Visualization of direct and diffusion-assisted RAD51 nucleation by full-length human BRCA2 protein

Homologous recombination (HR) is essential for error-free repair of DNA double-strand breaks, perturbed replication forks (RFs), and post-replicative single-stranded DNA (ssDNA) gaps. To initiate HR, the recombination mediator and tumor suppressor protein BRCA2 facilitates nucleation of RAD51 on ssDNA prior to stimulation of RAD51 filament growth by RAD51 paralogs. Although ssDNA binding by BRCA2 has been implicated in RAD51 nucleation, the function of double-stranded DNA (dsDNA) binding by BRCA2 remains unclear. Here, we exploit single-molecule (SM) imaging to visualize BRCA2-mediated RAD51 nucleation in real time using purified proteins. We report that BRCA2 nucleates and stabilizes RAD51 on ssDNA either directly or through an unappreciated diffusion-assisted delivery mechanism involving binding to and sliding along dsDNA, which requires the cooperative action of multiple dsDNA-binding modules in BRCA2. Collectively, our work reveals two distinct mechanisms of BRCA2-dependent RAD51 loading onto ssDNA, which we propose are critical for its diverse functions in maintaining genome stability and cancer suppression.

HELQ is a dual-function DSB repair enzyme modulated by RPA and RAD51

DNA double-stranded breaks (DSBs) are deleterious lesions, and their incorrect repair can drive cancer development1. HELQ is a superfamily 2 helicase with 3' to 5' polarity, and its disruption in mice confers germ cells loss, infertility and increased predisposition to ovarian and pituitary tumours2-4. At the cellular level, defects in HELQ result in hypersensitivity to cisplatin and mitomycin C, and persistence of RAD51 foci after DNA damage3,5. Notably, HELQ binds to RPA and the RAD51-paralogue BCDX2 complex, but the relevance of these interactions and how HELQ functions in DSB repair remains unclear3,5,6. Here we show that HELQ helicase activity and a previously unappreciated DNA strand annealing function are differentially regulated by RPA and RAD51. Using biochemistry analyses and single-molecule imaging, we establish that RAD51 forms a complex with and strongly stimulates HELQ as it translocates during DNA unwinding. By contrast, RPA inhibits DNA unwinding by HELQ but strongly stimulates DNA strand annealing. Mechanistically, we show that HELQ possesses an intrinsic ability to capture RPA-bound DNA strands and then displace RPA to facilitate annealing of complementary sequences. Finally, we show that HELQ deficiency in cells compromises single-strand annealing and microhomology-mediated end-joining pathways and leads to bias towards long-tract gene conversion tracts during homologous recombination. Thus, our results implicate HELQ in multiple arms of DSB repair through co-factor-dependent modulation of intrinsic translocase and DNA strand annealing activities.

Generation of versatile ss-dsDNA hybrid substrates for single-molecule analysis

Here, we describe a rapid and versatile protocol to generate gapped DNA substrates for single-molecule (SM) analysis using optical tweezers via site-specific Cas9 nicking and force-induced melting. We provide examples of single-stranded (ss) DNA gaps of different length and position. We outline protocols to visualize these substrates by replication protein A-enhanced Green Fluorescent Protein (RPA-eGFP) and SYTOX Orange staining using commercially available optical tweezers (C-TRAP). Finally, we demonstrate the utility of these substrates for SM analysis of bidirectional growth of RAD-51-ssDNA filaments. For complete details on the use and execution of this protocol, please refer to Belan et al. (2021).

A critical role for linker DNA in higher-order folding of chromatin fibers

Nucleosome-nucleosome interactions drive the folding of nucleosomal arrays into dense chromatin fibers. A better physical account of the folding of chromatin fibers is necessary to understand the role of chromatin in regulating DNA transactions. Here, we studied the unfolding pathway of regular chromatin fibers as a function of single base pair increments in linker length, using both rigid base-pair Monte Carlo simulations and single-molecule force spectroscopy. Both computational and experimental results reveal a periodic variation of the folding energies due to the limited flexibility of the linker DNA. We show that twist is more restrictive for nucleosome stacking than bend, and find the most stable stacking interactions for linker lengths of multiples of 10 bp. We analyzed nucleosomes stacking in both 1- and 2-start topologies and show that stacking preferences are determined by the length of the linker DNA. Moreover, we present evidence that the sequence of the linker DNA also modulates nucleosome stacking and that the effect of the deletion of the H4 tail depends on the linker length. Importantly, these results imply that nucleosome positioning in vivo not only affects the phasing of nucleosomes relative to DNA but also directs the higher-order structure of chromatin.

