Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
Synergistic and supportive interactions among genes can be incorporated in engineering biology to enhance and stabilize the performance of biological systems, but combinatorial numerical explosion challenges the analysis of multigene interactions. The incorporation of DNA barcodes to mark genes coupled with next-generation sequencing offers a solution to this challenge. We describe improvements for a key method in this space, CombiGEM, to broaden its application to assembling typical gene-sized DNA fragments and to reduce the cost of sequencing for prevalent small-scale projects. The expanded reach of the method beyond currently targeted small RNA genes promotes the discovery and incorporation of gene synergy in natural and engineered processes such as biocontainment, the production of desired compounds, and previously uncharacterized fundamental biological mechanisms.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10510714 | PMC |
| http://dx.doi.org/10.1021/acssynbio.3c00183 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
The ability to synthesize 50-kb+ DNA molecules has tremendous potential in the fields of genome engineering, metabolic engineering, and synthetic regulatory genomics. Despite tremendous achievements in these fields, such as the completion of the first synthetic eukaryotic genome, assembling custom big DNAs remains slow, expensive, and laborious. In this work, we present a set of improvements to yeast-based DNA assembly methods that enable medium-to high-throughput big DNA experiments.
View Article and Find Full Text PDFGenome content reorganization in the non-model ciliate : insights into nuclear architecture, DNA content, and chromosome fragmentation during macronuclear development.
mSphere
June 2025
Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA.
Unlabelled: Ciliates are a model lineage for studies of genome architecture given their unusual genome structures. All ciliates have both somatic macronuclei (MAC) and germline micronuclei (MIC), both of which develop from a zygotic nucleus following sex (i.e.
View Article and Find Full Text PDFEfficient and Precise Integration of Large DNA Sequences Using Precise Interstrand Cross-Linking of Long ssDNA and sgRNA.
ACS Synth Biol
May 2025
Department of Polymer Science and Engineering, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China.
Homology-directed repair (HDR) allows the precise introduction of functional constructs into the human genome through nonviral gene-editing reagents. However, its application in large DNA sequence gene editing remains limited due to challenges such as low efficiency and the off-target effect. To address these limitations, a new method named AOLP was developed to synthesize chemically modified long single-stranded DNA (lssDNA) as the template donor for Cas9-based gene editing, which has been proven to be more stable than that prepared using the commercial phosphorylation method.
View Article and Find Full Text PDFWidespread 3D genome reorganization precedes programmed DNA rearrangement in .
bioRxiv
January 2025
Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY 10032, USA.
Genome organization recapitulates function, yet ciliates like possess highly-specialized germline genomes, which are largely transcriptionally silent. During post-zygotic development, 's germline undergoes large-scale genome editing, rearranging precursor genome elements into a transcriptionally-active genome with thousands of gene-sized nanochromosomes. Transgenerationally-inherited RNAs, derived from the parental somatic genome, program the retention and reordering of germline fragments.
View Article and Find Full Text PDFChromomeres, Topologically Associating Domains and Structural Organization of Chromatin Bodies in Somatic Nuclei (Macronuclei) of Ciliates.
Front Biosci (Landmark Ed)
November 2024
Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
Background: In the twentieth century, the textbook idea of packaging genomic material in the cell nucleus and metaphase chromosomes was the presence of a hierarchy of structural levels of chromatin organization: nucleosomes - nucleosomal fibrils -30 nm fibrils - chromomeres - chromonemata - mitotic chromosomes. Chromomeres were observed in partially decondensed chromosomes and interphase chromatin as ~100 nm globular structures. They were thought to consist of loops of chromatin fibres attached at their bases to a central protein core.
View Article and Find Full Text PDF