Instantaneous Derivatization Technology for Simultaneous and Homogeneous Determination of Multiple DNA Targets

Abstract

There are potential advantages, in terms of simplicity and speed, for detecting DNA hybridization steps directly without using any external labels, especially for the multiplexed assays. In the current paper, we describe the use of a carrier-resolved label-free multiplexed assay for the simultaneous detection of multiple DNA targets. Herein we demonstrate that this protocol, using three homogeneous carriers thermosensitive poly(N-isopropylacrylamide), polystyrene beads, and magnetic beads, respectively, for simultaneous determination of three short DNA fragments specific to hepatitis B virus. Briefly, one hybridization occurs between a mixture of three different capture probe DNAs immobilized onto three carriers and three targets in a single vessel, and then chemiluminescence (CL) detection proceeds via an instantaneous derivatization reaction between the specific CL reagent 3,4,5-trimethoxylphenylglyoxal (TMPG) and the guanine nucleotide-rich regions within the target DNA. An excellent linearity is found within the range between 0.1 and 6.0 pmol with the lowest detection limit of 100 fmol. In contrast to current encoding strategies, every hybridization signal for the corresponding DNA target in our protocol is uniquely immobilized onto one carrier vehicle with a unique and intrinsic physical-chemical signature. Moreover, an instantaneous derivatization reaction is employed for the label-free determination of three targets in a single vessel. In addition, a simple CL setup is employed to read the carrier code instead of an expensive and complicated flow cytometer or imaging system commonly used for multiplexed assays. Further signal amplification is achieved by employing three amplified DNAs for second hybridization, which include a guanine nucleobase-rich sequence domain for the generation of light and an additional tethered nucleic acid domain complementary with one of the target DNA as an amplification platform. Such simple amplified CL transduction allows detection of DNA targets down to the 15-fmol level. This new protocol also provided a good capability in discriminating perfectly complementary DNA from single-base mismatches and noncomplementary sequences. Overall, the protocol described here may have value in a variety of clinical, environmental, and biodefense applications for which the accurate quantitative analysis of multiple DNA targets is desired.