Sensitive and label-free biosensing of RNA with predicted secondary structures by a triplex affinity capture method

A novel biosensing approach for the label-free detection of nucleic acid sequences of short and large lengths has been implemented, with special emphasis on targeting RNA sequences with secondary structures. The approach is based on selecting 8-aminoadenine-modified parallel-stranded DNA tail-clamps as affinity bioreceptors. These receptors have the ability of creating a stable triplex-stranded helix at neutral pH upon hybridization with the nucleic acid target. A surface plasmon resonance biosensor has been used for the detection. With this strategy, we have detected short DNA sequences (32-mer) and purified RNA (103-mer) at the femtomol level in a few minutes in an easy and level-free way. This approach is particularly suitable for the detection of RNA molecules with predicted secondary structures, reaching a limit of detection of 50 fmol without any label or amplification steps. Our methodology has shown a marked enhancement for the detection (18% for short DNA and 54% for RNA), when compared with the conventional duplex approach, highlighting the large difficulty of the duplex approach to detect nucleic acid sequences, especially those exhibiting stable secondary structures. We believe that our strategy could be of great interest to the RNA field

Gold nanorod rotary motors for ultra-sensitive DNA detection

Rotary nanomotors that convert electromagnetic energy into nanoscale mechanical motion provide a highly sensitive platform for studies of biomolecular interactions and biosensing. Here we demonstrate an ultra-sensitive method for detection of short DNA molecules and analysis of DNA melting using single rotating nanorod optically trapped in a focused laser beam

Superior LSPR substrates based on electromagnetic decoupling for on-a-chip high-throughput label-free biosensing

Localized surface plasmon resonance (LSPR) biosensing based on supported metal nanoparticles offers unparalleled possibilities for high-end miniaturization, multiplexing and high-throughput label-free molecular interaction analysis in real time when integrated within an opto-fluidic environment. However, such LSPR-sensing devices typically contain extremely large regions of dielectric materials that are open to molecular adsorption, which must be carefully blocked to avoid compromising the device readings. To address this issue, we made the support essentially invisible to the LSPR by carefully removing the dielectric material overlapping with the localized plasmonic fields through optimized wet-etching. The resulting LSPR substrate, which consists of gold nanodisks centered on narrow SiO2 pillars, exhibits markedly reduced vulnerability to nonspecific substrate adsorption, thus allowing, in an ideal case, the implementation of thicker and more efficient passivation layers. We demonstrate that this approach is effective and fully compatible with state-of-the-art multiplexed real-time biosensing technology and thus represents the ideal substrate design for high-throughput label-free biosensing systems with minimal sample consumption

Large-Scale Fabrication of Shaped High Index Dielectric Nanoparticles on a Substrate and in Solution

High index dielectric nanoparticles and metasurfaces have been proposed for many different applications, including light harvesting, sensing, and metalenses. However, widespread utilization in practice also requires large-scale fabrication methods able to produce homogeneous structures with engineered optical properties in a cost effective manner. Here, a facile fabrication method for silicon nanoparticles is presented that is scalable to 4 inch wafers and can produce a wide range of nanoparticle shapes on demand. Furthermore, it is shown that the fabricated nanoparticles can be detached from their support using a simple substrate removal technique and then transferred to colloidal suspension. The method is universal in the sense that it can be used to generate monodispersed colloidal solutions of nanoparticles of various shapes, sizes and compositions and it therefore opens up a range of new possibilities for applications, for example in nanomedicine and bionanotechnology

Photothermal DNA Release from Laser-Tweezed Individual Gold Nanomotors Driven by Photon Angular Momentum

Gold nanoparticles offer a unique possibility for contact-free bioanalysis and actuation with high spatial resolution that increases their potential for bioapplications such as affinity-based biosensing, drug delivery, and cancer treatment. Here we demonstrate an ultrasensitive optomechanical method for probing and releasing DNA cargo from individual gold nanoparticles trapped and manipulated by laser tweezers. Single nanorods are operated as rotational nanomotors, driven and controlled by circularly polarized laser light in aqueous solution. By rotational dynamics analysis, we resolve differences in the thickness of adsorbed ultrathin molecular layers, including different DNA conformations, with nanometer resolution. We then utilize photothermal heating to release DNA from single nanomotors while measuring the temperature-dependent kinetics and activation energy of the DNA melting process. The method opens new possibilities for optomechanical quantification and application of thermally induced molecular transitions in strongly confined geometries, such as inside microfluidic devices and single cells