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Synthetic single-stranded oligonucleotides play crucial roles in DNA amplification reactions for various applications, such as serving as primers, enabling magnetic separation, and generating dsDNA for subsequent digestion. Typically, these oligos are added in excess to ensure rapid binding to their intended targets. However, while performing rolling circle amplification (RCA) using phi29 DNA polymerase, we observed a decrease in amplification efficiency when oligos were present in the reaction. This phenomenon was consistently observed in two separate laboratories, prompting this study to delve into the root causes responsible for the decline in RCA efficiency. The lowered efficiency was consistent regardless of the manufacturer or any mutations in the phi29 polymerase. We identified several variables that influenced RCA efficiency, mainly the length of the oligos used and the presence of modifications, particularly those obstructing 3’ end digestion. This strongly suggests that the exonuclease domain of phi29 DNA polymerase is responsible for the competition-based inhibition. Our investigation shows that even picomole quantities of oligos can significantly reduce total DNA production during the phi29 DNA polymerase-mediated amplification process. Conversely, the addition of oligos to the reaction did not impede the efficiency of Bst 3.0 polymerase, likely due to the lack of an exonuclease domain of said polymerase. While increasing the quantity of phi29 DNA polymerase in the reaction partially alleviated the adverse effects of excess oligos, we believe it is crucial to carefully optimize the oligo quantities to achieve maximum amplification of the desired targets.

An attractive approach to increase the aqueous apparent solubility of poorly soluble drugs is to formulate them in their amorphous state. In the present study, celecoxib, a poorly soluble drug, was successfully loaded into mesoporous magnesium carbonate (MMC) in its amorphous state via a solvent evaporation method. Crystallization of celecoxib was suppressed, and no reaction with the carrier was detected. The MMC formulation was evaluated in vitro and in vivo in terms of oral bioavailability. Celebra®, a commercially available formulation, was used as a reference. The two celecoxib formulations were orally administrated in male rats (average of n = 6 animals per group), and blood samples for plasma were taken from all animals at different time points after administration. There was no statistical difference (p > 0.05) in AUCinf between the two formulations. The results showed that MMC may be a promising drug delivery excipient for increasing the bioavailability of compounds with solubility-limited absorption.

Detection of antibiotic resistance is paramount for accurate and effective treatment of infectious bacterial diseases. There is a growing interest for methods making it possible to identify the specific genes giving rise to antibiotic resistance. Molecular detection approaches have evolved to the point where many techniques can be performed in clinics, bedside setups or implemented in microfluidic chips as they require little equipment and training. Rolling circle amplification (RCA) is an isothermal DNA amplification technique that amplifies synthetic circular DNA probes that have been hybridized to a complementary target present in the sample. To increase the number of amplification products, several rounds of RCA may be performed on a single sample. This technique is denoted as circle-to-circle amplification (C2CA).

Nanomedicine is just starting to reshape clinical practice and since the last decade magnetic nanoparticles have drawn increasing attention to the development of different types of magnetic biosensors. This is because of their high physical and chemical stability and that they are not generally affected by reagent chemistry or exposure to light. Magnetic nanoparticle-based biosensors offer an attractive and cost-effective route for detection of biomolecules, since they are relatively inexpensive to produce and easily made biocompatible. We have developed a diagnostic method, based on oligonucleotide-functionalized magnetic nanoparticles, for detection of specific DNA sequences. These DNA sequences are amplified through an isothermal amplification technique called rolling circle amplification (RCA) which generates micrometer sized RCA products after one hour of amplification. The oligonucleotides attached to the surface of the magnetic nanoparticles are complementary to repeating sequences of the RCA products. In a high salt and high temperature environment, the oligonucleotide-functionalized magnetic nanoparticles bind to the RCA products and forms large aggregates visible to the naked eye. This allows for simple qualitative detection of specific DNA sequences where there is no need for complicated and expensive readout instrumentation. Our developed method yields visible aggregates in the presence of at least 1 amol of DNA target in less than 2 hours; targeting the antibiotic resistance gene sul1. Specificity tests shows that there is no non-specific aggregation detected in samples containing up to 20 fmol of non-complementary amplified DNA. This method is a versatile and simple tool for detecting pathogenic DNA with no read-out equipment required.

