Bio-Mediated Synthesis of Metal Nanomaterials for SERS Application

The discovery of nanomaterials (NMs) caused a great revolution in the field of science especially in material science. The highly exotic and tunable size and shape of NMs have devoted more interest due to their unique physiochemical properties. There are various methods and methodologies involved to prepare NMs in a desired morphology. Among these, the fabrication of bio-molecules mediated NMs are highly attractive because their size and shape can be easily tuned by simple, eco-friendly and reliable way. Deoxyribonucleic acid (DNA) is considered to be one of the most promising and well-studied bio-molecule in the fabrication of various types of NMs. The rich functionalities with the double-helix structure of DNA facilitate to accommodate a higher number of metal ions on its surface and results in perfect chain-like nano-assemblies. Moreover, the DNA mediated NMs can be highly useful for the Surface Enhanced Raman Scattering (SERS) studies with appropriate analytes. The SERS technique provides the fingerprint information of the analyte molecules even at very low concentration (such as even in ppm levels). The SERS intensity is greatly influenced by the size and shape of the NMs prepared using DNA scaffolds due to their assembly in a close proximity and generation of higher number of ‘hot spots’. In this present book chapter, we elaborated the numerous methodologies involved for the synthesis of DNA-based NMs considering their size, shapes, and also highlighted the possible mechanism involved for their growth with DNA scaffolds. In-addition, the possible application of DNA mediated NMs towards SERS studies has also been detailed in this book chapter.

Interaction of Antimicrobial Peptide Ponericin W1, Thanatin, and Mastatopara-S with Geotrichum citri-aurantii Genomic DNA

Antimicrobial peptides of mastatopara-S (M-S), thanatin, and ponericin W1(P W1) were able to disrupt the membrane integrity and alter the morphology of the hyphae of Geotrichum citri-aurantii and then reduced the sour rot of citrus fruit. In order to understand the mechanisms of thanatin, P W1 and M-S other than membrane disruption, the interaction betwixt the peptides and G. citri-aurantii DNA were investigated in this research. The laser confocal microscopy found that P W1, thanatin, and M-S could penetrate the cell membrane. Gel retardation assay demonstrated that P W1, thanatin, and M-S could bind to the G. citri-aurantii genomic DNA in vitro. UV-visible spectra and fluorescence spectra analysis further confirmed that the peptides can bind to the DNA, and then insert into the base pairs in the DNA helix, followed by wrecking the double-helix structure. In addition, M-S, thanatin, and P W1 can suppress the synthesis of DNA and RNA of G. citri-aurantii.

A magnon scattering platform

Scattering experiments have revolutionized our understanding of nature. Examples include the discovery of the nucleus [R. G. Newton, Scattering Theory of Waves and Particles (1982)], crystallography [U. Pietsch, V. Holý, T. Baumback, High-Resolution X-Ray Scattering (2004)], and the discovery of the double-helix structure of DNA [J. D. Watson, F. H. C. Crick, Nature 171, 737–738]. Scattering techniques differ by the type of particles used, the interaction these particles have with target materials, and the range of wavelengths used. Here, we demonstrate a two-dimensional table-top scattering platform for exploring magnetic properties of materials on mesoscopic length scales. Long-lived, coherent magnonic excitations are generated in a thin film of yttrium iron garnet and scattered off a magnetic target deposited on its surface. The scattered waves are then recorded using a scanning nitrogen vacancy center magnetometer that allows subwavelength imaging and operation under conditions ranging from cryogenic to ambient environment. While most scattering platforms measure only the intensity of the scattered waves, our imaging method allows for spatial determination of both amplitude and phase of the scattered waves, thereby allowing for a systematic reconstruction of the target scattering potential. Our experimental results are consistent with theoretical predictions for such a geometry and reveal several unusual features of the magnetic response of the target, including suppression near the target edges and a gradient in the direction perpendicular to the direction of surface wave propagation. Our results establish magnon scattering experiments as a platform for studying correlated many-body systems.

Més enllà de la doble hèlix: L’estructura G-quàdruplex de l’ADN

DNA is the fundamental biomolecule needed for correct cell functioning and, until very recently, it was associated to the double helix structure discovered over 70 years ago by Crick, Watson, and Franklin. However, other DNA structures and conformations have been described, like G-quadruplexes. These G-quadruplexes are formed in regions of the genome that are rich in guanine. They have tetramer structure and control biological processes such as genetic expression, protection against ageing, or the transmission of neural information. In this document, we describe their chemical and structural characteristics, besides presenting their main cellular functions. Lastly, we present G-quadruplexes as molecular targets for future cancer therapies.

