Thermodynamics and Kinetics-Directed Regulation of Nucleic Acid-Based Molecular Recognition

Nucleic acid-based molecular recognition plays crucial roles in various fields like biosensing and disease diagnostics. To achieve optimal detection and analysis, it is essential to regulate the response performance of nucleic acid probes or switches to match specific application requirements by regulating thermodynamics and kinetics properties. However, the impacts of thermodynamics and kinetics theories on recognition performance are sometimes obscure and the relative conclusions are not intuitive. To promote the thorough understanding and rational utilization of thermodynamics and kinetics theories, this review focuses on the landmarks and recent advances of nucleic acid thermodynamics and kinetics and summarizes the nucleic acid thermodynamics and kinetics-based strategies for regulation of nucleic acid-based molecular recognition. This work hopes such a review can provide reference and guidance for the development and optimization of nucleic acid probes and switches in the future, as well as for advancements in other nucleic acid-related fields.

Strategies for Anisotropic Fibrillar Hydrogels: Design, Cell Alignment, and Applications in Tissue Engineering

Efficient cellular alignment in biomaterials presents a considerable challenge, demanding the refinement of appropriate material morphologies, while ensuring effective cell-surface interactions. To address this, biomaterials are continuously researched with diverse coatings, hydrogels, and polymeric surfaces. In this context, we investigate the influence of physicochemical parameters on the architecture of fibrillar hydrogels that significantly orient the topography of flexible hydrogel substrates, thereby fostering cellular adhesion and spatial organization. Our Review comprehensively assesses various techniques for aligning polymer fibrils within hydrogels, specifically interventions applied during and after the cross-linking process. These methodologies include mechanical strains, precise temperature modulation, controlled fluidic dynamics, and chemical modulators, as well as the use of magnetic and electric fields. We highlight the intrinsic appeal of these methodologies in fabricating cell-aligning interfaces and discuss their potential implications within the fields of biomaterials and tissue engineering, particularly concerning the pursuit of optimal cellular alignment.

Methods to functionalize gold nanoparticles with tandem-phosphorothioate DNA: role of physicochemical properties of the phosphorothioate backbone in DNA adsorption to gold nanoparticles

Perception of the differences in the physicochemical properties of phosphorothioate DNA (PS-DNA) and phosphodiester DNA (PO-DNA) greatly aids in understanding the AuNP-DNA binding process. Replacing one non-bridging oxygen atom of the anionic phosphodiester backbone with a sulfur atom leads to a major change in the DNA adsorption mechanism of AuNPs. In this work, we investigated and compared salt-aging, low pH-assisted, and freeze-thaw methods for conjugating phosphorothioate-modified oligonucleotides to AuNPs. The results obtained clearly demonstrate that only the pH-assisted method can successfully bind tandem phosphorothioate DNA to gold nanoparticles and sufficiently maintain the colloidal stability of AuNPs. When a phosphate group is converted to a phosphorothioate group, the negative charge of the phosphate group is located on the sulfur atom. Due to the soft nature of sulfur (a very weak H-bond acceptor), the negative charge on the sulfur atom cannot be shielded even with the gradual addition of salt to increase the ionic strength, so, the pH-assisted based method is the best for the functionalization of AuNPs with tandem-PS DNA.

Gold nanocubes based optical detection of HIV-1 DNA via surface enhanced Raman spectroscopy