Visual detection of rolling circle amplification products (RCPs) has been achieved by specific aggregation with magnetic nanoparticles. The method presented here reliably generates aggregates in 1.5 h; these are visible to the naked eye in samples containing at least 0.4 fmol of RCPs. In addition, alternate current susceptometry and absorbance spectroscopy have also been used to quantify the amplified products. The specificity of the detection method was tested, and no non-specific aggregation was detected in samples containing up to 20 fmol of non-complementary amplified DNA. This method is a versatile tool for detecting pathogenic DNA in point-of-care diagnostics, with no readout equipment required. However, chips and automated assays can be used in conjugation with the developed method since detection and quantification can be achieved by commercially available readout instruments.

In the current work, mesoporous magnesium carbonate (MMC) was used to suppress crystallization of the poorly soluble drug celecoxib (CXB). This resulted in both a higher dissolution rate and supersaturation of the substance in vitro as well as an increased transfer of CXB over a Caco-2 cell membrane mimicking the membrane in the small intestine. The CXB flux over the cell membrane showed a linear behavior over the explored time period. These results indicate that MMC may be helpful in increasing the bioavailability and obtaining a continuous release of CXB, and similar substances, in vivo. Neusilin US2 was used as a reference material and showed a more rapid initial release with subsequent crystallization of the incorporated CXB in the release media. The presented results form the foundation of future development of MMC as a potential carrier for poorly soluble drugs.

Understanding the binding mechanism between probe-functionalized magnetic nanoparticles (MNPs) and DNA targets or amplification products thereof is essential in the optimization of magnetic biosensors for the detection of DNA. Herein, the molecular interaction forming hybrid structures upon hybridization between DNA-functionalized magnetic nanoparticles, exhibiting Brownian relaxation, and rolling circle amplification products (DNA-coils) is investigated by the use of atomic force microscopy in a liquid environment and magnetic biosensors measuring the frequency-dependent magnetic response and the frequency-dependent modulation of light transmission. This approach reveals the qualitative and quantitative correlations between the morphological features of the hybrid structures with their magnetic response. The suppression of the high-frequency peak in the magnetic response and the appearance of a new peak at lower frequencies match the formation of larger sized assemblies upon increasing the concentration of DNA-coils. Furthermore, an increase of the DNA-coil concentration induces an increase in the number of MNPs per hybrid structure. This study provides new insights into the DNA-MNP binding mechanism, and its versatility is of considerable importance for the mechanistic characterization of other DNA-nanoparticle biosensor systems.

Nanomedicine, the application of nanotechnology in medicine, is expected to have a revolutionary impact on health care. During the last decade, magnetic nanoparticles have drawn increasing attention in the development of different types of magnetic biosensors. Magnetic nanoparticle-based biosensors offer an attractive and cost-effective route for detection of biomolecules, since they are relatively inexpensive to produce, stable and easily made biocompatible. The detection principle presented at this seminar is based on measuring of the shift in Brownian relaxation frequency of functionalized magnetic nanoparticles. The frequency shift is a result of an increase of the hydrodynamic size of the particles as they bind to designated target molecules. The detection system has the potential of detecting DNA, for example those of pathogenic bacteria present in humans and animals.The aim of this project is to bring forward a sensitive, low-cost and easy-to-use diagnostic method, which can serve as an efficient analytical platform for rapid detection and characterization of bacteria resistant to antibiotics.

The binding kinetics of magnetic nanoparticles (MNPs) to rolling circle amplification products (RCPs) is investigated using a differential homogenous magnetic assay (DHMA)1. The DHMA utilizes a microfluidic device to measure the differential ac susceptibility signal between a reference and a test sample, taking advantage of the symmetry in a high-Tc SQUID gradiometer sensor2. The DHMA signal is related to the relative differences in the particle distribution of the two samples, and the background magnetic signal is thus eliminated. Therefore, minuscule changes in the nanoparticle’s concentration and size distribution of the test sample are directly detectable in the solution. This makes the DHMA a superior technique to characterize the binding interaction of the MNPs to biomolecules like RCPs specially at very low concentrations. The DHMA reveals that there is a competitive dynamic process between the MNP labelled RCPs and the unbound MNPs in the solution as a function of the RCP concentrations. The evidence of this dynamic in the signal fades as the MNP-RCP agglomerates are formed. The DHMA also shows that the smaller MNPs in the MNP size distribution take precedence over the larger MNP in immobilization on the RCPs. Comparing the DHMA responses with the turn-off detection method indicates that a full frequency range ac susceptibility observation is necessary when detecting low concentration of target RCPs. The findings are critical for understanding the underlying microscopic binding process and improving the assay performance. [1] Sepehri, S. et al, Differential homogeneous magnetic assay. Submitted. [2] Sepehri, S. et al. Volume-amplified magnetic bioassay integrated with microfluidic sample handling and high-Tc SQUID magnetic readout. APL Bioeng. 2, 016102 (2018).

