Oriented Soft DNA Curtains for Single-Molecule Imaging

Diamond nanoneedles for biosensing

Nanoparticles and nanomaterials are revolutionizing medicine by offering diverse tools for diagnosis and therapy, including devices, contrast agents, drug delivery systems, adjuvants, therapeutics, and theragnostic agents. Realizing full applied potential requires a deep understanding of the interactions of nano dimensional objects with biological cells. In this study, we investigate interaction of single-crystal diamond nanoneedles (SCDNNs) containing silicon vacancy (SiV-) color centers with biological substances. Four batches of the diamond needles with sizes ranging between 200 nm and 1300 nm and their water suspensions were used in these studies. The human lung fibroblast cells were used for the proof-of-concept demonstration. Employing micro-photoluminescence (PL) mapping, confocal microscopy, and lactate dehydrogenase (LDH) viability tests, we evaluated the cellular response to the SCDNNs. Intriguingly, our investigation with PL spectroscopy revealed that the cells and SCDNNs can coexist together with approved efficient registration of SiV-centers presence. Notably, LDH release remained minimal in cells exposed to optimally sized SCDNNs, suggesting a small number of lysed cells, and indicating non-cytotoxicity in concentrations of 2-32µg ml-1. The evidence obtained highlights the potential of SCDNNs for extra- or/and intracellular drug delivery when the surface of the needle is modified. In addition, fluorescent defects in the SCDNNs can be used for bioimaging as well as optical and quantum sensing.

Live-cell imaging reveals the trade-off between target search flexibility and efficiency for Cas9 and Cas12a

CRISPR-Cas systems have widely been adopted as genome editing tools, with two frequently employed Cas nucleases being SpyCas9 and LbCas12a. Although both nucleases use RNA guides to find and cleave target DNA sites, the two enzymes differ in terms of protospacer-adjacent motif (PAM) requirements, guide architecture and cleavage mechanism. In the last years, rational engineering led to the creation of PAM-relaxed variants SpRYCas9 and impLbCas12a to broaden the targetable DNA space. By employing their catalytically inactive variants (dCas9/dCas12a), we quantified how the protein-specific characteristics impact the target search process. To allow quantification, we fused these nucleases to the photoactivatable fluorescent protein PAmCherry2.1 and performed single-particle tracking in cells of Escherichia coli. From our tracking analysis, we derived kinetic parameters for each nuclease with a non-targeting RNA guide, strongly suggesting that interrogation of DNA by LbdCas12a variants proceeds faster than that of SpydCas9. In the presence of a targeting RNA guide, both simulations and imaging of cells confirmed that LbdCas12a variants are faster and more efficient in finding a specific target site. Our work demonstrates the trade-off of relaxing PAM requirements in SpydCas9 and LbdCas12a using a powerful framework, which can be applied to other nucleases to quantify their DNA target search.

smFRET Detection of Cis and Trans DNA Interactions by the BfiI Restriction Endonuclease

Protein-DNA interactions are fundamental to many biological processes. Proteins must find their target site on a DNA molecule to perform their function, and mechanisms for target search differ across proteins. Especially challenging phenomena to monitor and understand are transient binding events that occur across two DNA target sites, whether occurring in cis or trans. Type IIS restriction endonucleases rely on such interactions. They play a crucial role in safeguarding bacteria against foreign DNA, including viral genetic material. BfiI, a type IIS restriction endonuclease, acts upon a specific asymmetric sequence, 5-ACTGGG-3, and precisely cuts both upper and lower DNA strands at fixed locations downstream of this sequence. Here, we present two single-molecule Förster resonance energy-transfer-based assays to study such interactions in a BfiI-DNA system. The first assay focuses on DNA looping, detecting both "Phi"- and "U"-shaped DNA looping events. The second assay only allows in trans BfiI-target DNA interactions, improving the specificity and reducing the limits on observation time. With total internal reflection fluorescence microscopy, we directly observe on- and off-target binding events and characterize BfiI binding events. Our results show that BfiI binds longer to target sites and that BfiI rarely changes conformations during binding. This newly developed assay could be employed for other DNA-interacting proteins that bind two targets and for the dsDNA substrate BfiI-PAINT, a useful strategy for DNA stretch assays and other super-resolution fluorescence microscopy studies.

CRISPR/Cas14 provides a promising platform in facile and versatile aptasensing with improved sensitivity

CRISPR is reshaping biosensing technology due to its programmability, sensitivity, and specificity. Most current CRISPR-based biosensors are developed based on Cas12 and Cas13, while the biosensing potentials of the newly discovered Cas14 have not been fully elucidated yet. Herein, a fluorometric biosensor named HARRY (highly sensitive aptamer-regulated Cas14 R-loop for bioanalysis) was developed. The diblock ssDNA is designed to contain the activator sequence of Cas14 and the aptamer sequence of specific targets. In the absence of targets, the ssDNA activates Cas14a, then the Cas14a trans-cleavages the fluorescent reporter, causing fluorescence enhancement. In the presence of the targets, ssDNA-target assembly is formed via aptamer interaction, resulting in the inhibition of Cas14a activation. HARRY can detect ATP, Cd²⁺, histamine, aflatoxin B1, and thrombin with detection limits at the low-nanomolar level, which shows improvement compared with Cas12a-based aptasensors in sensitivity and versatility. We reasoned that the improvement is derived from the ssDNA specificity of Cas14a and found that the detection limit of HARRY is correlated to the binding affinities of aptamers. This study unlocks the potential of Cas14a in versatile aptasensing, which may inspire the development of CRISPR-based biosensors from the Cas14a branch.

