AI Article Synopsis
- Most single-molecule manipulation configurations for DNA and RNA involve multiple single-stranded strands with functional labels at both ends for surface attachment.
- We developed a new amplification-annealing (AA) assay that simplifies the creation of various DNA/RNA configurations in just two or three steps, avoiding complex digestion and ligation processes.
- These configurations can be used in advanced manipulation techniques like optical tweezers, magnetic tweezers, and atomic force microscopy, as well as other surface-tethering methods.
Article Abstract
Despite having a great variety of topologies, most DNA, RNA, and RNA-DNA hybrid (RDH) configurations for single-molecule manipulation are composed of several single-stranded (ss) DNA and ssRNA strands, with functional labels at the two ends for surface tethering. On this basis, we developed a simple, robust, and universal amplification-annealing (AA) assay for making all these configurations in two or three steps without inefficient digestion and ligation reactions. As examples, we made ssDNA, short ssDNA with double-stranded (ds) DNA handles, dsDNA with ssDNA handles, replication-fork shaped DNA/RDH/RNA, DNA holiday junction, three-site multiple-labeled and nicked DNA, torsion-constrained RNA/RDH, and short ssRNA with RDH handles. In addition to single-molecule manipulation techniques including optical tweezers, magnetic tweezers, and atomic force microscopy, these configurations can be applied in other surface-tethering techniques as well.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1021/acssynbio.9b00241 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Modulation of the Magnetic Anisotropy via the Ligand Field in Sandwiched Erbium Complexes.
Inorg Chem
December 2024
Institute of Nano Science and Technology, Sector-81, Mohali, Punjab 140306, India.
Among lanthanide-based single-molecule magnets (SMMs), erbium(III) is a Kramers ion, apart from dysprosium(III), which provides magnetic bistability in the presence of a suitable coordination environment. However, Er-based SMMs exhibit significantly less magnetic anisotropy than Dy because their prolate electronic density necessitates equatorially correlated ligands to minimize the charge contact with the Er atom. Here, in this work, we have computationally investigated the heteroleptic organometallic complexes with an Er(III) atom sandwiched between two distinct cyclic rings (five- and eight-membered) with the aim of tuning the magnetic anisotropy via exploiting the ligand field.
View Article and Find Full Text PDFGenome concentration limits cell growth and modulates proteome composition in .
Elife
December 2024
Howard Hughes Medical Institute, Stanford University, Stanford, United States.
Defining the cellular factors that drive growth rate and proteome composition is essential for understanding and manipulating cellular systems. In bacteria, ribosome concentration is known to be a constraining factor of cell growth rate, while gene concentration is usually assumed not to be limiting. Here, using single-molecule tracking, quantitative single-cell microscopy, and modeling, we show that genome dilution in cells arrested for DNA replication limits total RNA polymerase activity within physiological cell sizes across tested nutrient conditions.
View Article and Find Full Text PDFManipulating π-π Interactions between Single Molecules by Using Antenna Electrodes as Optical Tweezers.
Phys Rev Lett
December 2024
Center of Single-Molecule Sciences, Institute of Modern Optics, Tianjin Key Laboratory of Micro-scale Optical Information Science and Technology, Nankai University, Tianjin 300350, China.
Via conductance measurements of thousands of single-molecule junctions, we report that the π-π coupling between neighboring aromatic molecules can be manipulated by laser illumination. We reveal that this optical manipulation originates from the optical plasmonic gradient force generated inside the nanogaps, in which the gapped antenna electrodes act as optical tweezers pushing the neighboring molecules closer together. These findings offer a nondestructive approach to regulate the interaction of the molecules, deepening the understanding of the mechanism of π-π interaction, and open an avenue to manipulate the relative position of extremely small objects down to the scale of single molecules.
View Article and Find Full Text PDFMethods for Studying Motor-Driven Viral DNA Packaging in Bacteriophages phi29, Lambda, and T4 via Single DNA Molecule Manipulation and Rapid Solution Exchange.
Methods Mol Biol
December 2024
Department of Physics, University of California San Diego, La Jolla, CA, USA.
Viral DNA packaging is a required step in the assembly of many dsDNA viruses. A molecular motor fueled by ATP hydrolysis packages the viral genome to near crystalline density inside a pre-formed prohead shell in ~5 min at room temperature in vitro. We describe procedures for measuring the packaging of single DNA molecules into single viral proheads with optical tweezers.
View Article and Find Full Text PDFIsolation and Analysis of Rare Enzymatic Events with Multiplex Flow Magnetic Tweezers.
Methods Mol Biol
December 2024
Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany.
Article Synopsis
- New techniques in biomolecular dynamics allow manipulation of forces at the single-molecule level, helping to advance our understanding.
- A newly developed method significantly increases the throughput of force spectroscopy, enabling analysis of thousands of molecules simultaneously, including rare enzymatic events.
- The chapter includes experimental procedures for studying DNA gyrase's supercoiling dynamics and introduces a software platform to classify dynamic behaviors, making it applicable to various complex enzymatic processes.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!