A DNA-Based MRI Contrast Agent for Quantitative pH Measurement

Abstract

Extracellular pH is important in clinical measurements due to its correlation to cell metabolism and disease progression. In MRI, T 1 /T 2 ratiometric analysis and other methods have been previously applied to quantify pH using conventional pulse sequences. However, for nanoparticle-based approaches, heterogeneity in size and surface functionalization tends toward qualitative rather than quantitative results. To address this limitation, we developed a novel DNA-based MRI contrast agent, pH-DMRCA, which utilizes a highly programmable and reproducible nanostructure. The pH-DMRCA is a dendritic DNA scaffold that is functionalized with a pH-responsive MRI-sensitive construct, Gd(NP-DO3A), at the end of each DNA arm. We first evaluated the r 1 and r 2 response of our pH-DMRCA over a range of pH values (pH = 5−9) to establish a relaxometric model of pH. These MRIbased assessments of pH were validated in a separate set of samples using a pH electrode (n = 18) and resulted in a good linear correlation (R 2 = 0.99, slope = 0.98, intercept = 0). A Bland−Altman analysis of the results also showed reasonable agreement between the calculated pH and measured pH. Moreover, these pH comparisons were consistent across three different pH-DMRCA concentrations, demonstrating concentration-independence of the method. This MRI-based pH quantification methodology was further verified in human blood plasma. Given the versatility of the DNA-based nanostructures, the contrast agent has a potential to be applied to a wide variety of imaging applications where extracellular pH is important including cancer, stroke, cardiovascular disease, and other important diseases.

pH-responsive i-motif-conjugated nanoparticles for MRI analysis

“…Further developments in CA signal enhancement, paired with our quantitative analysis method 21 could work toward enabling accurate measurements of pH in vivo. The biggest advantage in using the i-motif as the MR signal modulating element is the ease of tunability of the i-motif response range by changes in the sequence.…”

“…The pHsensing mechanism of this CA, Gd(NP-DO3A) 20 , was dependent on changing the protonation state of the nitrophenol arm of the ligand, which consequently changes q (q = 1 vs q = 2). Using the same pH-responsive Gd-based CA, we developed a DNAdendrimer-based MRI CA that demonstrated a significant increase in relaxivity for use in quantitative pH measurement 21 .…”

Visible Fluorescent Light-up Probe for DNA Three-Way Junctions Provides Host–Guest Biosensing Applications

“…A simple aptasensor uses fluorescent light-up probes that bind specific DNA topologies in a label-free platform that does not require chemical modification of the aptamer. , Numerous label-free platforms have been developed for the G-quadruplex (GQ) motif that is also a common recognition element for aptasensors. − The platforms typically rely on structure switching, which may involve a GQ–duplex equilibrium or a GQ–GQ nanodevice due to the polymorphic nature of GQs . Both the duplex and GQs provide a stacking surface for π-extended visible chromophores, such as commercially available thiazole orange (TO), Thioflavin T (ThT), and SYBR Green I (SGI) .…”

“…1 They are produced during DNA replication and are viewed as druggable targets through creation of 3WJ-specific agents that can stabilize the structure to promote cell death in proliferating cancer cells. 2 The branched DNA 3WJ is also an important building block for the construction of DNA nanostructures 3,4 and serves as a motif for the creation of aptamer-based sensors (aptasensors) 5,6 for binding proteins, 7 small-molecule targets, 8,9 and even cells. 10 A simple aptasensor uses fluorescent light-up probes that bind specific DNA topologies in a label-free platform that does not require chemical modification of the aptamer.…”

Novel Self-Calibrating Amperometric and Ratiometric Electrochemical Nanotip Microsensor for pH Measurement in Rat Brain

“…The past decades have witnessed progressive developments in pH monitoring technologies, such as nuclear magnetic resonance, − fluorescence, − surface-enhanced Raman scattering, , and electrochemical methods. − At present, the most common method for measuring pH is the electrochemical assay based on conventional microelectrodes with high spatial resolution, simplicity, and high sensitivity. However, most pH detections were performed using potentiometric sensors, and only a few of them were used to measure the pH e of cells, and even fewer were used to in vivo measure the pH e of mammalian cells. − Recently, a different approach for pH measurement involves the use of voltammetric techniques.…”