Q3: A Compact Device for Quick, High Precision qPCR.

Marco Cereda,Pietro Ferrari,Francesco Ferrara,Alessandro Cocci,Valentina Pavanati,Lillo Raia,Giorgia Calisti,Alessandro Bramanti,Danilo Pirola,Marco Bianchessi,Davide Cucchi,Lorenzo Bruno

doi:10.3390/s18082583

Abstract

An accurate and easy-to-use Q3 system for on-chip quantitative real-time Polymerase Chain Reaction (qPCR) is hereby demonstrated, and described in detail. The qPCR reactions take place inside a single-use Lab-on-a-Chip with multiple wells, each with 5 to 15 µL capacity. The same chip hosts a printed metal heater coupled with a calibrated sensor, for rapid and accurate temperature control inside the reaction mixture. The rest of the system is non-disposable and encased in a 7 × 14 × 8.5 (height) cm plastic shell weighing 300 g. Included in the non-disposable part is a fluorescence read-out system featuring up to four channels and a self-contained control and data storage system, interfacing with an external user-friendly software suite. Hereby, we illustrate the engineering details of the Q3 system and benchmark it with seamlessly ported testing protocols, showing that Q3 equals the performance of standard commercial systems. Overall, to the best of our knowledge, this is one of the most mature general-purpose systems for on-chip qPCR currently available.

Highlights

Polymerase Chain Reaction (PCR) amplification of nucleic acids increases the concentration of target nucleotide sequences, when present, exploiting the peculiar characteristics of the macromolecule [1].Whenever DNA or RNA must be searched for, starting from undetectable concentrations, PCR is the gold standard technique [2]
Four Q3-Plus V2 (Q3) cartridges were loaded in parallel with four standard PCR plates
Assuming accurate loading with the same quantities of reagents and sample, the reliability across the wells typically depends on uniform temperature distribution and optical read-out characteristics, as well as on the quantitative real-time Polymerase Chain Reaction (qPCR)-compatibility of the cartridge materials contacting the reagents

Summary

Introduction

Polymerase Chain Reaction (PCR) amplification of nucleic acids increases the concentration of target nucleotide sequences, when present, exploiting the peculiar characteristics of the macromolecule [1].Whenever DNA or RNA must be searched for, starting from undetectable concentrations, PCR is the gold standard technique [2]. Polymerase Chain Reaction (PCR) amplification of nucleic acids increases the concentration of target nucleotide sequences, when present, exploiting the peculiar characteristics of the macromolecule [1]. In its quantitative version (quantitative real-time PCR, or qPCR) it provides an estimation of the initial concentration of target sequences, which is useful in many cases [3]. Examples include Human Immunodeficiency Virus (HIV) monitoring in seropositive patients, for therapy tuning [4], and quantification of alimentary pathogens in some foodstuff (such as seafood) where toxicity depends on the concentration [5]. The already huge importance of molecular diagnostics is bound to grow hand in hand with our knowledge of the genome; and the latter, in turn, is increasing at a fast pace. QPCR-based monitoring and diagnostics will be more and more pervasive within the medical and biological sciences

Methods

Results

Conclusion