Large-scale discovery of recombinases for integrating DNA into the human genome

Recent microbial genome sequencing efforts have revealed a vast reservoir of mobile genetic elements containing integrases that could be useful genome engineering tools. Large serine recombinases (LSRs), such as Bxb1 and PhiC31, are bacteriophage-encoded integrases that can facilitate the insertion of phage DNA into bacterial genomes. However, only a few LSRs have been previously characterized and they have limited efficiency in human cells. Here, we developed a systematic computational discovery workflow that searches across the bacterial tree of life to expand the diversity of known LSRs and their cognate DNA attachment sites by >100-fold. We validated this approach via experimental characterization of LSRs, leading to three classes of LSRs distinguished from one another by their efficiency and specificity. We identify landing pad LSRs that efficiently integrate into native attachment sites in a human cell context, human genome-targeting LSRs with computationally predictable pseudosites, and multi-targeting LSRs that can unidirectionally integrate cargos with similar efficiency and superior specificity to commonly used transposases. LSRs from each category were functionally characterized in human cells, overall achieving up to 7-fold higher plasmid recombination than Bxb1 and genome insertion efficiencies of 40-70% with cargo sizes over 7 kb. Overall, we establish a paradigm for the large-scale discovery of microbial recombinases directly from sequencing data and the reconstruction of their target sites. This strategy provided a rich resource of over 60 experimentally characterized LSRs that can function in human cells and thousands of additional candidates for large-payload genome editing without double-stranded DNA breaks.

Benzoic Acid Derivatives of Ifloga spicata (Forssk.) Sch.Bip. as Potential Anti-Leishmanial against Leishmania tropica

This study aimed to appraise the anti-leishmanial potentials of benzoic acid derivatives, including methyl 3,4-dihydroxybenzoate (compound 1) and octadecyl benzoate (compound 2), isolated from the ethnomedicinally important plant Ifloga spicata (I. spicata). Chemical structures were elucidated via FT-IR, mass spectrometry, and multinuclear (1H and 13C) NMR spectroscopy. Anti-leishmanial potentials of the compounds were assessed using Leishmania tropica promastigotes. Moreover, acridine orange fluorescent staining was performed to visualize the apoptosis-associated changes in promastigotes under a fluorescent microscope. A SYTOX assay was used to check rupturing of Leishmania promastigote cell membranes using 0.1% Triton X-100 as positive control. A DNA interaction assay was carried out to assess DNA attachment potential. AutoDock software was used to check the binding affinity of compounds with surface enzyme leishmanolysin gp63 (1LML). Both compounds exhibited considerable anti-leishmanial potential, with LD50 values of 10.40 ± 0.09 and 14.11 ± 0.11 μg/mL for compound 1 and compound 2, respectively. Both compounds showed higher binding affinity with the leishmanolysin (gp63) receptor/protease of Leishmania, as assessed using computational analysis. The binding scores of compounds 1 and 2 with target gp63 were −5.3 and −5.6, respectively. The attachment of compounds with this receptor resulted in their entry into the cell where they bound with Leishmania DNA, causing apoptosis. The results confirmed that the investigated compounds have anti-leishmanial potential and are potential substitutes as natural anti-leishmanial agents against L. tropica.

DNA Vaccines—How Far From Clinical Use?

Two decades ago successful transfection of antigen presenting cells (APC) in vivo was demonstrated which resulted in the induction of primary adaptive immune responses. Due to the good biocompatibility of plasmid DNA, their cost-efficient production and long shelf life, many researchers aimed to develop DNA vaccine-based immunotherapeutic strategies for treatment of infections and cancer, but also autoimmune diseases and allergies. This review aims to summarize our current knowledge on the course of action of DNA vaccines, and which factors are responsible for the poor immunogenicity in human so far. Important optimization steps that improve DNA transfection efficiency comprise the introduction of DNA-complexing nano-carriers aimed to prevent extracellular DNA degradation, enabling APC targeting, and enhanced endo/lysosomal escape of DNA. Attachment of virus-derived nuclear localization sequences facilitates nuclear entry of DNA. Improvements in DNA vaccine design include the use of APC-specific promotors for transcriptional targeting, the arrangement of multiple antigen sequences, the co-delivery of molecular adjuvants to prevent tolerance induction, and strategies to circumvent potential inhibitory effects of the vector backbone. Successful clinical use of DNA vaccines may require combined employment of all of these parameters, and combination treatment with additional drugs.

Solution-stable anisotropic carbon nanotube/graphene hybrids based on slanted columnar thin films for chemical sensing

Because of their structural anisotropy and stability in liquids, carbon nanotube/graphene hybrid structures are promising for biosensing applications, as shown in a proof-of-concept experiment on in situ ellipsometry monitoring of pyrene-functionalized DNA attachment.

Studying Effect Dimensions of Design and Simulation Silicon Nanowire Filed Effect Biosensor

We investigated into report a study biosensor based on silicon into an effect on the dimensions of conductance design and simulation nanowire surface with molecular DNA for sensitivity. In the design nanowire of A biosensor with 3 layers starting with polyisilicon nanowire of radius 8 NM surrounded by a 50-nm electrode layer, and the substrate by a 300nm. COMSOL Multiphysics software used to provide interaction with molecules such as DNA and the distribution of the electrostatic potential in the narrower due to the dimensions, surface nanowire charge was computed using Poisson equation with Boltzmann statistics. In the result of the effect geometry was also studied and the different dimension yield different space charge and the surface charge at interactive site were also investigated and the study demonstrate steps wise identification of all critical parameters for (DNA) attachment with surface nanowires.