Isothermal amplification of DNA using quadruplex primers with fluorescent pteridine base analogue 3-methyl isoxanthopterin

Quadruplex-Based Reactions for Dynamic DNA Nanotechnology

The stringent base-pairing rules of DNA make it an exceptionally powerful bottom-up nanoscale material for dynamic nanotechnologies. However, current nanomachines are based on rearrangements between DNA duplexes, which limits structural versatility and introduces detrimental background activity. Specifically, to make the reactions unidirectional, product duplexes are designed to be thermodynamically more favorable than their respective substrate duplexes. As a result, the reactions are thermodynamically driven, which represents the main source for the background activity. Here we test an alternative approach based on a structural transformation (ST) between a monomolecular DNA substrate and a quadruplex product. The quadruplex sequence is incorporated into a hairpin substrate. ST reaction is initiated by an addition of a target molecule, which through toehold-mediated strand displacement releases the quadruplex-forming sequence. The liberated sequence folds into a stable quadruplex and stays folded after dissociation of the target molecule. This Article analyzes the thermodynamic principles of ST reactions and demonstrates that the unidirectional nonenzymatic reaction can be run without thermodynamic favorability by transforming thermodynamically stable substrates into metastable products. In other words, ST is capable to drive nanomachines using thermodynamically uphill reactions. This allows for (i) running nanodevices without detrimental background activity and (ii) charging the product molecules with potential energy, which could be used in downstream endergonic activities.

Isothermal amplification of long DNA segments by quadruplex priming amplification

Amplification of long DNA segments with the highest possible specificity and lowest bias is one of the main goals of modern genomics. Quadruplex priming amplification (QPA) is a single-primer isothermal method, which employs the free energy of quadruplex structures as the driving force for DNA amplification without any extra reaction components. As a result, QPA represents one of the simplest isothermal assays and was previously shown to be suitable for amplification of relatively short DNA sequences. The current study reveals that single-primer QPA can be used for both exponential and linear amplification of relatively long DNA segments (>100 nt), and switching between these modes can be accomplished by simple re-design of the primer used. While exponential amplification resulted in production of some undesired higher molecular weight species, linear QPA demonstrated highly specific amplification of the target molecules without any side products.

On chip quadruplex priming amplification for quantitative isothermal diagnostics

Nucleic acid testing is a common technique for medical diagnostics. For example, it is used to detect HIV treatment failure by monitoring viral load levels. Quadruplex Priming Amplification (QPA) is an isothermal nucleic acid amplification technique that requires little power and few chemical reagents per assay, all features that make QPA well suited for point-of-care (POC) diagnostics. The QPA assay can be further optimized by integrating it with microfluidic devices that can automate and combine multiple reaction steps and reduce the quantity and cost of reagents per test. In this study, a real-time, exponential QPA reaction is demonstrated for the first time in a microfluidic chip, where the reaction was not inhibited and supported performance levels comparable to a commercially-available, non-microfluidics setup.

Universally applicable, quantitative PCR method utilizing fluorescent nucleobase analogs

We herein describe a novel quantitative PCR (qPCR) method, which operates in both signal-off and on manners, by utilizing a unique property of fluorescent nucleobase analogs. The first, signal-off method is developed by designing the primers to contain pyrrolo-dC (PdC), one of the most common fluorescent nucleobase analogs. The specially designed single-stranded primer is extended to form double-stranded DNA during PCR and the fluorescence signal from the PdCs incorporated in the primer is accordingly reduced due to its conformation-dependent fluorescence properties. In addition, the second, signal-on method is devised by designing the primers to contain 5′-overhang sequences complementary to the PdC-incorporated DNA probes. At the initial phase, the PdC-incorporated DNA probes are hybridized to the 5′-overhang sequences of the primer, exhibiting the significantly quenched fluorescence signal, but are detached by either hydrolysis or strand displacement reaction during PCR, leading to the highly enhanced fluorescence signal. This method is more advanced than the first one since it produces signal-on fluorescence response and permits the use of a single PdC-incorporated DNA probe for the detection of multiple target nucleic acids, remarkably decreasing the assay cost. With these novel qPCR methods, we successfully quantified target nucleic acids derived from sexually transmitted disease (STD) pathogens with high accuracy. Importantly, the proposed strategies overcome the major drawbacks in the current SYBR Green and TaqMan probe-based qPCR methods such as low specificity and high assay cost.

A novel quantitative PCR (qPCR) method was developed by utilizing a unique property of fluorescent nucleobase analogs (PdCs).

Exponential quadruplex priming amplification for DNA-based isothermal diagnostics

Polymerase chain reaction (PCR) is a method of choice for molecular diagnostics. However, PCR relies on thermal cycling, which is not compatible with the goals of point-of-care diagnostics. A simple strategy to turn PCR into an isothermal method would be to use specific primers, which upon polymerase elongation can self-dissociate from the primer-binding sites. We recently demonstrated that a monomolecular DNA quadruplex, GGGTGGGTGGGTGGG, meets these requirements, which led to the development of the linear versions of quadruplex priming amplification (QPA). Here we demonstrate exponential version of isothermal QPA, which allows an unprecedented 10(10)-fold amplification of DNA signal in less than 40 min.

Quadruplex priming amplification for the detection of mRNA from surrogate patient samples

Simple and rapid methods for detecting mRNA biomarkers from patient samples are valuable in settings with limited access to laboratory resources. In this report, we describe the development and evaluation of a self-contained assay to extract and quantify mRNA biomarkers from complex samples using a novel nucleic acid-based molecular sensor called quadruplex priming amplification (QPA). QPA is a simple and robust isothermal nucleic acid amplification method that exploits the stability of the G-quadruplex nucleotide structure to drive spontaneous strand melting from a specific DNA template sequence. Quantification of mRNA was enabled by integrating QPA with a magnetic bead-based extraction method using an mRNA-QPA interface reagent. The assay was found to maintain >90% of the maximum signal over a 4 °C range of operational temperatures (64-68 °C). QPA had a dynamic range spanning four orders of magnitude, with a limit of detection of ~20 pM template molecules using a highly controlled heating and optical system and a limit of detection of ~250 pM using a less optimal water bath and plate reader. These results demonstrate that this integrated approach has potential as a simple and effective mRNA biomarker extraction and detection assay for use in limited resource settings.