DNA-coated Beads Research Articles

Efficient multi-gene expression in cell-free droplet microreactors

Cell-free transcription and translation systems promise to accelerate and simplify the engineering of proteins, biological circuits and metabolic pathways. Their encapsulation on microfluidic platforms can generate millions of cell-free reactions in picoliter volume droplets. However, current methods struggle to create DNA diversity between droplets while also reaching sufficient protein expression levels. In particular, efficient multi-gene expression has remained elusive. We here demonstrate that co-encapsulation of DNA-coated beads with a defined cell-free system allows high protein expression while also supporting genetic diversity between individual droplets. We optimize DNA loading on commercially available microbeads through direct binding as well as through the sequential coupling of up to three genes via a solid-phase Golden Gate assembly or BxB1 integrase-based recombineering. Encapsulation with an off-the-shelf microfluidics device allows for single or multiple protein expression from a single DNA-coated bead per 14 pL droplet. We envision that this approach will help to scale up and parallelize the rapid prototyping of more complex biological systems.

Rezidüel Tümör Tespiti İçin Bir Sıvı Biyopsi Yöntemi Olarak Alelspesifik Emülsiyon PCR (asePCR)

AimThis study aimed to develop an allele-specific emulsion polymerase chain reaction (asePCR)technique for detection of cell-free circulating tumor DNA (ctDNA) in the blood plasma of cancer patients. Materials and MethodsGenomic DNA extracted from normal (wild-type) and thyroid cancer (mutant) cell lines (MCF10A and B-CPAP) were used to obtain specific dilution series (spike-in) of mutant DNA with wild-type DNA. Two sequential PCR steps (regular and asePCR) were performed with specifically designed primers for each step to detect the spiked-in mutant DNA fraction within the wild-type normal DNA. The DNA products amplified by regular PCR were used as templates in the asePCR where specific reverse primers were designed to amplify either the mutant or wild-type allele while a common forward primer was covalently bound to the beads. The asePCR reaction mix was encapsulated in water-in-oil emulsion compartments and incubated in a thermocycler with specific PCR program settings. At the end of asePCR reaction, oil compartments were broken and DNA-coated beads were evaluated by FACS to determine the mutant and wild-type fractions for each sample.ResultsThe asePCR technique successfully detected the mutant DNA in the background of wildtype DNA (0% mutant) as a proof-of-principle. A strong correlation (r2>0.99) was found between the expected mutant fraction and the fraction measured by asePCR. asePCR was sensitive and specific enough to consistently detect various low mutant DNA fractions in the background of wild-type DNA with no false positives in the wild-type sample.Discussion and Conclusion Our asePCR can be used to detect mutant ctDNA in the plasma of cancer patients as a liquid biopsy method for tumor response evaluation and early detection of possible relapses.

Measurement of the position-dependent electrophoretic force on DNA in a glass nanocapillary.

The electrophoretic force on a single DNA molecule inside a glass nanocapillary depends on the opening size and varies with the distance along the symmetrical axis of the nanocapillary. Using optical tweezers and DNA-coated beads, we measured the stalling forces and mapped the position-dependent force profiles acting on DNA inside nanocapillaries of different sizes. We showed that the stalling force is higher in nanocapillaries of smaller diameters. The position-dependent force profiles strongly depend on the size of the nanocapillary opening, and for openings smaller than 20 nm, the profiles resemble the behavior observed in solid-state nanopores. To characterize the position-dependent force profiles in nanocapillaries of different sizes, we used a model that combines information from both analytical approximations and numerical calculations.

