Unraveling the complexity of the interactions of DNA nucleotides with gold by single molecule force spectroscopy

Hierarchical Mechanical Transduction of Precision-Engineered DNA Hydrogels with Sacrificial Bonds

Engineering the response to external signals in mechanically switchable hydrogels is important to promote smart materials applications. However, comparably little attention has focused on embedded precision mechanisms for autonomous nonlinear response in mechanical profiles in hydrogels, and we lack understanding of how the behavior from the molecular scale transduces to the macroscale. Here, we design a nonlinear stress-strain response into hydrogels by engineering sacrificial DNA hairpin loops into model network hydrogels formed from star-shaped building blocks. We characterize the force-extension response of single DNA hairpins and are able to describe how the specific topology influences the nonlinear mechanical behavior at different length scales. For this purpose, we utilize force spectroscopy as well as microscopic and macroscopic deformation tests. This study contributes to a better understanding of designing nonlinear strain-adaptive features into hydrogel materials.

Adsorbing DNA to Mica by Cations: Influence of Valency and Ion Type

Ion-mediated attraction between DNA and mica plays a crucial role in biotechnological applications and molecular imaging. Here, we combine molecular dynamics simulations and single-molecule atomic force microscopy experiments to characterize the detachment forces of single-stranded DNA at mica surfaces mediated by the metal cations Li+, Na+, K+, Cs+, Mg2+, and Ca2+. Ion-specific adsorption at the mica/water interface compensates (Li+ and Na+) or overcompensates (K+, Cs+, Mg2+, and Ca2+) the bare negative surface charge of mica. In addition, direct and water-mediated contacts are formed between the ions, the phosphate oxygens of DNA, and mica. The different contact types give rise to low- and high-force pathways and a broad distribution of detachment forces. Weakly hydrated ions, such as Cs+ and water-mediated contacts, lead to low detachment forces and high mobility of the DNA on the surface. Direct ion-DNA or ion-surface contacts lead to significantly higher forces. The comprehensive view gained from our combined approach allows us to highlight the most promising cations for imaging in physiological conditions: K+, which overcompensates the negative mica charge and induces long-ranged attractions. Mg2+ and Ca2+, which form a few specific and long-lived contacts to bind DNA with high affinity.

Adsorption of DNA Fragments at Aqueous Graphite and Au(111) via Integration of Experiment and Simulation

We combine single molecule force spectroscopy measurements with all-atom metadynamics simulations to investigate the cross-materials binding strength trends of DNA fragments adsorbed at the aqueous graphite C(0001) and Au(111) interfaces. Our simulations predict this adsorption at the level of the nucleobase, nucleoside, and nucleotide. We find that despite challenges in making clear, careful connections between the experimental and simulation data, reasonable consistency between the binding trends between the two approaches and two substrates was evident. On C(0001), our simulations predict a binding trend of dG > dA ≈ dT > dC, which broadly aligns with the experimental trend. On Au(111), the simulation-based binding strength trends reveal stronger adsorption for the purines relative to the pyrimadines, with dG ≈ dA > dT ≈ dC. Moreover, our simulations provide structural insights into the origins of the similarities and differences in adsorption of the nucleic acid fragments at the two interfaces. In particular, our simulation data offer an explanation for the differences observed in the relative binding trend between adenosine and guanine on the two substrates.

Impedimetric monitoring of apoptosis using cytochrome-aptamer bioconjugated silver nanocluster

It is well known that cytochrome c (Cyt c) is a crucial death regulator that triggers programmed cell death, apoptosis. Here, we report on the successful application of an aptamer bioconjugated nanoclusters for the detection of apoptosis based on release of cytochrome c from mitochondria in lysates human embryonic kidney cells HEK293T. The aptamer-conjugated silver nanoclusters (Apt@AgNCs) were synthesized and immobilized on gold electrode for impedimetric detection of Cyt c over the range of 0.15-375nM. It was found that the presence of Ag(I) ions shell at the surface of prepared NCs could increase their affinity to the donor groups (COO^- and some amine groups in its deprotonated form, NH₂) of cysteine attached on the gold electrode surface. The use of NCs, which play the role of conductive holders, established a simple immobilization procedure based on a low cost non-functionalized DNA sequence. To diminish the probable nonspecific impedance changes and decrease time of measurement, a rapid single frequency measurements (SFM) was assessed based on recording total impedance |Z| in different individual frequencies.

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.