Resonator nanophotonic standing-wave array trap for single-molecule manipulation and measurement

RNA Polymerase II is a Polar Roadblock to a Progressing DNA Fork

DNA replication and transcription occur simultaneously on the same DNA template, leading to inevitable conflicts between the replisome and RNA polymerase. These conflicts can stall the replication fork and threaten genome stability. Although numerous studies show that head-on conflicts are more detrimental and more prone to promoting R-loop formation than co-directional conflicts, the fundamental cause for the RNA polymerase roadblock polarity remains unclear, and the structure of these R-loops is speculative. In this work, we use a simple model system to address this complex question by examining the Pol II roadblock to a DNA fork advanced via mechanical unzipping to mimic the replisome progression. We found that the Pol II binds more stably to resist removal in the head-on configuration, even with minimal transcript size, demonstrating that the Pol II roadblock has an inherent polarity. However, an elongating Pol II with a long RNA transcript becomes an even more potent and persistent roadblock while retaining the polarity, and the formation of an RNA-DNA hybrid mediates this enhancement. Surprisingly, we discovered that when a Pol II collides with the DNA fork head-on and becomes backtracked, an RNA-DNA hybrid can form on the lagging strand in front of Pol II, creating a topological lock that traps Pol II at the fork. TFIIS facilitates RNA-DNA hybrid removal by severing the connection of Pol II with the hybrid. We further demonstrate that this RNA-DNA hybrid can prime lagging strand replication by T7 DNA polymerase while Pol II is still bound to DNA. Our findings capture basal properties of the interactions of Pol II with a DNA fork, revealing significant implications for transcription-replication conflicts.

Optical tweezing of microparticles and cells using silicon-photonics-based optical phased arrays

Integrated optical tweezers have the potential to enable highly-compact, low-cost, mass-manufactured, and broadly-accessible optical manipulation when compared to standard bulk-optical tweezers. However, integrated demonstrations to date have been fundamentally limited to micron-scale standoff distances and, often, passive trapping functionality, making them incompatible with many existing applications and significantly limiting their utility, especially for biological studies. In this work, we demonstrate optical trapping and tweezing using an integrated OPA for the first time, increasing the standoff distance of integrated optical tweezers by over two orders of magnitude compared to prior demonstrations. First, we demonstrate trapping of polystyrene microspheres 5 mm above the surface of the chip and calibrate the trap force. Next, we show tweezing of polystyrene microspheres in one dimension by non-mechanically steering the trap by varying the input laser wavelength. Finally, we use the OPA tweezers to demonstrate, to the best of our knowledge, the first cell experiments using single-beam integrated optical tweezers, showing controlled deformation of mouse lymphoblast cells. This work introduces a new modality for integrated optical tweezers, significantly expanding their utility and compatibility with existing applications, especially for biological experiments.

Optical torque calculations and measurements for DNA torsional studies

The angular optical trap (AOT) is a powerful instrument for measuring the torsional and rotational properties of a biological molecule. Thus far, AOT studies of DNA torsional mechanics have been carried out using a high numerical aperture oil-immersion objective, which permits strong trapping but inevitably introduces spherical aberrations due to the glass-aqueous interface. However, the impact of these aberrations on torque measurements is not fully understood experimentally, partly due to a lack of theoretical guidance. Here, we present a numerical platform based on the finite element method to calculate forces and torques on a trapped quartz cylinder. We have also developed a new experimental method to accurately determine the shift in the trapping position due to the spherical aberrations by using a DNA molecule as a distance ruler. We found that the calculated and measured focal shift ratios are in good agreement. We further determined how the angular trap stiffness depends on the trap height and the cylinder displacement from the trap center and found full agreement between predictions and measurements. As a further verification of the methodology, we showed that DNA torsional properties, which are intrinsic to DNA, could be determined robustly under different trap heights and cylinder displacements. Thus, this work has laid both a theoretical and experimental framework that can be readily extended to investigate the trapping forces and torques exerted on particles with arbitrary shapes and optical properties.