The MRN-CtIP Pathway Is Required for Metaphase Chromosome Alignment

Faithful duplication of the genome in S phase followed by its accurate segregation in mitosis is essential to maintain genomic integrity. Recent studies have suggested that proteins involved in DNA transactions are also required for whole-chromosome stability. Here we demonstrate that the MRN (Mre11, Rad50, and Nbs1) complex and CtIP are required for accurate chromosome segregation. Depletion of Mre11 or CtIP, antibody-mediated inhibition of Mre11, or small-molecule inhibition of MRN using mirin results in metaphase chromosome alignment defects in Xenopus egg extracts. Similarly, loss of MRN function adversely affects spindle assembly around DNA-coated beads in egg extracts. Inhibition of MRN function in mammalian cells triggers a metaphase delay and disrupts the RCC1-dependent RanGTP gradient. Addition of the Mre11 inhibitor mirin to egg extracts and mammalian cells reduces RCC1 association with mitotic chromosomes. Thus, the MRN-CtIP pathway contributes to Ran-dependent mitotic spindle assembly by modulating RCC1 chromosome association.

The Ran GTPase Mediates Chromatin Signaling to Control Cortical Polarity during Polar Body Extrusion in Mouse Oocytes

The molecular basis for asymmetric meiotic divisions in mammalian oocytes that give rise to mature eggs and polar bodies remains poorly understood. Previous studies demonstrated that the asymmetrically positioned meiotic chromosomes provide the cue for cortical polarity in mouse oocytes. Here we show that the chromatin-induced cortical response can be fully reconstituted by injecting DNA-coated beads into metaphase II-arrested eggs. The injected DNA beads induce a cortical actin cap, surrounded by a myosin II ring, in a manner that depends on the number of beads and their distance from the cortex. The Ran GTPase plays a critical role in this process, because dominant-negative and constitutively active Ran mutants disrupt DNA-induced cortical polarization. The Ran-mediated signaling to the cortex is independent of the spindle but requires cortical myosin II assembly. We hypothesize that a Ran(GTP) gradient serves as a molecular ruler to interpret the asymmetric position of the meiotic chromatin.

Innate Immune Collectin Surfactant Protein D Enhances the Clearance of DNA by Macrophages and Minimizes Anti-DNA Antibody Generation

Dying microbes and necrotic cells release highly viscous DNA that induces inflammation and septic shock, and apoptotic cells display DNA, a potential autoantigen, on their surfaces. However, innate immune proteins that mediate the clearance of free DNA and surface DNA-containing cells are not clearly established. Pulmonary surfactant proteins (SP-) A and D are innate immune pattern recognition collectins that contain fibrillar collagen-like regions and globular carbohydrate recognition domains (CRDs). We have recently shown that collectins SP-A, SP-D, and mannose binding lectin recognize DNA and RNA via their collagen-like regions and CRDs. Here we show that SP-D enhances the uptake of Cy3-labeled fragments of DNA and DNA-coated beads by U937 human monocytic cells, in vitro. Analysis of DNA uptake by freshly isolated mouse alveolar macrophages shows that SP-D, but not SP-A, deficiency results in reduced clearance of DNA, ex vivo. Analysis of bronchoalveolar lavage fluid shows that SP-D- but not SP-A-deficient mice are defective in clearing free DNA from the lung. Additionally, both SP-A- and SP-D-deficient mice accumulate anti-DNA Abs in sera in an age-dependent manner. Thus, we conclude that collectins such as SP-A and SP-D reduce the generation of anti-DNA autoantibody, which may be explained in part by the defective clearance of DNA from the lungs in the absence of these proteins. Our findings establish two new roles for these innate immune proteins and that SP-D enhances efficient pinocytosis and phagocytosis of DNA by macrophages and minimizes anti-DNA Ab generation.

The condensin complex is required for proper spindle assembly and chromosome segregation in Xenopus egg extracts.

Chromosome condensation is required for the physical resolution and segregation of sister chromatids during cell division, but the precise role of higher order chromatin structure in mitotic chromosome functions is unclear. Here, we address the role of the major condensation machinery, the condensin complex, in spindle assembly and function in Xenopus laevis egg extracts. Immunodepletion of condensin inhibited microtubule growth and organization around chromosomes, reducing the percentage of sperm nuclei capable of forming spindles, and causing dramatic defects in anaphase chromosome segregation. Although the motor CENP-E was recruited to kinetochores pulled poleward during anaphase, the disorganized chromosome mass was not resolved. Inhibition of condensin function during anaphase also inhibited chromosome segregation, indicating its continuous requirement. Spindle assembly around DNA-coated beads in the absence of kinetochores was also impaired upon condensin inhibition. These results support an important role for condensin in establishing chromosomal architecture necessary for proper spindle assembly and chromosome segregation.

