Real‐time analysis of switchable nanocomposites of magnesium pyrophosphates and rolling circle amplification products

Abstract

Rolling circle amplification (RCA) is a robust isothermal nucleic acid amplification method producing nanocomposites of DNA and inorganic magnesium pyrophosphate precipitates. Although the conformation and structure of such nanocomposites impact applications, most studies of them have been performed at the end‐point after exposure to a treatment. Here, we use real‐time optomagnetic measurements of the hydrodynamic size of magnetic nanoparticles (MNPs) to study the growth of RCA products grafted onto MNPs as well as the effect of post‐RCA temperature annealing and chemical treatment. As a key result, we show that secondary structures in the RCA products trap and partially protect magnesium pyrophosphate precipitates and that these are reversibly released upon heating above a characteristic temperature defined by the sequence of the RCA product. These findings provide a deeper mechanistic understanding of the synthesis and structure of DNA nanocomposites, which impacts applications of DNA nanocomposites in sensing and drug delivery.

Insights into the Formation of DNA–Magnetic Nanoparticle Hybrid Structures: Correlations between Morphological Characterization and Output from Magnetic Biosensor Measurements

“…The characteristic frequency for Brownian relaxation dynamics, for MNPs having a mean hydrodynamic diameter ( D h ), is expressed as where η is the dynamic viscosity of the carrier liquid and k B T is the thermal energy. 24 , 26 , 27 , 59 …”

“…Here, it was assumed that the DNA–MNP assemblies have spherical shapes. Noteworthy, in the case of the optomagnetic measurements, the Brownian relaxation frequency at low magnetic fields in the linear response regime is related to the peak frequency as 59 …”

“…where η is the dynamic viscosity of the carrier liquid and k B T is the thermal energy. 24,26,27,59 The frequency-dependent imaginary part of the complex magnetic susceptibility (χ″) exhibits a peak in the frequency range between 75 and 121 Hz (Figure 5A). As expected, the peak amplitude diminishes with increasing DNA-coil concentration because of that the number of immobilized MNPs becomes higher.…”

“…Since the MNPs used in our study exhibit blocked magnetic moments, the physical rotation of the particle (Brownian relaxation) is the dominating relaxation mechanism. The characteristic frequency for Brownian relaxation dynamics, for MNPs having a mean hydrodynamic diameter ( D h ), is expressed as where η is the dynamic viscosity of the carrier liquid and k B T is the thermal energy. ,,, …”