Optical detection of HIV-1 DNA with surface enhanced Raman spectroscopy (SERS) is a quick and versatile method, having great potential in screening and characterization of HIV-1 virus particle. We have synthesized and applied novel gold nanocubes (AuNCs) for signal enhancement of SERS to study HIV-1 DNA strands by taking into account the specific vibrational bands of functional groups. Raman peaks at 562 cm^-1, 800 cm^-1, 1094 cm^-1 were observed in both Human Random Control DNA and HIV-1 DNA, while three new peaks were detected in infected DNA at 421 cm^-1, 1069 cm^-1 and 1254 cm^-1. Raman bands in case of AuNCs coated HIV-1 DNA molecules were observed with enhanced intensity values as compared to the silver nanoparticles-based SERS substrate. In case of silver nanoparticles (AgNPs) conjugate DNA, we get all signatures of HIV-1 virus at almost the same position with peak distortions, peak alterations and intensities reductions. We overall molecularly observed HIV-1 infected DNA and Human Random Control DNA, with high sensitivity and selectivity using highly sensitive and stable AuNCs in SERS. This technique can be utilized to identify molecular structures and chemical identification of biomacromolecules which can further be investigated as biomarkers for the screening of whole-body HIV-1 virus particles.

Visible wavelength spectral tuning of absorption and circular dichroism of DNA-assembled Au/Ag core-shell nanorod assemblies

Plasmonic nanoparticles have unique properties which can be harnessed to manipulate light at the nanoscale. With recent advances in synthesis protocols that increase their stability, gold-silver core-shell nanoparticles have become suitable building blocks for plasmonic nanostructures to expand the range of attainable optical properties. Here we tune the plasmonic response of gold-silver core-shell nanorods over the visible spectrum by varying the thickness of the silver shell. Through the chiral arrangement of the nanorods with the help of various DNA origami designs, the spectral tunability of the plasmon resonance frequencies is transferred into circular dichroism signals covering the spectrum from 400 nm to 700 nm. Our approach could aid in the construction of better sensors as well as metamaterials with a tunable optical response in the visible region.

Modulation of DNAzyme Activity via Butanol Dehydration

Understanding the activity of biomolecules in cosolvent systems is important for catalysis, separation and developing biosensors. The majority of previously studied solvents are either phase separated with water or miscible with water. Butanol was recently used to extract water for the conjugation of DNA to gold nanoparticles. In this work, the effect of butanol on the activity of a few RNA-cleaving DNAzymes was studied. A 130-fold improvement in sensitivity for the Na⁺ -specific EtNa DNAzyme was observed, and butanol also improved the activity of another Na⁺ -specific DNAzyme, NaA43T by a few folds. However, when divalent metal ions were used for both EtNa and 17E DNAzymes, the activity was inhibited. A main driven force for enhanced DNAzyme activity is the concentration effect due to butanol dehydration. This study provides insights into the interplay between DNA, metal ions and organic solvents, and such an understanding might be useful for developing sensitive biosensors.

Comparison of Two DNA Aptamers for Dopamine Using Homogeneous Binding Assays

Dopamine is an essential neurotransmitter and its detection is important for bioanalytical chemistry. Two very different DNA aptamers have been reported for dopamine, one derived from an RNA aptamer (named Apt1) and other obtained via direct aptamer selection (named Apt2). In this study, we used four homogeneous binding assays to compare these two DNA dopamine aptamers. Thiazole orange (TO) fluorescence assay indicated that the Apt2 specifically bound with dopamine with a K_d of 2.37 μM, which was consistent with that from the isothermal titration calorimetry (ITC) assay. However, Apt1 had much less TO fluorescence change and also no signal from ITC. By labeling the two ends of the two aptamers by a fluorophore and a quencher, the aptamer beacons showed binding of dopamine only for Apt2. Finally, the label-free AuNP-based colorimetric assay showed no difference between these two aptamer sequences, and even non-binding random DNA showed the same response, indicating that AuNPs were not a good probe for detecting dopamine. According to the data, Apt1 does not appear to be able to bind dopamine specifically, while Apt2 showed specific binding and could be used for developing related biosensors.

