Freezing promoted hybridization of very short DNA oligonucleotides

Freezing Functional Nucleic Acids: From Molecular Reactions to Surface Immobilization

Biochemical reactions are typically slowed down by decreasing temperature. However, accelerated reaction kinetics have been observed for a long time. More recent examples have highlighted the unique role of freezing in fabricating supermaterials, degrading environmental contaminants, and accelerating bioreactions. Functional nucleic acids are DNA or RNA oligonucleotides with versatile properties, including target recognition, catalysis, and molecular co4mputing. In this review, we discuss the current observations and understanding of freezing-facilitated reactions involving functional nucleic acids. Molecular reactions such as ligation/conjugation, cleavage, and hybridization are discussed. Moreover, freezing-induced DNA-nanoparticle conjugations are introduced. Then, we describe our effect in immobilizing DNA on bulk surfaces. Finally, we address some critical questions and research opportunities in the field.

Self-assembly of a multimeric genomic hydrogel via multi-primed chain reaction of dual single-stranded circular plasmids for cell-free protein production

Recent technical advances in cell-free protein synthesis (CFPS) offer several advantages over cell-based expression systems, including the application of cellular machinery, such as transcription and translation, in the test tube. Inspired by the advantages of CFPS, we have fabricated a multimeric genomic DNA hydrogel (mGD-gel) via rolling circle chain amplification (RCCA) using dual single-stranded circular plasmids with multiple primers. The mGD-gel exhibited significantly enhanced protein yield. In addition, mGD-gel can be reused at least five times, and the shape of the mGD-gel can be easily manipulated without losing the feasibility of protein expression. The mGD-gel platform based on the self-assembly of multimeric genomic DNA strands (mGD strands) has the potential to be used in CFPS systems for a variety of biotechnological applications.

Freeze-Driven Adsorption of Poly-A DNA on Gold Nanoparticles: From a Stable Biointerface to Plasmonic Dimers

Increasing attention is paid to poly-adenine (poly-A) DNA-functionalized gold nanoparticles due to the high cost of thiols. Freezing is an effective approach for immobilizing poly-A DNA on gold nanoparticles, but its mechanism remains elusive. To cope with this issue, in this paper, some experimental insights are provided. It is shown that (1) the DNA loading density is independent of the length of poly-A. (2) DNA is densely packed on gold nanoparticles, and the biointerface is peculiarly stable, which is not in line with the existing "wrapping" model. (3) Using a DNA-staining dye, thiazole orange, it is shown that poly-A duplex structures are formed on the surface of gold nanoparticles, with evidence given by fluorescence and Raman measurements. An alternative model involving stable poly-A duplexes anchored by finite terminal adenines is proposed. Based on it, a strategy for constructing plasmonic dimers is developed, using freeze-driven adsorption of a DNA sequence with poly-adenine at both ends. This work provides insights into the reaction between poly-A DNA and AuNPs upon freezing and is expected to facilitate related research in biosensor development and nanotechnology.

Factors and methods to modulate DNA hybridization kinetics

DNA oligonucleotides are widely used in a diverse range of research fields from analytical chemistry, molecular biology, nanotechnology to drug delivery. In these applications, DNA hybridization is often the most important enabling reaction. Achieving control over hybridization kinetics and a high yield of hybridized products is needed to ensure high-quality and reproducible results. Since DNA strands are highly negatively charged and can also fold upon itself to form various intramolecular structures, DNA hybridization needs to overcome these barriers. Nucleation and diffusion are two main kinetic limiting steps although their relative importance differs in different conditions. The effects of length and sequence, temperature, pH, salt concentration, cationic polymers, organic solvents, freezing and crowding agents are summarized in the context of overcoming these barriers. This article will help researchers in the biotechnology-related fields to better understand and control DNA hybridization, as well as provide a landscape for future work in simulation and experiment to optimize DNA hybridization systems.

DNA Assembly-Based Stimuli-Responsive Systems

Stimuli-responsive designs with exogenous stimuli enable remote and reversible control of DNA nanostructures, which break many limitations of static nanostructures and inspired development of dynamic DNA nanotechnology. Moreover, the introduction of various types of organic molecules, polymers, chemical bonds, and chemical reactions with stimuli-responsive properties development has greatly expand the application scope of dynamic DNA nanotechnology. Here, DNA assembly-based stimuli-responsive systems are reviewed, with the focus on response units and mechanisms that depend on different exogenous stimuli (DNA strand, pH, light, temperature, electricity, metal ions, etc.), and their applications in fields of nanofabrication (DNA architectures, hybrid architectures, nanomachines, and constitutional dynamic networks) and biomedical research (biosensing, bioimaging, therapeutics, and theranostics) are discussed. Finally, the opportunities and challenges for DNA assembly-based stimuli-responsive systems are overviewed and discussed.

Freezing-Assisted Conjugation of Unmodified Diblock DNA to Hydrogel Nanoparticles and Monoliths for DNA and Hg2+ Sensing

Acrydite-modified DNA is the most frequently used reagent to prepare DNA-functionalized hydrogels. Herein, we show that unmodified penta-adenine (A₅ ) can reach up to 75 % conjugation efficiency in 8 h under a freezing polymerization condition in polyacrylamide hydrogels. DNA incorporation efficiency was reduced by forming duplex or other folded structures and by removing the freezing condition. By designing diblock DNA containing an A₅ block, various functional DNA sequences were attached. Such hydrogels were designed for ultrasensitive DNA hybridization and Hg²⁺ detection, with detection limits of 50 pM and 10 nM, respectively, demonstrating the feasibility of using unmodified DNA to replace acrydite-DNA. The same method worked for both gel nanoparticles and monoliths. This work revealed interesting reaction products by exploiting freezing and has provided a cost-effective way to attach DNA to hydrogels.

Gold Nanoparticles Adsorb DNA and Aptamer Probes Too Strongly and a Comparison with Graphene Oxide for Biosensing

Using fluorescently labeled DNA oligonucleotides and nanomaterials for developing biosensors has been extensively reported for gold nanoparticles (AuNPs) and graphene oxide (GO) among others. These materials have vastly different affinities and mechanisms for interacting with DNA, and their analytical performance is likely to be different. In this work, we used several DNA sequences and, respectively, adsorbed them on AuNPs and GO to quench fluorescence. Different from previous work, we used KCN to fully dissolve the AuNPs to calculate the percentage of the desorbed DNA due to the complementary DNA (cDNA) and aptamer target. The desorbed probe DNA from the AuNPs was less than 5% for all of the targets including DNA, adenosine, Hg²⁺, and lysozyme, indicating a very strong DNA adsorption affinity. Desorption of DNA was achieved by adding HEPES buffer, NaCl, and As(III), but such desorption was attributed to the adsorption of these molecules or ions by the AuNPs instead of their interaction with the adsorbed DNA. For GO, more probes desorbed with addition of target analytes but so did nonspecific desorption by random DNA and proteins. In summary, AuNPs are unlikely to be a good surface for developing biosensors relying solely on the desorption of probe DNA, while for GO the main problem is nonspecific desorption.