On the Feasibility of Using the Intrinsic Fluorescence of Nucleotides for DNA Sequencing

Protein coupled thionine acetate probed silica nanoparticles: An integrated laser-assisted therapeutic approach for treating cancer

Herein, we report a multifaceted nanoformulation, developed by binding thionine acetate (TA) in silica matrix to form TA loaded silica nanoparticles (STA Nps), which were characterized using various physicochemical techniques. STA NPs were spherical shaped having size 40-50 nm and exhibited good heating efficiency, improved photostability and singlet oxygen production rate than TA alone. In PDT experiment, the rate of degradation for ABDMA was enhanced from 0.1367 min-1 for TA alone to 0.1774 min-1 for STA Nps, depicting an increase in the reactive oxygen species (ROS) generation ability of STA Nps. Further, the cytotoxicity of STA Nps was investigated by carrying out the biophysical studies with Calf thymus DNA (Ct-DNA) and Human Serum Albumin (HSA). The results indicated that the binding of STA Nps to Ct-DNA causes alterations in the double helix structure of DNA and as a result, STA Nps can impart chemotherapeutic effects via targeting DNA. STA Nps showed good binding affinity with HSA without compromising the structure of HSA, which is important for STA Nps sustainable biodistribution and pharmacokinetics. Based on this study, it is suggested that because of the synergistic effect of chemo and phototherapy, STA Nps can be extensively utilized as potential candidates for treating cancer.

Using the Intrinsic Fluorescence of DNA to Characterize Aptamer Binding

The reliable, readily accessible and label-free measurement of aptamer binding remains a challenge in the field. Recent reports have shown large changes in the intrinsic fluorescence of DNA upon the formation of G-quadruplex and i-motif structures. In this work, we examined whether DNA intrinsic fluorescence can be used for studying aptamer binding. First, DNA hybridization resulted in a drop in the fluorescence, which was observed for A30/T30 and a 24-mer random DNA sequence. Next, a series of DNA aptamers were studied. Cortisol and Hg²⁺ induced fluorescence increases for their respective aptamers. For the cortisol aptamer, the length of the terminal stem needs to be short to produce a fluorescence change. However, caffeine and adenosine failed to produce a fluorescence change, regardless of the stem length. Overall, using the intrinsic fluorescence of DNA may be a reliable and accessible method to study a limited number of aptamers that can produce fluorescence changes.

Laser-Induced Periodic Ag Surface Structure with Au Nanorods Plasmonic Nanocavity Metasurface for Strong Enhancement of Adenosine Nucleotide Label-Free Photoluminescence Imaging

The label-free detection of biomolecules by means of fluorescence spectroscopy and imaging is topical. The developed surface-enhanced fluorescence technique has been applied to achieve progress in the label-free detection of biomolecules including deoxyribonucleic acid (DNA) bases. In this study, the effect of a strong enhancement of photoluminescence of 5'-deoxyadenosine-monophosphate (dAMP) by the plasmonic nanocavity metasurface composed of the silver femtosecond laser-induced periodic surface structure (LIPSS) and gold nanorods or nanospheres has been realized at room temperature. The highest value of 1220 for dAMP on the Ag-LIPSS/Au nanorod metasurface has been explained to be a result of the synergetic effect of the generation of hot spots near the sharp edges of LIPSS and Au nanorod tips together with the excitation of collective gap mode of the cavity due to strong near-field plasmonic coupling. A stronger plasmonic enhancement of the phosphorescence compared to the fluorescence is achieved due to a greater overlap of the phosphorescence spectrum with the surface plasmon spectral region. The photoluminescence imaging of dAMP on the metasurfaces shows a high intensity in the blue range. The comparison of Ag-LIPSS/Au nanorod and Ag-LIPSS/Au-nanosphere metasurfaces shows a considerably higher enhancement for the metasurface containing Au nanorods. Thus, the hybrid cavity metasurfaces containing metal LIPSS and nonspherical metal nanoparticles with sharp edges are promising for high-sensitive label-free detection and imaging of biomolecules at room temperature.

Enhancement of the intrinsic fluorescence of adenine using aluminum nanoparticle arrays

This study demonstrates the metal-enhanced fluorescence of adenine using aluminum nanoparticle arrays in the deep UV range. It achieves the reproducible intensity enhancement of intrinsic fluorescence up to 80 on well-defined aluminum nanoparticle arrays at 257 nm excitation. In addition to a high signal enhancement, a strong modification of the fluorescence emission spectrum of adenine is observed. This study illustrates that the label-free detection of DNA bases and proteins that have low intrinsic fluorescence and absorption bands in the deep UV range can be facilitated using aluminum nanostructures.

Experimental and simulative study on surface enhanced Raman scattering of rhodamine 6G adsorbed on big bulk-nanocrystalline metal substrates

Big bulk-nanocrystalline metal materials of silver (Ag) and aluminum (Al) for surface-enhanced Raman scattering (SERS) spectroscopy have been synthesized in a mold under different pressures using vacuum-warm-compaction (VWC) technology.