DNA Origami-Enabled Plasmonic Sensing

The reliable programmability of DNA origami makes it an extremely attractive tool for bottom-up self-assembly of complex nanostructures. Utilizing this property for the tuned arrangement of plasmonic nanoparticles holds great promise particularly in the field of biosensing. Plasmonic particles are beneficial for sensing in multiple ways, from enhancing fluorescence to enabling a visualization of the nanoscale dynamic actuation via chiral rearrangements. In this Perspective, we discuss the recent developments and possible future directions of DNA origami-enabled plasmonic sensing systems. We start by discussing recent advancements in the area of fluorescence-based plasmonic sensing using DNA origami. We then move on to surface-enhanced Raman spectroscopy sensors followed by chiral sensing, both utilizing DNA origami nanostructures. We conclude by providing our own views on the future prospects for plasmonic biosensors enabled using DNA origami.

Pt-S Bond-Mediated Nanoflares for High-Fidelity Intracellular Applications by Avoiding Thiol Cleavage

The Au-S bond is the classic way to functionalize gold nanoparticles (AuNPs). However, cleavage of the bond by biothiols and other chemicals is a long-standing problem hindering practical applications, especially in cells. Instead of replacing the thiol by a carbene or selenol for stronger adsorption, it is now shown that the Pt-S bond is much more stable, fully avoiding cleavage by biothiols. AuNPs were deposited with a thin layer of platinum, and an AuNP@Pt-S nanoflare was constructed to detect the miRNA-21 microRNA in living cells. This design retained the optical and cellular uptake properties of DNA-functionalized AuNPs, while showing high-fidelity signaling. It discriminated target cancer cells even in a mixed-cell culture system, where the Au-S based nanoflare was less sensitive. Compared to previous methods of changing the ligand chemistry, coating a Pt shell is more accessible, and previously developed methods for AuNPs can be directly adapted.

Nucleic Acid Catalysis under Potential Prebiotic Conditions

Catalysis by nucleic acids is indispensable for extant cellular life, and it is widely accepted that nucleic acid enzymes were crucial for the emergence of primitive life 3.5-4 billion years ago. However, geochemical conditions on early Earth must have differed greatly from the constant internal milieus of today's cells. In order to explore plausible scenarios for early molecular evolution, it is therefore essential to understand how different physicochemical parameters, such as temperature, pH, and ionic composition, influence nucleic acid catalysis and to explore to what extent nucleic acid enzymes can adapt to non-physiological conditions. In this article, we give an overview of the research on catalysis of nucleic acids, in particular catalytic RNAs (ribozymes) and DNAs (deoxyribozymes), under extreme and/or unusual conditions that may relate to prebiotic environments.

Aptamer Induced Multicolored AuNCs-WS2 "Turn on" FRET Nano Platform for Dual-Color Simultaneous Detection of AflatoxinB1 and Zearalenone

Mycotoxins posit serious threats to human and animal health, and numerous efforts have been performed to detect the multiple toxins by a single diagnostic approach. To best of our knowledge, for the first time, we synthesized an aptamer induced "turn on" fluorescence resonance energy transfer (FRET) biosensor using dual-color gold nanoclusters (AuNCs), l-proline, and BSA synthesized AuNCs (Lp-AuNCs and BSA-AuNCs), with WS₂ nanosheet for simultaneous recognition of aflatoxinB₁ (AFB₁) and zearalenone (ZEN) by single excitation. Here, AFB₁ aptamer stabilized blue-emitting AuNCs (AFB₁-apt-Lp-AuNCs) (at 442 nm) and ZEN aptamer functionalized with red-colored AuNCs (ZEN-apt-BSA-AuNCs) (at 650 nm) were employed as an energy donor and WS₂ nanosheet as a fluorescence quencher. With the addition of AFB₁ and ZEN, the change in fluorescence intensity (F.I) was recorded at 442 and 650 nm and can be used for simultaneous recognition with a detection limit of 0.34 pg mL^-1 (R² = 0.9931) and 0.53 pg mL^-1 (R² = 0.9934), respectively. Most importantly, the semiquantitative determination of AFB₁ and ZEN can also be realized through photovisualization. The current approach paves a new way to develop sensitive, selective, and convenient metal nanocluster-based fluorescent "switch-on" probes with potential applications in multipurpose biosensing.