A high throughput screen to identify secreted and transmembrane proteins involved in Drosophila embryogenesis.

Secreted and transmembrane proteins play an essential role in intercellular communication during the development of multicellular organisms. Because only a small number of these genes have been characterized, we developed a screen for genes encoding extracellular proteins that are differentially expressed during Drosophila embryogenesis. Our approach utilizes a new method for screening large numbers of cDNAs by whole-embryo in situ hybridization. The cDNA library for the screen was prepared from rough endoplasmic reticulum-bound mRNA and is therefore enriched in clones encoding membrane and secreted proteins. To increase the prevalence of rare cDNAs in the library, the library was normalized using a method based on cDNA hybridization to genomic DNA-coated beads. In total, 2,518 individual cDNAs from the normalized library were screened by in situ hybridization, and 917 of these cDNAs represent genes differentially expressed during embryonic development. Sequence analysis of 1,001 cDNAs indicated that 811 represent genes not previously described in Drosophila. Expression pattern photographs and partial DNA sequences have been assembled in a database publicly available at the Berkeley Drosophila Genome Project website (). The identification of a large number of genes encoding proteins involved in cell-cell contact and signaling will advance our knowledge of the mechanisms by which multicellular organisms and their specialized organs develop.

Self-organization of microtubules into bipolar spindles around artificial chromosomes in Xenopus egg extracts.

Functional nuclei and mitotic spindles are shown to assemble around DNA-coated beads incubated in Xenopus egg extracts. Bipolar spindles assemble in the absence of centrosomes and kinetochores, indicating that bipolarity is an intrinsic property of microtubules assembling around chromatin in a mitotic cytoplasm. Microtubules nucleated at dispersed sites with random polarity rearrange into two arrays of uniform polarity. Spindle-pole formation requires cytoplasmic dynein-dependent translocation of microtubules across one another. It is proposed that spindles form in the absence of centrosomes by motor-dependent sorting of microtubules according to their polarity.

Enrichment of IgG anti-DNA-producing lymphoblastoid cell lines by antigen-coated immunomagnetic beads

In this paper we describe the establishment of four anti-DNA-producing lymphoblastoid cell lines (LCL) by Epstein-Barr virus (EBV) infection of peripheral blood B-cells from a patient with systemic lupus erythematosus. The LCL showed a heterogeneous cell composition: the frequencies of cells in active proliferation, cells secreting IgG or IgM, and cells effectively producing IgG or IgM anti-DNA were estimated by limiting dilution analysis. The cells producing anti-DNA antibodies were a small fraction of the whole cell population constituting the LCL. In order to enrich the fraction of cells producing the desired antibody we performed a positive selection by DNA-coated immunomagnetic beads. Results show that in two out of three IgG anti-DNA-secreting LCL the frequency of DNA-producing cells increased after incubation with DNA-coated beads. At variance, IgM anti-DNA-secreting cells were completely lost after immunomagnetic separation. This approach could represent a further tool to obtain better fusion partners to construct stable hybrids secreting human monoclonal antibodies. The advantages of the presented technique would be: (a) removing of the fraction of low-affinity IgM-producing cells, which is often prevalent in EBV-induced LCL; and (b) the enrichment of IgG anti-DNA producing cells, which better represent the antibodies involved in the pathogenesis of the disease.

A system for photographing cell-sized particles moving at high velocities

A system is described that was used to photograph 3.9 micron diameter DNA-coated beads traveling at speeds up to 30,000 cm/s. The resolution of the optics is 1 micron, so smaller particles moving more slowly could also be photographed. A useful feature is the 15 cm working distance between the optical components and the object to be photographed. Some alternative applications for this type of equipment include studies of cell behavior in turbulence, microbial disruption processes, and membrane poration techniques.