Optical trapping and manipulating with a transmissive and polarization-insensitive metalens

Trapping and manipulating micro-objects and achieving high-precision measurements of tiny forces and displacements are of paramount importance in both physical and biological research. While conventional optical tweezers rely on tightly focused beams generated by bulky microscope systems, the emergence of flat lenses, particularly metalenses, has revolutionized miniature optical tweezers applications. In contrast to traditional objectives, the metalenses can be seamlessly integrated into sample chambers, facilitating flat-optics-based light manipulation. In this study, we propose an experimentally realized transmissive and polarization-insensitive water-immersion metalens, constructed using adaptive nano-antennas. This metalens boasts an ultra-high numerical aperture of 1.28 and achieves a remarkable focusing efficiency of approximately 50 % at a wavelength of 532 nm. Employing this metalens, we successfully demonstrate stable optical trapping, achieving lateral trapping stiffness exceeding 500 pN/(μm W). This stiffness magnitude aligns with that of conventional objectives and surpasses the performance of previously reported flat lenses. Furthermore, our bead steering experiment showcases a lateral manipulation range exceeding 2 μm, including a region of around 0.5 μm exhibiting minimal changes in stiffness for smoothly optical manipulation. We believe that this metalens paves the way for flat-optics-based optical tweezers, simplifying and enhancing optical trapping and manipulation processes, attributing ease of use, reliability, high performance, and compatibility with prevalent optical tweezers applications, including single-molecule and single-cell experiments.

Magnetic tweezers principles and promises

Magnetic tweezers have become popular with the outbreak of single molecule micromanipulation: catching a single molecule of DNA, RNA or a single protein and applying mechanical constrains using micron-size magnetic beads and magnets turn out to be easy. Various factors have made this possible: the fact that manufacturers have been preparing these beads to catch various biological entities-the ease of use provided by magnets which apply a force or a torque at a distance thus inside a flow cell-some chance: since the forces so generated are in the right range to stretch a single molecule. This is a little less true for torque. Finally, one feature which also appears very important is the simplicity of their calibration using Brownian motion. Here we start by describing magnetic tweezers used routinely in our laboratory where we have tried to develop a device as simple as possible so that the experimentalist can really focus on the biological aspect of the biomolecules that he/she is interested in. We discuss the implications of the various components and their important features. Next, we summarize what is easy to achieve and what is less easy. Then we refer to contributions by other groups who have brought valuable insights to improve magnetic tweezers.

High-precision micro-displacement sensing based on an optical filter and optoelectronic oscillators

High-precision micro-displacement sensing based on an optical filter and optoelectronic oscillators (OEOs) is proposed and experimentally demonstrated. In this scheme, an optical filter is utilized to separate the carriers of the measurement and reference OEO loops. Through the optical filter, the common path structure can be consequently achieved. The two OEO loops share all optical/electrical components, except for the micro-displacement to be measured. Measurement and reference OEOs are alternately oscillated by using a magneto-optic switch. Therefore, self-calibration is achieved without additional cavity length control circuits, greatly simplifying the system. A theoretical analysis of the system is developed, and this analysis is then demonstrated with experiments. Regarding the micro-displacement measurements, we achieved a sensitivity of 312.058 kHz/mm and a measurement resolution of 356 pm. The measurement precision is less than 130 nm over a measurement range of 19 mm.

Influence of Single Deuterium Replacement on Frequency of Hydrogen Bond Dissociation in IFNA17 under the Highest Critical Energy Range

The effect of single substitutions of protium for deuterium in hydrogen bonds between pairs of nitrogenous bases on the open states occurrence probability at high critical breaking energies of these bonds has been studied. The study was carried out using numerical methods based on the angular mathematical model of DNA. The IFNA17 gene was divided into three approximately equal parts. A comparison of the open states occurrence probability in these parts of the gene was done. To improve the accuracy of the results, a special data processing algorithm was developed. The developed methods have shown their suitability for taking into account the occurrence of open states in the entire range of high critical energies. It has been established that single ²H/¹H substitutions in certain nitrogenous bases can be a mechanism for maintaining the vital activity of IFNA17 under critical conditions. In general, the developed method of the mathematical modeling provide unprecedented insight into the DNA behavior under the highest critical energy range, which greatly expands scientific understanding of nucleobases interaction.