SERS Spectra of Oligonucleotides as Fingerprints to Detect Label-Free RNA in Microfluidic Devices

Probing specific RNA sequences is an issue of major significance for which fluorescence dominates most of the investigation strategies and relies heavily on the use of specific labels. In this paper, we report the detection by SERS (surface-enhanced Raman scattering) of unlabeled model purified oligonucleotides RNA polyadenosine (5′-AAA­AAA­AAA­A-3′) and polycytosine (5′-CCC­CCC­CCC­C-3′) combining silver nanoparticles as enhancing surfaces with microfluidic platforms to control species movement and the aggregation state of the nanoparticles, which is critical for the sensitivity. Two types of microfluidic platforms have been evaluated and compared: one based on laminar streams and the other involving flowing droplets acting as chemical reactors. Both platforms provide homogeneous and controlled mixing conditions of nanoparticles with oligonucleotides: laminar streams induce mixing driven by diffusion, whereas droplets permit fast and efficient mixing through internal fluid recirculation and prevent channel clogging by nanoparticles. We demonstrate that in both cases, the bases can be detected selectively. In the droplet microfluidic system, the Raman maximum enhancement is localized in the center of the droplet and observed after a certain period of mixing time that appears specific for each base, after droplet formation. It appears to be a highly promising approach for probing unlabeled nucleotides using SERS

Effect of the Interaction of the Amyloid β (1–42) Peptide with Short Single-Stranded Synthetic Nucleotide Sequences: Morphological Characterization of the Inhibition of Fibrils Formation and Fibrils Disassembly

The formation of extracellular neuritic plaques in the brain of individuals who suffered from Alzheimer’s disease (AD) is a major pathological hallmark. These plaques consist of filamentous aggregates of the amyloid beta (1–42) (Aβ₄₂) proteins. Prevention or reduction of the formation of these fibrils is foreseen as a potential therapeutic approach. In this context, we investigated the interactions between the Aβ₄₂ protein and polyions, in particular short single stranded synthetic nucleotide sequences. The experimental outcomes reported herein provide evidence of the inhibition of amyloid fibril genesis as well as disassembly of existing fibers through electrostatic interaction between the Aβ₄₂ protein and the polyions. Since the polyions and the Aβ₄₂ protein are oppositely charged, the formation of (micellar) inter polyelectrolyte complexes (IPECs) is likely to occur. Since the abnormal deposition of amyloid fibers is an archetype of AD, the outcomes of these investigations, supported by atomic force microscopy imaging in the dry and liquid states, as well as circular dichroism and Fourier transform infrared spectroscopy, are of high interest for the development of future strategies to cure a disease that concerns an ever aging population

Interaction of Polycationic Ni(II)-Salophen Complexes with G‑Quadruplex DNA

A series of nine Ni­(II) salophen complexes involving one, two, or three alkyl-imidazolium side-chains was prepared. The lengths of the side-chains were varied from one to three carbons. The crystal structure of one complex revealed a square planar geometry of the nickel ion. Fluorescence resonance energy transfer melting of G-quadruplex structures in the presence of salophen complex were performed. The G-quadruplex DNA structures were stabilized in the presence of the complexes, but a duplex DNA was not. The binding constants of the complexes for parallel and antiparallel G-quadruplex DNA, as well as hairpin DNA, were measured by surface plasmon resonance. The compounds were selective for G-quadruplex DNA, as reflected by equilibrium dissociation constant <i>K</i>_D values in the region 0.1–1 μM for G-quadruplexes and greater than 2 μM for duplex DNA. Complexes with more and shorter side-chains had the highest binding constants. The structural basis for the interaction of the complexes with the human telomeric G-quadruplex DNA was investigated by computational studies: the aromatic core of the complex stacked over the last tetrad of the G-quadruplex with peripherical cationic side chains inserted into opposite grooves. Biochemical studies (telomeric repeat amplification protocol assays) indicated that the complexes significantly inhibited telomerase activity with IC₅₀ values as low as 700 nM; the complexes did not significantly inhibit polymerase activity

Interaction of Polycationic Ni(II)-Salophen Complexes with G‑Quadruplex DNA

A series of nine Ni­(II) salophen complexes involving one, two, or three alkyl-imidazolium side-chains was prepared. The lengths of the side-chains were varied from one to three carbons. The crystal structure of one complex revealed a square planar geometry of the nickel ion. Fluorescence resonance energy transfer melting of G-quadruplex structures in the presence of salophen complex were performed. The G-quadruplex DNA structures were stabilized in the presence of the complexes, but a duplex DNA was not. The binding constants of the complexes for parallel and antiparallel G-quadruplex DNA, as well as hairpin DNA, were measured by surface plasmon resonance. The compounds were selective for G-quadruplex DNA, as reflected by equilibrium dissociation constant <i>K</i>_D values in the region 0.1–1 μM for G-quadruplexes and greater than 2 μM for duplex DNA. Complexes with more and shorter side-chains had the highest binding constants. The structural basis for the interaction of the complexes with the human telomeric G-quadruplex DNA was investigated by computational studies: the aromatic core of the complex stacked over the last tetrad of the G-quadruplex with peripherical cationic side chains inserted into opposite grooves. Biochemical studies (telomeric repeat amplification protocol assays) indicated that the complexes significantly inhibited telomerase activity with IC₅₀ values as low as 700 nM; the complexes did not significantly inhibit polymerase activity