Chromatin fibers stabilize nucleosomes under torsional stress

Torsional stress generated during DNA replication and transcription has been suggested to facilitate nucleosome unwrapping and thereby the progression of polymerases. However, the propagation of twist in condensed chromatin remains yet unresolved. Here, we measure how force and torque impact chromatin fibers with a nucleosome repeat length of 167 and 197. We find that both types of fibers fold into a left-handed superhelix that can be stabilized by positive torsion. We observe that the structural changes induced by twist were reversible, indicating that chromatin has a large degree of elasticity. Our direct measurements of torque confirmed the hypothesis of chromatin fibers as a twist buffer. Using a statistical mechanics-based torsional spring model, we extracted values of the chromatin twist modulus and the linking number per stacked nucleosome that were in good agreement with values measured here experimentally. Overall, our findings indicate that the supercoiling generated by DNA-processing enzymes, predicted by the twin-supercoiled domain model, can be largely accommodated by the higher-order structure of chromatin.

Rigid Basepair Monte Carlo Simulations of One-Start and Two-Start Chromatin Fiber Unfolding by Force

The organization of chromatin in 30 nm fibers remains a topic of debate. Here, we quantify the mechanical properties of the linker DNA and evaluate the impact of these properties on chromatin fiber folding. We extended a rigid basepair DNA model to include (un)wrapping of nucleosomal DNA and (un)stacking of nucleosomes in one-start and two-start chromatin fibers. Monte Carlo simulations that mimic single-molecule force spectroscopy experiments of folded nucleosomal arrays reveal different stages of unfolding as a function of force and are largely consistent with a two-start folding for 167 and one-start folding for 197 nucleosome repeat length fibers. The major insight is that nucleosome unstacking and subsequent unwrapping is not necessary to obtain quantitative agreement with experimental force extension curves up to the overstretching plateau of folded chromatin fibers at 3-5 pN. Nucleosome stacking appears better accommodated in one-start than in two-start conformations, and we suggest that this difference can compensate the increased energy for bending the linker DNA. Overall, these simulations capture the dynamic structure of chromatin fibers while maintaining realistic physical properties of the linker DNA.

Unraveling DNA Organization with Single-Molecule Force Spectroscopy Using Magnetic Tweezers

Genomes carry the genetic blueprint of all living organisms. Their organization requires strong condensation as well as carefully regulated accessibility to specific genes for proper functioning of their hosts. The study of the structure and dynamics of the proteins that organize the genome has benefited tremendously from the development of single-molecule force spectroscopy techniques that allow for real-time, nanometer accuracy measurements of the compaction of DNA and manipulation with pico-Newton scale forces. Magnetic tweezers in particular have the unique ability to complement such force spectroscopy with the control over the linking number of the DNA molecule, which plays an important role when DNA organizing proteins form or release wraps, loops, and bends in DNA. Here, we describe all the necessary steps to prepare DNA substrates for magnetic tweezers experiments, assemble flow cells, tether DNA to magnetics bead inside flow cell, and manipulate and record the extension of such DNA tethers. Furthermore, we explain how mechanical parameters of nucleo-protein filaments can be extracted from the data.

Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding

The eukaryotic genome is highly compacted into a protein-DNA complex called chromatin. The cell controls access of transcriptional regulators to chromosomal DNA via several mechanisms that act on chromatin-associated proteins and provide a rich spectrum of epigenetic regulation. Elucidating the mechanisms that fold chromatin fibers into higher-order structures is therefore key to understanding the epigenetic regulation of DNA accessibility. Here, using histone H4-V21C and histone H2A-E64C mutations, we employed single-molecule force spectroscopy to measure the unfolding of individual chromatin fibers that are reversibly cross-linked through the histone H4 tail. Fibers with covalently linked nucleosomes featured the same folding characteristics as fibers containing wild-type histones but exhibited increased stability against stretching forces. By stabilizing the secondary structure of chromatin, we confirmed a nucleosome repeat length (NRL)-dependent folding. Consistent with previous crystallographic and cryo-EM studies, the obtained force-extension curves on arrays with 167-bp NRLs best supported an underlying structure consisting of zig-zag, two-start fibers. For arrays with 197-bp NRLs, we previously inferred solenoidal folding, which was further corroborated by force-extension curves of the cross-linked fibers. The different unfolding pathways exhibited by these two types of arrays and reported here extend our understanding of chromatin structure and its potential roles in gene regulation. Importantly, these findings imply that chromatin compaction by nucleosome stacking protects nucleosomal DNA from external forces up to 4 piconewtons.

Strain-Induced Spatial and Spectral Isolation of Quantum Emitters in Mono- and Bilayer WSe2

Two-dimensional transition metal dichalcogenide semiconductors are intriguing hosts for quantum light sources due to their unique optoelectronic properties. Here, we report that strain gradients, either unintentionally induced or generated by substrate patterning, result in spatially and spectrally isolated quantum emitters in mono- and bilayer WSe2. By correlating localized excitons with localized strain variations, we show that the quantum emitter emission energy can be red-tuned up to a remarkable ∼170 meV. We probe the fine-structure, magneto-optics, and second-order coherence of a strained emitter. These results raise the prospect of strain-engineering quantum emitter properties and deterministically creating arrays of quantum emitters in two-dimensional semiconductors.

Influence of surgical resection on plasma endoglin (CD105) level in non‑small cell lung cancer patients

BACKGROUND AND AIM

Endoglin is a proliferation-associated antigen on endothelial cells and essential for angiogenesis. Soluble endoglin (s‑endoglin), formed by proteolytic cleavage of ectodomain of membrane receptor could be an indicator of tumor‑activated endothelium. The aim of present study was to analyze changes of s‑endoglin level in plasma of lung cancer patients following surgical resection and to estimate the correlation of s‑endoglin with other soluble receptors, sTie2 and sVEGF R1.

PATIENTS AND METHODS

The study group consisted of 37 patients with stage I of non-small cell lung cancer. Plasma concentrations of s‑endoglin, sTie2 and sVEGF R1 were evaluated by ELISA, three times: before surgical resection and on postoperative day 7 and 30.

RESULTS

The median of s‑endoglin concentration decreased significantly on postoperative day 7 when compared with preoperative level and next increased on 30(th) day and it was comparable with that before surgery. s-Endoglin correlated with another soluble receptors, with sTie2 both before surgery (r=0.44) and on postoperative day 7 (r=0.52) and on 30(th) day (r=0.58), with sVEGF R1 - only on postoperative day 7 (r=0.75).

CONCLUSION

The increased level of serum endoglin in lung cancer patients compared to controls and its changes after surgical treatment suggest potential application of soluble form of endoglin as potential tumor marker.

Plasma concentration of angiopoietin-1, angiopoietin-2 and Tie-2 in cervical cancer

PURPOSE OF INVESTIGATION

Angiogenesis is important in the promotion and progression of malignancy. The formation of new blood vessels is coordinated by many factors, angiopoietins among others. Overexpression of angiopoietins has been observed in various tumors. The aim of the study was to evaluate plasma concentration of Ang-1, Ang-2 and Tie-2 in cervical cancer.

METHODS

The study group consisted of 34 patients with cervical cancer and the control group of 20 healthy volunteers. Plasma concentrations of Ang-1, Ang-2 and Tie-2 were evaluated by ELISA.

RESULTS

Plasma concentrations of Ang-1, Ang-2, Tie-2 and Ang-1/Ang-2 ratios were significantly higher in cervical cancer patients than in controls. Although there was no correlation between concentration of Ang-1, Ang-2, Tie-2 and clinical stage (FIGO), the Ang-1/Ang-2 ratio was higher in Stage I than in II-III. Ang-1 correlated positively with Ang-2 and Tie-2 in a subgroup with Stage II-III and Ang-2 with Tie-2 in a subgroup with Stage I.