The specific binding of oligonucleotide-tagged 100 nm magnetic nanoparticles (MNPs) to rolling circle products (RCPs) is investigated using our newly developed differential homogenous magnetic assay (DHMA). The DHMA measures ac magnetic susceptibility from a test and a control samples simultaneously and eliminates magnetic background signal. Therefore, the DHMA can reveal details of binding kinetics of magnetic nanoparticles at very low concentrations of RCPs. From the analysis of the imaginary part of the DHMA signal, we find that smaller MNPs in the particle ensemble bind first to the RCPs. When the RCP concentration increases, we observe the formation of agglomerates, which leads to lower number of MNPs per RCP at higher concentrations of RCPs. The results thus indicate that a full frequency range of ac susceptibility observation is necessary to detect low concentrations of target RCPs and a long amplification time is not required as it does not significantly increase the number of MNPs per RCP. The findings are critical for understanding the underlying microscopic binding process for improving the assay performance. They furthermore suggest DHMA is a powerful technique for dynamically characterizing the binding interactions between MNPs and biomolecules in fluid volumes.

Assays are widely used for detection of various targets, including pathogens, drugs, and toxins. Homogeneous assays are promising for the realization of point-of-care diagnostics as they do not require separation, immobilization, or washing steps. For low concentrations of target molecules, the speed and sensitivity of homogeneous assays have hitherto been limited by slow binding kinetics, time-consuming amplification steps, and the presence of a high background signal. Here, we present a homogeneous differential magnetic assay that utilizes a differential magnetic readout that eliminates previous limitations of homogeneous assays. The assay uses a gradiometer sensor configuration combined with precise microfluidic sample handling. This enables simultaneous differential measurement sample containing a synthesized Vibrio cholerae target and a negative control sample, which reduces the background signal and increases the readout speed. Very low concentrations of targets down to femtomolar levels are thus detectable without any additional amplification of the number of targets. Our homogeneous differential magnetic assay method opens new possibilities for rapid and highly sensitive diagnostics at the point of care.

We developed a novel biodetection method for influenza virus based on AC magnetic susceptibility measurement techniques (the DynoMag induction technique) together with functionalized multi-core magnetic nanoparticles. The sample consisting of an incubated mixture of magnetic nanoparticles and rolling circle amplified DNA coils is injected into a tube by a peristaltic pump. The sample is moved as a plug to the two well-balanced detection coils and the dynamic magnetic moment in each position is read over a range of excitation frequencies. The time for making a complete frequency sweep over the relaxation peak is about 5 minutes (10 Hz⁻10 kHz with 20 data points). The obtained standard deviation of the magnetic signal at the relaxation frequency (around 100 Hz) is equal to about 10-5 (volume susceptibility SI units), which is in the same range obtained with the DynoMag system. The limit of detection with this method is found to be in the range of 1 pM.

A bioassay based on a high-Tc superconducting quantum interference device (SQUID) reading out functionalized magnetic nanoparticles (fMNPs) in a prototype microfluidic platform is presented. The target molecule recognition is based on volume amplification using padlock-probe-ligation followed by rolling circle amplification (RCA). The MNPs are functionalized with single-stranded oligonucleotides, which give a specific binding of the MNPs to the large RCA coil product, resulting in a large change in the amplitude of the imaginary part of the ac magnetic susceptibility. The RCA products from amplification of synthetic Vibrio cholera target DNA were investigated using our SQUID ac susceptibility system in microfluidic channel with an equivalent sample volume of 3 μl. From extrapolation of the linear dependence of the SQUID signal versus concentration of the RCA coils, it is found that the projected limit of detection for our system is about 1.0 × 105 RCA coils (0.2 × 10−18 mol), which is equivalent to 66 fM in the 3 μl sample volume. This ultra-high magnetic sensitivity and integration with microfluidic sample handling are critical steps towards magnetic bioassays for rapid detection of DNA and RNA targets at the point of care.

We use functionalized iron oxide magnetic multi-core particles of 100 nm in size (hydrodynamic particle diameter) and AC susceptometry (ACS) methods to measure the binding reactions between the magnetic nanoparticles (MNPs) and bio-analyte products produced from DNA segments using the rolling circle amplification (RCA) method. We use sensitive induction detection techniques in order to measure the ACS response. The DNA is amplified via RCA to generate RCA coils with a specific size that is dependent on the amplification time. After about 75 min of amplification we obtain an average RCA coil diameter of about 1 µm. We determine a theoretical limit of detection (LOD) in the range of 11 attomole (corresponding to an analyte concentration of 55 fM for a sample volume of 200 µL) from the ACS dynamic response after the MNPs have bound to the RCA coils and the measured ACS readout noise. We also discuss further possible improvements of the LOD.

