On the formation of the double helix between adenine single strands at acidic pH from synchrotron radiation circular dichroism experiments

Synchrotron X-Ray Tomography for Rechargeable Battery Research: Fundamentals, Setups and Applications

Understanding the complicated interplay of the continuously evolving electrode materials in their inherent 3D states during the battery operating condition is of great importance for advancing rechargeable battery research. In this regard, the synchrotron X-ray tomography technique, which enables non-destructive, multi-scale, and 3D imaging of a variety of electrode components before/during/after battery operation, becomes an essential tool to deepen this understanding. The past few years have witnessed an increasingly growing interest in applying this technique in battery research. Hence, it is time to not only summarize the already obtained battery-related knowledge by using this technique, but also to present a fundamental elucidation of this technique to boost future studies in battery research. To this end, this review firstly introduces the fundamental principles and experimental setups of the synchrotron X-ray tomography technique. After that, a user guide to its application in battery research and examples of its applications in research of various types of batteries are presented. The current review ends with a discussion of the future opportunities of this technique for next-generation rechargeable batteries research. It is expected that this review can enhance the reader's understanding of the synchrotron X-ray tomography technique and stimulate new ideas and opportunities in battery research.

On the delocalization length in RNA single strands of cytosine: how many bases see the light?

The interplay between multiple chromophores in nucleic acids and photosynthetic proteins gives rise to complex electronic phenomena and largely governs the de-excitation dynamics.

Synchrotron-radiation vacuum-ultraviolet circular dichroism spectroscopy in structural biology: an overview

Circular dichroism spectroscopy is widely used for analyzing the structures of chiral molecules, including biomolecules. Vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy using synchrotron radiation can extend the short-wavelength limit into the vacuum-ultraviolet region (down to ~160 nm) to provide detailed and new information about the structures of biomolecules in combination with theoretical analysis and bioinformatics. The VUVCD spectra of saccharides can detect the high-energy transitions of chromophores such as hydroxy and acetal groups, disclosing the contributions of inter- or intramolecular hydrogen bonds to the equilibrium configuration of monosaccharides in aqueous solution. The roles of hydration in the fluctuation of the dihedral angles of carboxyl and amino groups of amino acids can be clarified by comparing the observed VUVCD spectra with those calculated theoretically. The VUVCD spectra of proteins markedly improves the accuracy of predicting the contents and number of segments of the secondary structures, and their amino acid sequences when combined with bioinformatics, for not only native but also nonnative and membrane-bound proteins. The VUVCD spectra of nucleic acids confirm the contributions of the base composition and sequence to the conformation in comparative analyses of synthetic poly-nucleotides composed of selected bases. This review surveys these recent applications of synchrotron-radiation VUVCD spectroscopy in structural biology, covering saccharides, amino acids, proteins, and nucleic acids.

Parallel Polyadenine Duplex Formation at Low pH Facilitates DNA Conjugation onto Gold Nanoparticles

DNA-functionalized gold nanoparticles (AuNPs) have been extensively used in sensing, drug delivery, and materials science. A key step is to attach DNA to AuNPs, forming a stable and functional conjugate. Although the traditional salt-aging method takes a full day or longer, a recent low-pH method allows DNA conjugation in a few minutes. The effect of low pH was attributed to the protonation of adenine (A) and cytosine (C), resulting in an overall lower negative charge density on DNA. In this work, the effect of DNA conformation at low pH is studied. Using circular dichroism (CD) spectroscopy, the parallel poly-A duplex (A-motif) is detected when a poly-A segment is linked to a random DNA, a design typically used for DNA conjugation. A DNA staining dye, thiazole orange, is identified for detecting such A-motifs. The A-motif structure is ideal for DNA conjugation because it exposes the thiol group to directly react with the gold surface while minimizing nonspecific DNA base adsorption. For nonthiolated DNA, the optimal procedure is to incubate DNA and AuNPs followed by lowering the pH. The i-motif formed by poly-C DNA at low pH is less favorable to the conjugation reaction because of its unique way of folding. The stability of poly-A and poly-G DNA at low pH is examined. An excellent stability of poly-A DNA is confirmed, but poly-G has lower stability. This study provides new fundamental insights into a practically useful technique of conjugating DNA to AuNPs.

Electronic coupling between photo-excited stacked bases in DNA and RNA strands with emphasis on the bright states initially populated

In biology the interplay between multiple light-absorbers gives rise to complex quantum effects such as superposition states that are of extreme importance for life, both for harvesting solar energy and likely protecting nucleic acids from radiation damage. Still the characteristics of these states and their quantum dynamics are a much debated issue. While the electronic properties of single bases are fairly well understood, the situation for strands is complicated by the fact that stacked bases electronically couple when photoexcited. These newly arising states are denoted as exciton states and are simply linear combinations of localised wavefunctions that involve N - 1 ground-state bases and one base in its excited state (cf. the Frenkel exciton model). There is disagreement over the number of bases, N, that coherently couple, i.e., the spatial extent of the exciton, and how electronic deexcitation back to the ground state occurs. The importance of dark charge-transfer states has been inferred both from time-resolved fluorescence and transient absorption experiments. These states were suggested to be responsible for long deexcitation times but it is unclear whether 'long' is tens of picoseconds or nanoseconds. In this review paper, we focus on the bright states initially populated and discuss their nature based on information obtained from systematic absorption and circular dichroism experiments on single strands of different lengths. Our results from the last five years are compared with those from other groups, and are discussed in the context of successive deexcitation schemes. Pieces to the puzzle have come from different experiments and theory but a complete description has yet to emerge. As such the story about DNA/RNA photophysical decay mechanisms resembles the tale about the blind men and the elephant where all see the beast in different, correct but incomplete ways.

Probing electronic coupling between adenine bases in RNA strands from synchrotron radiation circular dichroism experiments

Circular dichroism spectra (176-330 nm) of RNA adenine oligomers, (rA)(n) (n = 1-10, 12, 15, and 20), reveal electronic coupling between two bases in short strands. The number of interacting bases in long strands is more and larger than that reported previously for the corresponding DNA strands.