DNA molecules that encode a small, high-speed self-hydrolyzing deoxyribozyme are used as templates for rolling circle amplification (RCA) to produce single-stranded DNAs (ssDNAs) of single- and multiple-unit lengths. Including self-cleaving deoxyribozymes in RCA products can generate large amounts of ssDNAs with defined sequence and length as well as precise termini. We also demonstrate the use of this method to efficiently generate ssDNA size markers by using deoxyribozyme reaction conditions that permit partial processing.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5325123 | PMC |
http://dx.doi.org/10.2144/000114009 | DOI Listing |
Biochem J
January 2025
Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.
The bacterial transcription terminator Rho is a hexameric ATP-dependent RNA helicase that dislodges elongating RNA polymerases. It has an N-terminal primary RNA binding site (PBS) on each subunit and a C-terminal secondary RNA binding site at the central channel. Here, we show that Rho also binds to linear longer double-stranded DNAs (dsDNA) and the circular plasmids non-specifically using its PBS.
View Article and Find Full Text PDFACS Appl Mater Interfaces
January 2025
School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China.
Sensitive and accurate determination of acetamiprid is highly desirable for guaranteeing food safety. In this Letter, an energy-transfer-based dual-mode biosensor was developed using zinc-based metal-organic frameworks (Zn-MOFs) acting as both photoelectrochemical (PEC) and electrochemiluminescent (ECL) donors and Pt@CuO cubic nanocrystals (CNs) as the energy acceptor for detecting acetamiprid. By integration of aptamer recognition with two-step DNA circuit amplification (entropy-driven DNA cycle and DNA walker), the detection of acetamiprid was converted into the assay of abundant intermediate DNA strands.
View Article and Find Full Text PDFComput Biol Chem
December 2024
Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5400, Oulu 90014, Finland; Biocenter Oulu, University of Oulu, PO Box 5400, Oulu 90014, Finland. Electronic address:
Single-stranded breaks (SSBs) are the most frequent DNA lesions threatening genomic integrity-understanding how DNA sensor proteins recognize certain SSB types is crucial for studies of the DNA repair pathways. During repair of damaged DNA the final SSB that is to be ligated contains a 5'-phosphorylated end. The present work employed molecular simulation (MD) of DNA with a phosphorylated break in solution to address multiple questions regarding the dynamics of the break site.
View Article and Find Full Text PDFDNA Repair (Amst)
December 2024
Agriculture and Marine Science Program, Graduate School of Integrated Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan; Agricultural Science, Graduate School of Integrated Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan. Electronic address:
Most giant viruses including Mimiviridae family build large viral factories within the host cytoplasms. These giant viruses are presumed to possess specific genes that enable the rapid and massive replication of their large double-stranded DNA genomes within viral factories. It has been revealed that a functionally uncharacterized protein, MutS7, is expressed during the operational phase of the viral factory.
View Article and Find Full Text PDFJ Chem Inf Model
January 2025
Department of Chemistry and Institute of Functional Materials, Pusan National University, Busan 46241, South Korea.
The amber-OL21 force field (ff) was developed to better describe noncanonical DNA, including Z-DNA. Despite its improvements for DNA simulations, this study found that OL21's scope of application was limited by embedded ff artifacts. In a benchmark set of seven DNA molecules, including two double-stranded DNAs transitioning between B- and Z-DNA and five single-stranded DNAs folding into mini-dumbbell or G-quadruplex structures, the free energy landscapes obtained using OL21 revealed several issues: Z-DNA was overly stabilized; misfolded states in mini-dumbbell DNAs were most stable; DNA GQ folding was consistently biased toward an antiparallel topology.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!