The need to combat poor water solubility has increased interest in supersaturating drug delivery systems. In this study, amorphous mesoporous magnesium carbonate (MMC) was used as a drug carrier to achieve supersaturation of tolfenamic acid and rimonabant, two drug compounds with low aqueous solubility. The potential synergy between MMC and hydroxypropyl methylcellulose (HPMC), a polymer commonly included as a precipitation inhibitor in drug delivery systems, was explored with the aim of extending the time that high supersaturation levels were maintained. Release was studied under physiological conditions using USP-2 dissolution baths. A new small-scale method was developed to enable measurement of the initial drug release occurring when the MMC is immersed in the water phase. It was shown that MMC and HPMC together resulted in significant supersaturation and that the polymer enabled both the achievement of a higher API concentration and extension of the supersaturation period. The new small-scale release method showed that the release was linearly increasing with the dose and that similar release rates were observed for the two model compounds. It was hence concluded that the MMC release was diffusion limited for the compounds explored.

The presented measurement and data analysis procedure reduces the read-out time for the volume-amplified magnetic nanobead detection assay from ~30 min to only 2 min, providing fast, sensitive detection of DNA molecules. The molecular detection and amplification protocol was verified using samples containing rolling circle-amplified DNA products formed from synthetic Vibrio cholerae target DNA, with a limit of detection of 5 pM. The developed read-out method could be used to rapidly identify pathogens in a variety of applications including target screening in hospitals with limited resources, in out-patient settings and in the field.

Benefiting from their rapid readout, highly flexible devices and low-cost portable systems, optomagnetic biosensors have drawn increased attention in recent years as bioassay technologies for small molecules, biomarkers, DNA, and bacteria. Herein, an optomagnetic bioassay strategy suitable for point-of-care diagnostics, utilizing functionalized magnetic nanoparticles (100 nm) with Brownian relaxation behavior is optimized in order to obtain higher detection sensitivity for DNA molecules and bacteria. Presence of target DNA sequences or bacteria changes the dynamic behavior of the magnetic nanoparticles (binding to the target) and thus the optomagnetic response of the sample, which is measured by an optomagnetic setup including a 405 nm laser and a photodetector. The limit of detection is mainly set by the lowest measurable concentration of magnetic nanoparticles. Herein, as new results compared to previous work, we systematically optimize the concentration of 100 nm magnetic nanoparticles to increase the assay sensitivity and lower the limit of detection. To enable biplex detection, we perform this optimization in the presence of larger 250 nm magnetic nanoparticles that do not interact with the target. We show that the optimization and lowering of the 100 nm magnetic nanoparticle concentration result in a limit of detection of 780 fM of DNA coils formed by rolling circle amplification (size of about 1 μm) and 105 CFU per mL Salmonella (for immunoassay). These values are 15 times lower than those reported previously for this readout principle. Finally, we show that the 250 nm magnetic nanoparticles can serve as a second detection label for qualitative biplex detection of DNA coils formed by rolling circle amplification from V. cholerae and E. coli DNA coils using 100 nm and 250 nm magnetic detection nanoparticles, respectively.

Rapid and sensitive diagnostic methods based on isothermal amplification are ideal substitutes for PCR in out-of-lab settings. However, there are bottlenecks in terms of establishing low-cost and user-friendly readout methods for isothermal amplification schemes. Combining the high amplification efficiency of loop-mediated isothermal amplification (LAMP) with an optomagnetic' nanoparticle-based readout system, we demonstrate ultrasensitive and rapid detection of Newcastle disease virus RNA. Biotinylated amplicons of LAMP and reverse transcription LAMP (RT-LAMP) bind to streptavidin-coated magnetic nanoparticles (MNPs) resulting in a dramatical increase in the hydrodynamic size of the MNPs. This increase was measured by an optomagnetic readout system and provided quantitative information on the amount of LAMP target sequence. Our assay resulted in a limit of detection of 10 aM of target sequence with a total assay time of 30 min. The assay has also been tested on clinical samples (vaccine and tissue specimens) with a performance comparable to real-time RT-PCR By changing the LAMP primers, this strategy can serve as a general method for the detection of other DNA/RNA targets with high specificity and sensitivity.