The Importance and Challenges for Analytical Chemistry in Proteomics Analysis

Although Linus Pauling had an exceptional scientific contribution to the study of chemical bonds, reported in his book The Nature of Chemical Bond, the lousy image he got for the X-ray diffraction drove him to an unstable structure with an unreal DNA triple helix publication. Oppositely, for the consecration of James Watson & Francis Crick, they had the opportunity to enter science history using the right image of X-ray to propose the famous DNA double helix structure correctly. This chapter of science is an excellent example of how analytical chemistry performance affects horizons and scientific advances. Today the complexity of the systems is more significant and understanding how all proteins truly work into cells and organisms is the current challenge from proteomics. Comprehending how analysis is carried out and how instruments work could promote new insights to improve the analytical performance in proteomics. Here we described an overview based on our expertise on the analytical chemistry toolkit for proteomics analysis: shotgun, bottom-up, middle-down, top-down, and native proteomics, and their inherent instrumentation technologies. In addition, a detailed discussion of the analytical figures of merit in proteomics analysis is provided. We also address the limitations in multidimensional liquid chromatography and tandem mass spectrometry platforms. Furthermore, we present some perspectives in bioinformatics, mathematical modeling simulations, and chemometrics tools, as well.

Triclosan: Electrochemistry, Spontaneous Degradation and Effects on Double-Stranded DNA

Triclosan (TCS) is an antiseptic agent widely used mainly in personal care products and an important contaminant, which degrades in the environment causing toxicity on health, including negative effects on DNA. In this context, an electrochemical investigation of TCS in aqueous solution was studied by voltammetric techniques. The TCS underwent irreversible oxidation in a pH-dependent process, leading to the formation of two reversibly oxidized and pH-dependent oxidation products. An oxidation mechanism for TCS and its oxidation products in neutral aqueous medium was proposed. Besides that, the TCS spontaneously degraded into supporting eletrolytes with 3.4 ≤ pH ≤ 12.04 over the incubation time and the degraded TCS in solution was detected by electrochemical and spectrophotometric techniques. A higher degradation of TCS was observed in alkaline medium. In addition, the interaction in situ of this anti-microbial with DNA was investigated using dsDNA incubated solutions and dsDNA electrochemical bisosensor, by voltammetry. TCS and degraded TCS interacted with dsDNA causing the condensation of the double helix structure, release of guanine (by TCS and dedraded TCS) and adenine (by degraded TCS) bases from dsDNA and a possible intercalation of degraded TCS in the polynucleotide chain. No dsDNA oxidative damage was detected.

A Nonresonant Hybridized Electromagnetic-Triboelectric Nanogenerator for Irregular and Ultralow Frequency Blue Energy Harvesting

As a promising renewable energy source, it is a challenging task to obtain blue energy, which is irregular and has an ultralow frequency, due to the limitation of technology. Herein, a nonresonant hybridized electromagnetic-triboelectric nanogenerator was presented to efficiently obtain the ultralow frequency energy. The instrument adopted the flexible pendulum structure with a precise design and combined the working principle of electromagnetism and triboelectricity to realize the all-directional vibration energy acquisition successfully. The results confirmed that the triboelectric nanogenerator (TENG) had the potential to deliver the maximum power point of about 470 μW while the electromagnetic nanogenerator (EMG) can provide 523 mW at most. The conversion efficiency of energy of the system reached 48.48%, which exhibited a remarkable improvement by about 2.96 times, due to the elastic buffering effect of the TENG with the double helix structure. Furthermore, its ability to collect low frequency wave energy was successfully proven by a buoy in Jialing River. This woke provides an effective candidate to harvest irregular and ultralow frequency blue energy on a large scale.

C3′ Stereocentre of Furanose Determines the Helicity of Double-Stranded Nucleic Acids: Towards Etiology of Nucleic Acids

ABSTRACTRibose containing double-stranded nucleic acids exhibit helical structure, whereas sugar modified (xeno) nucleic acids may exhibit different structural features. The structural landscape of four stereo variants of furanosal nucleic acids and their C2′ deoxy counterparts, explored with molecular dynamics simulations, suggest that the configuration at the C3′ position plays a pivotal role in determining the helicity. The C3′ stereocentre acts as toggle-switch for the helix to ladder structural transformation by changing the nature of intra-strand interactions resulting in the optimal helices for ribose containing double-stranded nucleic acids. Interestingly, lack of chirality at the C2′ position results in better quality helices than inversion of stereochemistry relative to ribose. The etiology of furanosal-RNA over other furanoses can be hypothesized based on the helical structure, which can effectively be exploited by the biological machinery.SIGNIFICANCEThe double helix structure of furanosal RNA is governed by the configuration at the C3′ position. Furanose sugars such as xylose and lyxose where in the configuration at the C3′ position is inverted relative to the ribose do not form double helix structure, instead result in ladder-like structure. The configuration at the C3′ position acts as a toggle switch for the helix to ladder structural transition. Among four furanose sugars viz., ribose, arabinose, xylose, and lyxose, the double-stranded nucleic acids incorporating ribose form helices with best aspect ratio between major and minor grooves.