CTAB enhancement of FRET in DNA structures

Colorimetric detection of Salmonella typhimurium based on hexadecyl trimethyl ammonium bromide-induced supramolecular assembly of β-cyclodextrin-capped gold nanoparticles

We developed an effective and specific colorimetric strategy to detect Salmonella typhimurium (S. typhimurium) based on hexadecyl trimethyl ammonium bromide (CTAB)-induced supramolecular assembly of β-cyclodextrin-capped gold nanoparticles (β-CD-AuNPs). In this study, ssDNA aptamer of S. typhimurium could combine with CTAB to form the supramolecular ssDNA-CTAB composite, so the ssDNA aptamer was applied to control the concentration of CTAB. In the presence of S. typhimurium, ssDNA aptamers selectively bound to S. typhimurium but not to CTAB, leading to the host-guest chemistry reaction of CTAB and β-CD resulting in β-CD-AuNP supramolecular assembly aggregation with an obvious color change. The ratio of absorption at 650 and 520 nm (A_650nm/A_520nm) has a linear correlation to the log scale of the concentration of the bacteria (1 × 10²-1 × 10⁷ CFU/mL) with a low limit of detection (LOD) of 13 CFU/mL. In addition, this optical sensor has good selectivity and practicability. In milk samples, the recovery was 93.55-111.32%, which suggested its potential application in real samples.

Influence of the Sequestration Effect of CTAB on the Biofunctionalization of Gold Nanorods

Gold nanorods (GNRs) can be functionalized with multiple biomolecules allowing efficient cell targeting and delivery into specific cells. However, various issues have to be addressed prior to any clinical applications. They involve controlled biofunctionalization to be able to deliver a known dose of drug by immobilizing a known number of active molecules to GNRs while protecting their surface from degradation. The most widely used synthesis method of GNRs is seed-mediated growth. It requires the use of cetyltrimethylammonium bromide (CTAB) that acts as a strong capping agent stabilizing the colloidal solution. The problem is that not only is CTAB cytotoxic to most cells but it also induces the sequestration of biomolecules in solution during the functionalization steps of GNRs. The presence of CTAB therefore makes it difficult to control the immobilization of biomolecules to GNRs while removing CTAB from the colloidal solution, leading to the aggregation of GNRs. The sequestration effect of ssDNA in solution by CTAB was studied in detail as a function of the CTAB concentration and the nature of the solution (water or buffer) using Forster resonance energy transfer as a detection tool. The conditions in which DNA sequestration did and did not occur could be clearly defined. Using gel electrophoresis, we could demonstrate how strongly the ssDNA sequestration effect in solution impacts the GNR surface biofunctionalization.

The mechanism and regularity of quenching the effect of bases on fluorophores: the base-quenched probe method

The base-quenched probe method for detecting single nucleotide polymorphisms (SNPs) relies on real-time PCR and melting-curve analysis, which might require only one pair of primers and one probe.

Single-probe multistate detection of DNA via aggregation-induced emission on a graphene oxide platform

Graphene and graphene oxides (GO), or their reduced forms, have been introduced in a variety of biosensing platforms and have exhibited enhanced performance levels in these forms. We herein report a DNA sensing platform consisting of aggregation-induced emission (AIE) molecules and complementary DNA (comDNA) adsorbed on GO. We experimentally turned the AIE molecule on and off by adjusting its distance, which correlates with DNA structures as shown in our computational results, from the GO sheet, which quenches depending on its distance from the graphene plane. The changes in florescence are reproducible, which demonstrates the probe's ability to identify the binding state of the DNA. Our molecular dynamics simulation results reveal strong π-π interactions between single-strand DNA (ssDNA) and GO, which enable the ssDNA molecule to move closer to the graphene oxide. This reduces the center of mass and binding free energies in the simulation. When hybridized with comDNA, the increased distance, evidenced by the reduced interaction, eliminates the quenching effect and turns on the AIE molecule. Our protocol use of the AIE molecule as a probe thus avoids the complicated steps involved in covalent functionalization and allows the rapid and label-free detection of DNA molecules.

STATEMENT OF SIGNIFICANCE

A simple, rapid method of fluorescent measurement of DNA hybridization in the presence of graphene (oxide) is presented. Conventional fluorescent dyes offer high performance in biosensors. However, labeling procedures are synthetically demanding in time and resources making it less cost-effective. Molecules with aggregation-induced-emission (AIE) property have advantages over traditional fluorescent molecules because of their intrinsic preference for detection as a turn-on probe and their single-molecule detection ability. Previous work has shown AIE dyes act as excellent "label-free" bioprobes with high sensitivity but with limited selectivity. Graphene oxide (GO) with its unique optical properties and affinity to different kinds of biomolecules can be used as an auxiliary to enhance selectivity of AIE dyes. In this work, we report a label-free strategy to detect DNA of particular sequence by water-soluble AIE probes with the aid of GO, supported by the computational explanations for this phenomenon.

Enhancement of fluorescent resonant energy transfer and the antenna effect in DNA structures with multiple fluorescent dyes

This study examines the use of surfactants and metal cations to enhance the long range fluorescent resonant energy transfer (FRET) and the antenna effect from three TAMRA donor dyes to one Texas Red acceptor dye conjugated in dsDNA structure.

Enhanced fluorescent resonant energy transfer of DNA conjugates complexed with surfactants and divalent metal ions

Dimerization and resultant quenching of donor and acceptor dyes conjugated on DNA causes loss of fluorescent resonant energy transfer (FRET) efficiency. However, when complexed with surfactants and divalent metal ions, sheathing effects insulate and shield the DNA structures, reducing dimerization and quenching which leads to significant enhancement of FRET efficiency.