Phase behaviour and adsorption of deoxyribonucleic acid onto an azobenzene liquid crystalline ligand at the interfaces

Azobenzene liquid crystalline (ALC) ligand contains a cholesteryl group linked to an azobenzene moiety through a carbonyl dioxy spacer (C7) and terminated with an amine group as a polar head. The phase behaviour of the C7 ALC ligand at the air-water (A-W) interface is investigated employing surface manometry. The surface pressure-area per molecule isotherm shows that C7 ALC ligand exhibit two different phases following the phase sequence viz., liquid expanded (LE₁ and LE₂) and then collapse to three-dimensional crystallites. Further, our investigations under different pH conditions and in the presence of DNA reveal the following. Compared to the bulk, the acid dissociation constant (pK_a) of an individual amine reduces to 5 at the interfaces. For pH (3.5) < pK_a, the protonation of amine groups of C7 ALC ligand facilitates the condensation of the film and enhances the stability. For pH values > pK_a, the phase behaviour of the ligand remains the same due to the partial dissociation of the amine groups. The presence of DNA in the sub-phase result in the expansion of isotherm to the higher area per molecule and the compressional modulus extracted reveals the phase sequence; liquid expanded, liquid condensed, followed by a collapse. Further, the kinetics of adsorption of DNA to the amine groups of the ligand is investigated, suggesting the interactions are influenced by surface pressure corresponding to different phases and pH of the sub-phase. Brewster angle microscope studies are carried out at different surface densities of the ligand as well as in the presence of DNA also supports this inference. Atomic force microscope is employed to acquire the surface topography and height profile of C7 ALC ligand (1 layer) after transferring on onto a silicon substrate using Langmuir Blodgett deposition. The difference in the surface topography and thickness of the film indicates the adsorption of DNA onto the amine groups of the ligand. The characteristic UV-visible absorption bands of the ligand films (10 layers) at the air-solid interface are tracked and the hypsochromic shift of these bands is also attributed to these DNA interactions.

The miEye: Bench-top super-resolution microscope with cost-effective equipment

Commercial super-resolution (SR) imaging systems require a high budget, while current more affordable open source microscopy systems lack modularity and sometimes are too complex or lack reliability. We present miEye - a cost-effective microscope designed for high-resolution wide-field fluorescence imaging. The build is constructed using a CNC milled aluminum microscope body and commercially available optomechanics, with open-source Python-based microscope control, data visualization, and analysis software integration. The data acquisition software works robustly with commonly used industrial-grade complementary metal oxide semiconductor (iCMOS) cameras, performs IR beam back-reflection-based automatic focus stabilization, and allows for laser control via an Arduino-based laser relay. The open-source nature of the design is aimed to facilitate adaptation by the community. The build can be constructed for a cost of roughly 50 k €. It contains SM-fiber and MM-fiber excitation paths that are easy to interchange and an adaptable emission path. Also, it ensures <5 nm/min stability of the sample on all axes, and allows achieving <30 nm lateral resolution for dSTORM and DNA-PAINT single-molecule localization microscopy (SMLM) experiments. Thus it serves as a cost-effective and adaptable addition to the open source microscopy community and potentially will allow high-quality SR imaging even for limited-budget research groups.

Disarming of type I-F CRISPR-Cas surveillance complex by anti-CRISPR proteins AcrIF6 and AcrIF9

CRISPR-Cas systems are prokaryotic adaptive immune systems that protect against phages and other invading nucleic acids. The evolutionary arms race between prokaryotes and phages gave rise to phage anti-CRISPR (Acr) proteins that act as a counter defence against CRISPR-Cas systems by inhibiting the effector complex. Here, we used a combination of bulk biochemical experiments, X-ray crystallography and single-molecule techniques to explore the inhibitory activity of AcrIF6 and AcrIF9 proteins against the type I-F CRISPR-Cas system from Aggregatibacter actinomycetemcomitans (Aa). We showed that AcrIF6 and AcrIF9 proteins hinder Aa-Cascade complex binding to target DNA. We solved a crystal structure of Aa1-AcrIF9 protein, which differ from other known AcrIF9 proteins by an additional structurally important loop presumably involved in the interaction with Cascade. We revealed that AcrIF9 association with Aa-Cascade promotes its binding to off-target DNA sites, which facilitates inhibition of CRISPR-Cas protection.