Optical Micromachines for Biological Studies

Insights into the Dynamics and Helicase Activity of RecD2 of Deinococcus radiodurans during DNA Repair: A Single-Molecule Perspective

While the double helix is the most stable conformation of DNA inside cells, its transient unwinding and subsequent partial separation of the two complementary strands yields an intermediate single-stranded DNA (ssDNA). The ssDNA is involved in all major DNA transactions such as replication, transcription, recombination, and repair. The process of DNA unwinding and translocation is shouldered by helicases that transduce the chemical energy derived from nucleotide triphosphate (NTP) hydrolysis to mechanical energy and utilize it to destabilize hydrogen bonds between complementary base pairs. Consequently, a comprehensive understanding of the molecular mechanisms of these enzymes is essential. In the last few decades, a combination of single-molecule techniques (force-based manipulation and visualization) have been employed to study helicase action. These approaches have allowed researchers to study the single helicase-DNA complex in real-time and the free energy landscape of their interaction together with the detection of conformational intermediates and molecular heterogeneity during the course of helicase action. Furthermore, the unique ability of these techniques to resolve helicase motion at nanometer and millisecond spatial and temporal resolutions, respectively, provided surprising insights into their mechanism of action. This perspective outlines the contribution of single-molecule methods in deciphering molecular details of helicase activities. It also exemplifies how each technique was or can be used to study the helicase action of RecD2 in recombination DNA repair.

Spin Hall Effect in the Paraxial Light Beams with Multiple Polarization Singularities

Elements of micromachines can be driven by light, including structured light with phase and/or polarization singularities. We investigate a paraxial vectorial Gaussian beam with multiple polarization singularities residing on a circle. Such a beam is a superposition of a cylindrically polarized Laguerre-Gaussian beam with a linearly polarized Gaussian beam. We demonstrate that, despite linear polarization in the initial plane, on propagation in space, alternating areas are generated with a spin angular momentum (SAM) density of opposite sign, that manifest about the spin Hall effect. We derive that in each transverse plane, maximal SAM magnitude is on a certain-radius circle. We obtain an approximate expression for the distance to the transverse plane with the maximal SAM density. Besides, we define the singularities circle radius, for which the achievable SAM density is maximal. It turns out that in this case the energies of the Laguerre-Gaussian and of the Gaussian beams are equal. We obtain an expression for the orbital angular momentum density and find that it is equal to the SAM density, multiplied by -m/2 with m being the order of the Laguerre-Gaussian beam, equal to the number of the polarization singularities. We consider an analogy with plane waves and find that the spin Hall affect arises due to the different divergence between the linearly polarized Gaussian beam and cylindrically polarized Laguerre-Gaussian beam. Application areas of the obtained results are designing micromachines with optically driven elements.

Spin Hall Effect of Double-Index Cylindrical Vector Beams in a Tight Focus

We investigate the spin angular momentum (SAM) of double-index cylindrical vector beams in tight focus. Such a set of beams is a generalization of the conventional cylindrical vector beams since the polarization order is different for the different transverse field components. Based on the Richards-Wolf theory, we obtain an expression for the SAM distribution and show that if the polarization orders are of different parity, then the spin Hall effect occurs in the tight focus, which is there are alternating areas with positive and negative spin angular momentum, despite linear polarization of the initial field. We also analyze the orbital angular momentum spectrum of all the components of the focused light field and determine the overwhelming angular harmonics. Neglecting the weak harmonics, we predict the SAM distribution and demonstrate the ability to generate the focal distribution where the areas with the positive and negative spin angular momentum reside on a ring and are alternating in pairs, or separated in different semicircles. Application areas of the obtained results are designing micromachines with optically driven elements.

Optical microlever assisted DNA stretching

Optical microrobotics is an emerging field that has the potential to improve upon current optical tweezer studies through avenues such as limiting the exposure of biological molecules of interest to laser radiation and overcoming the current limitations of low forces and unwanted interactions between nearby optical traps. However, optical microrobotics has been historically limited to rigid, single-body end-effectors rather than even simple machines, limiting the tasks that can be performed. Additionally, while multi-body machines such as microlevers exist in the literature, they have not yet been successfully demonstrated as tools for biological studies, such as molecule stretching. In this work we have taken a step towards moving the field forward by developing two types of microlever, produced using two-photon absorption polymerisation, to perform the first lever-assisted stretches of double-stranded DNA. The aim of the work is to provide a proof of concept for using optical micromachines for single molecule studies. Both styles of microlevers were successfully used to stretch single duplexes of DNA, and the results were analysed with the worm-like chain model to show that they were in good agreement.

Single laser trapping for optical folding and rotation of red blood cells in sickle cell disease in response to hydroxyurea treatment

Optical folding and rotation behavior of red blood cells (RBCs) in polarized laser tweezers are considerably important for understanding the biophysical and biomechanical properties using the fast probing method. Here, a dual-mode polarized single-laser tweezers technique with distinct principal axes exhibiting different polarization states is presented and designed to investigate the deformation, optical folding, and rotation of single living cells with one measurement. RBC optical folding and rotation speed are measured in patients with sickle cell disease (SCD), including follow up of patients after hydroxyurea (HU) treatment for at least three months. Folding angle and rotation speed are significantly lower in patients with SCD and do not significantly differ in patients treated by HU compared with the healthy control group. The RBC folding angle and rotation speed in patients treated with HU drug increase linearly at lower laser powers and rapidly at higher powers, and increase much slowly in patients not treated with HU. The difference in the folding angle and rotation speed of RBCs could be useful for drug response in SCD or predicting pain crisis in SCD.

Genetic Material Manipulation and Modification by Optical Trapping and Nanosurgery-A Perspective

Light can be employed as a tool to alter and manipulate matter in many ways. An example has been the implementation of optical trapping, the so called optical tweezers, in which light can hold and move small objects with 3D control. Of interest for the Life Sciences and Biotechnology is the fact that biological objects in the size range from tens of nanometers to hundreds of microns can be precisely manipulated through this technology. In particular, it has been shown possible to optically trap and move genetic material (DNA and chromatin) using optical tweezers. Also, these biological entities can be severed, rearranged and reconstructed by the combined use of laser scissors and optical tweezers. In this review, the background, current state and future possibilities of optical tweezers and laser scissors to manipulate, rearrange and alter genetic material (DNA, chromatin and chromosomes) will be presented. Sources of undesirable effects by the optical procedure and measures to avoid them will be discussed. In addition, first tentative approaches at cellular-level genetic and organelle surgery, in which genetic material or DNA-carrying organelles are extracted out or introduced into cells, will be presented.

Editorial for the Special Issue on Optical Trapping and Manipulation: From Fundamentals to Applications

This Special Issue of Micromachines is devoted to optical trapping, and the enormous range of uses the method has found in the decades since its first demonstration [...].