Previously, we described a method for a recombinase-directed stacking of new DNA to an existing transgenic locus. Here, we describe how we can similarly stack DNA molecules in vitro and that the in vitro derived gene stack can be incorporated into an Agrobacterium transformation vector by in vitro recombination. After transfer to the chromosome by Agroinfection, the transgenic locus harbors a new target site that can be used for the subsequent in vivo stacking of new DNA. Alternatively, the in vitro derived gene stack has the potential to be integrated directly into the plant genome in vivo at a preexisting chromosomal target. Being able to stack DNA in vitro as well as in vivo, and with compatibility between the two systems, brings new flexibility for using the recombinase-mediated approach for transgene stacking.
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http://dx.doi.org/10.1007/978-1-4939-4931-1_3 | DOI Listing |
Eng Biol
December 2024
Analytik Jena AG Analytik Jena UK Ltd London UK.
Breakthroughs in engineering biology will solve the challenges facing humanity, by harnessing life itself. Standing in the way of these breakthroughs are the technical challenges of collecting the requisite data. Data variability and reproducibility problems, mean the odds are stacked against emerging biotechs.
View Article and Find Full Text PDFSmall
December 2024
Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo, 182-8585, Japan.
This paper discusses the controlled morphology of hierarchical liquid crystalline DNA assemblies. Through a process of heating and slow cooling, double-stranded DNAs (dsDNAs) having 23 complementary bases and two base overhangs (a pair of 25mer oligonucleotides) spontaneously assemble into micro-sized hexagonal platelets in a solution containing poly(ethylene glycol) (PEG) and salt. Remarkably, the addition of a shorter dsDNA with AA/TT overhangs (a pair of 18mer oligonucleotides) to a PEG-salt solution of 25mer DNA with AA/TT overhangs results in the formation of molecular tubes, each with a central blockage.
View Article and Find Full Text PDFAnal Chem
December 2024
Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba DistrictChongqing 400038, China.
CRISPR/Cas12a-based diagnostics have great potential for sensing nucleic acids, but their application is limited by the sequence-dependent property. A platform termed miR-Cabiner (a universal NA sensing platform based on self-stacking scaded cyclic DA circuit-mdiated CISPR/Cas12a) is demonstrated herein that is sensitive and universal for analyzing miRNAs. This platform combines catalytic hairpin assembly (CHA) and hybrid chain reaction (HCR) into a unified circuit and finally cascades to CRISPR/Cas12a.
View Article and Find Full Text PDFNucleic Acids Res
December 2024
Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA, 19081USA.
Left-handed G-quadruplexes (LHG4s) belong to a class of recently discovered noncanonical DNA structures under the larger umbrella of G-quadruplex DNAs (G4s). The biological relevance of these structures and their ability to be targeted with classical G4 ligands is underexplored. Here, we explore whether the putative LHG4 DNA sequence from the SLC2A1 oncogene promoter maintains its left-handed characteristics upon addition of nucleotides in the 5'- and 3'-direction from its genomic context.
View Article and Find Full Text PDFbioRxiv
December 2024
Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Most eukaryotes possess two Rad51/RecA family DNA recombinases that are thought to have arisen from an ancient gene duplication event: Rad51, which is expressed in both mitosis and meiosis; and Dmc1, which is only expressed in meiosis. To explore the evolutionary relationship between these recombinases, here, we present high-resolution CryoEM structures of Rad51 filaments and Dmc1 filaments bound to ssDNA, which reveal a pair of stacked interfacial aromatic amino acid residues that are nearly universally conserved in Rad51 but are absent from Dmc1. We use a combination of bioinformatics, genetic analysis of natural sequence variation, and deep mutational analysis to probe the functionally tolerated sequence space for these stacked aromatic residues.
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