DNA Hybridization Assay Using Gold Nanoparticles and Electrophoresis Separation Provides 1 pM Sensitivity

Effect of DNA density immobilized on gold nanoparticles on nucleic acid detection

Gold nanoparticles (AuNPs) have been utilized as colorimetric biosensors, where target molecule-induced AuNP aggregation can be recognized by a colour change from red to blue. Particularly, single-stranded DNA (ssDNA)-immobilized AuNPs (ssDNA-AuNPs) have been applied to genetic diagnosis due to their rapid and sequence-specific aggregation properties. However, the effect of the density of immobilized ssDNA have not been investigated yet. In this study, we developed a method to control the amount of immobilized ssDNA by use of ethylene glycol, which is expected to control the ice crystal spacing in a freezing-thawing ssDNA-AuNP synthesis method. We also investigated the effect of the DNA density on the sensitivity of the target ssDNA detection, and found that the detection sensitivity was improved at lower DNA densities. To discuss the reason for the improved detection sensitivity, we modified the ssDNA-AuNPs with alkane thiol for better dispersion stability against salt. The results suggest that the DNA density, rather than the dispersion stability, has a significant impact on detection sensitivity.

A Simple and Fast Assay Based on Carboxyfluorescein-Loaded Liposome for Quantitative DNA Detection

The development of an innovative and easy way to run assays for the quantitative detection of DNA present in biological fluids (i.e., blood, urine, and saliva) is of great interest for early diagnosis (e.g., tumors) and personalized medicine. Herein, a new quantitative assay based on the use of highly sensitive carboxyfluorescein-loaded liposomes as signal amplification systems is reported. The method has been tested for the detection of low amounts of DNA sequences. The reported proof of concept exploits a target DNA molecule as a linker between two complementary oligonucleotides. One oligonucleotide is biotinylated at its 3' end and binds to streptavidin-coupled magnetic beads, whereas the other one is conjugated to a cholesterol molecule incorporated in the phospholipidic bilayer of the fluorescent liposomes. In the presence of the target fragment, the correct formation of a construct takes place as witnessed by a strong fluorescence signal, amplified by dissolving lipidic nanoparticles with Triton X-100. The system is able to detect specific nucleotide sequences with a very low detection threshold of target DNA (tens of picomolar). The assay allows the detection of both single- and double-stranded DNA. Studies performed in human blood serum show the correct assembling of the probe but with a reduction of limit of detection (up to ∼1 nM). This liposome signal amplification strategy could be used not only for the detection of DNA but also for other nucleic acids (mRNA; microRNA) that are difficult to be quantified by currently available protocols.

Non-Cross-Linking Aggregation of DNA-Carrying Polymer Micelles Triggered by Duplex Formation

Colloidal behaviors of particles functionalized with biomolecules are generally complicated. This study describes that colloidal behaviors of double-stranded (ds) DNA-carrying polymer micelles are well controlled by altering the molar ratio of single-stranded (ss) DNA moiety in the dsDNA shell. ssDNA-carrying micelles composed of a poly( N-isopropylacrylamide) (PNIPAAm) core surrounded by a dense shell of ssDNAs were prepared through self-assembly of PNIPAAm grafted with ssDNA by incubating its solution above the lower critical solution temperature. Spontaneous, non-cross-linking aggregation of the micelles was triggered by DNA duplex formation on the surface. Comparison of the critical coagulation concentration of NaCl among a series of the DNA-carrying micelles revealed the relationship between the helical structure of the surface-bound DNA and the colloidal stability of the micelles. The electrophoretic mobility analysis of the micelles indicated that the duplex formation reduced the structural flexibility of the surface-bound DNA, thereby decreasing the interparticle entropic repulsion. It is also suggested that the augmented rigidity of the surface-bound DNA increases the number of terminal base pairs facing the solvent, which could lead to multiple blunt-end stacking interaction among the micelles. Therefore, small DNA molecules could be considered unique surface-modifiers capable of controlling interactions between the surfaces of materials.