Feasibility of Using Bimetallic Plasmonic Nanostructures to Enhance the Intrinsic Emission of Biomolecules

Detection of the intrinsic fluorescence from proteins is important in bio-assays because it can potentially eliminate the labeling of external fluorophores to proteins. This is advantageous because using external fluorescent labels to tag biomolecules requires chemical modification and additional incubation and washing steps which can potentially perturb the native functionality of the biomolecules. Hence the external labeling steps add expense and complexity to bio-assays. In this paper, we investigate for the first time the feasibility of using bimetallic nanostructures made of silver (Ag) and aluminum (Al) to implement the metal enhanced fluorescence (MEF) phenomenon for enhancing the intrinsic emission of biomolecules in the ultra-violet (UV) spectral region. Fluorescence intensities and lifetimes of a tryptophan analogue N-acetyl-L-tryptophanamide (NATA) and a tyrosine analogue N-acetyl-L-tyrosinamide (NATA-tyr) were measured. Increase in fluorescence intensities of upto 10-fold and concurrent decrease in lifetimes for the amino acids were recorded in the presence of the bimetallic nanostructures when compared to quartz controls. We performed a model protein assay involving biotinylated bovine serum albumin (bt-BSA) and streptavidin on the bimetallic nanostructured substrate to investigate the distance dependent effects on the extent of MEF from the bimetallic nanostructures and found a maximum enhancement of over 15-fold for two layers of bt-BSA and streptavidin. We also used finite difference time domain (FDTD) calculations to explore how bimetallic nanostructures interact with plane waves and excited state fluorophores in the UV region and demonstrate that the bimetallic substrates are an effective platform for enhancing the intrinsic emission of proteins and other biomolecules.

Ensemble and Single Molecule Studies on the Use of Metallic Nanostructures to Enhance the Intrinsic Emission of Enzyme Cofactors

We present a strategy for enhancing the intrinsic emission of the enzyme cofactors flavin adenine dinucleotide (FAD), flavin mononucleotide (FMN) and nicotinamide adenine dinucleotide (NADH). Ensemble studies show that silver island films (SIFs) are the optimal metal enhanced fluorescence (MEF) substrates for flavins and gave emission enhancements of over 10-fold for both FAD and FMN. A reduction in the lifetime of FAD and FMN on SIFs was also observed. Thermally evaporated aluminum films on quartz slides were found to be the optimal MEF substrate for NADH and gave a 5-fold increase in the emission intensity of NADH. We present finite-difference time-domain (FDTD) calculations that compute the enhancement in the radiated power emitting from an excited state dipole emitting in the wavelength range of NADH in close proximity to an aluminum nanoparticle, and a dipole emitting in the emission wavelength of flavins next to a silver nanoparticle. These calculations confirm that aluminum serves as the optimal MEF substrate for NADH and silver was the optimal MEF substrate for flavins. This is because the plasmon resonance properties of aluminum lie in the UV-blue regime and that of silver lie in the visible region. We also present the results of single molecule studies on FMN which show SIFs can both significantly enhance the intrinsic emission from single FMN molecules, significantly reduce their lifetimes and also significantly reduce FMN blinking. This is the first report of the observation of MEF from cofactors both at the ensemble and single molecule level. We hope this study will serve as a platform to encourage the future use of metallic nanostructures to study cofactors using their intrinsic fluorescence to directly monitor enzyme binding reactions without the need of extrinsic labeling of the molecules.

Metallic-Nanostructure-Enhanced Fluorescence of Single Flavin Cofactor and Single Flavoenzyme Molecules

The enzyme cofactors are intrinsically fluorescent and participate directly in the single molecule enzymology studies. Due to photobleaching, one cannot follow kinetics continuously by cofactor fluorescence for more than several minutes typically. Modification of spectral properties of fluorophores, such as the amplification of emission intensity, can be achieved through coupling with surface plasmons in close proximity to metallic nanostructures. This process, referred to as metal-enhanced fluorescence, offers promise for a range of applications, including bioassays, sensor technology, microarrays, and single-molecule studies. Here, we demonstrated up to a 100-fold increase in the emission of the single cofactors and flavoenzymes near silver nanostructures. Amplified fluorescence of different types of flavins and flavoenzymes has been interpreted by using time-resolved single molecule fluorescence data. The results show considerable promise for the studies of enzyme kinetics using the intrinsic fluorescence from the cofactors.

The use of aluminum nanostructures as platforms for metal enhanced fluorescence of the intrinsic emission of biomolecules in the ultra-violet

We consider the possibility of using aluminum nanostructures for enhancing the intrinsic emission of biomolecules. We used the finite-difference time-domain (FDTD) method to calculate the effects of aluminum nanoparticles on nearby fluorophores that emit in the ultra-violet (UV). We find that the radiated power of UV fluorophores is significantly increased when they are in close proximity to aluminum nanostructures. We show that there will be increased localized excitation near aluminum particles at wavelengths used to excite intrinsic biomolecule emission. We also examine the effect of excited-state fluorophores on the near-field around the nanoparticles. Finally we present experimental evidence showing that a thin film of amino acids and nucleotides display enhanced emission when in close proximity to aluminum nanostructured surfaces. Our results suggest that biomolecules can be detected and identified using aluminum nanostructures that enhance their intrinsic emission. We hope this study will ignite interest in the broader scientific community to take advantage of the plasmonic properties of aluminum and the potential benefits of its interaction with biomolecules to generate momentum towards implementing fluorescence-based bioassays using their intrinsic emission.