allowed an accurate detection of eight different proteases, indicating that fluorescence signal acquisition from a single compartment containing a mixture of ssDNAs is an effective strategy for the characterization of the target proteins. Additionally, the sensor could identify proteins, which are potential targets for disease diagnosis, in a protease and inhibitor mixture of different composition ratios. As our sensor benefits from simple construction and measurement procedures, and uses accessible materials, it offers a rapid and simple platform for the detection of proteins.

Highlights

The detection and identification of proteins plays an important role in the diagnosis of various diseases [1]
To develop a pattern-recognition-based protein-sensing system that can accurately identify analytes, it is necessary to design molecular probes capable of producing multivariate differential pattern data that are specific to individual protein analytes
In order to generate differential optical patterns from a single compartment, we employed these single-stranded DNAs (ssDNAs) that were conjugated with three different fluorophores (DNA-G, DNA-Y, and DNA-R)

Summary

Introduction

The detection and identification of proteins plays an important role in the diagnosis of various diseases [1]. The “lock-and-key” approach, which uses protein-specific molecular probes, such as antibodies [2], aptamers [3], and small organic molecules [4], has been developed to serve this purpose. Such molecular probes often interact with non-target proteins whose structure is similar to that of the target protein in a cross-reactive manner [5,6,7], which complicates the preparation or synthesis of probes that are completely specific to a target protein. The molecular probes used to construct systems that generate optical response patterns. A number of highly sensitive pattern-recognition-based protein sensing systems has been reported that employ materials capable of multi-contact interactions with the macromolecular structure of proteins, such as chromogenic or fluorogenic polymers [11,12,13] and nanoparticles [14,15,16]

Methods

Results

Conclusion