CONCLUSION

Plasma concentrations of Ang- 1, Ang-2 and Tie-2 may be useful additional tumor markers in cervical cancer.

Ultrastructural changes associated with cryopreservation of potato (Solanum tuberosum l.) shoot tips

The ultrastructure of cells within shoot tips of S. tuberosum 'Désirée' was studied after different steps of the DMSO droplet cryopreservation method. After 2 h of DMSO treatment, cells contained numerous small vesicles, while at the same time mitochondria and chloroplasts had increased in size and vacuoles had assumed an irregular shape. After rapid cooling in liquid nitrogen, subsequent rewarming, and 1 h incubation there were no apparent changes in the ultrastructural organization of the cells, suggesting that they might be still intact. However, two days after rewarming, the meristematic dome area and part of the epidermis showed signs of extensive damage. Rupture of plasmalemma, plasmolysis and destruction of cell organelles as well as strong heterochromatisation of nuclei were observed. Survival and regeneration of cells were found mainly in leaf primordial regions. Here cells were very active, containing many mitochondria and intact or regenerating chloroplasts. Alternating temperature preculture of donor plants before shoot tip isolation improved the cryopreservation results (plant regeneration 46.5 percent) as compared to constantly warm precultured shoot tips (plant regeneration 20.0 percent), which showed slightly stronger damage after rewarming from liquid nitrogen.

Drugs of abuse--an analysis based on cases from the Kraków Department of Clinical Toxicology of Jagiellonian University College of Medicine in 1997-2000

The aim of the study was to present the frequency of acute drug overdosing by dependent patients in the years 1997, 1998, 1999 and 2000, and to compare the numbers of poisoned addicts suffering withdrawal syndrome and seeking detoxification. The analysis includes data for all drug addicts treated at the Kraków Department of Clinical Toxicology in years 1997, 1998, 1999 and 2000 because of drug overdosing and resultant acute intoxication, because of withdrawal syndrome and also the opiate dependent patients qualified to methadone maintenance programme. The patients dependent on ethanol were excluded. A progressive increase in number of poisonings with psychoactive substances was noted in analysed years, respectively 231, 298, 331 and 442 patients. Drugs of abuse, were the most frequent cause of admission. Also incidence rate of poisoning expressed per 10,000 of Kraków inhabitants was highest for the cases admitted because of overdosing or craving for narcotics. Opiate derivatives produced at home from poppy straw or from juice of poppy head (so called "kompot" or "Polish heroin") were the most common cause of admission in all the analysed years: increase in number of acutely poisoned, and also increase in number of opiate dependent patients who suffered withdrawal syndrome and sought detoxification was noted in 2000 as compared to years 1998 and 1999. Opiate derivatives followed by amphetamine, as the single toxic agent or in mixed combinations, were still the most common drugs of abuse detected in body fluids. The men were dominant in all the analysed years, but the increase in number of depended women was observed through the years under analysis.

Synthesis and tumor-uptake study of phosphate esters of polyhedral hydroxyboranes

The phosphorylations of B12H11OH2-,B12H10(OH)2-2-, and B20H17OH4-with POCl3 and (C6H5O)2POCl were investigated and the following derivatives were isolated: B12H11OPO3H3-,B12H11OPO3H2-2-,B12H11OPO(OC6H5)-2-2 minus, B12H11OPO(OC6H5)OH2 minus, b12h10(op2o6h2)2-4 minus, B12H10(OPO3H2)2-2 minus, B12Br10(OPO3H)2-4 minus, B12H10[O-PO(OC6H5)2]2-2 minus, B20H18OP2O6H2-4 minus, B20H18OPO3H2-3 minus. The B-O-P bonds proved very resistant to hydrolysis and the phosphates were administered in the for of Na+ salts at pH 7.2 to rats bearing subcutaneous glioma. The boron concentrations in tumors and the tumor/blood concentration ratios were compared with those of parent hydroxy derivatives. Except when the POH function was blocked by phenyl groups the phosphorylation invariably resulted in a greatly enhanced uptake of the borane into tumors and improved the tumor/blood boron ratio. The phopshate function appears to be one of the most effective handles for the incorporation of boron into brain tumors and the compounds show considerable promise for use in the neutron capture therapy of brain tumors.