Mapping the nicking efficiencies of nickase R.BbvCI for side-specific LNA-substituted substrates using rolling circle amplification

Sequencing and Optical Genome Mapping for the Adventurous Chemist

This review provides a comprehensive overview of the chemistries and workflows of the sequencing methods that have been or are currently commercially available, providing a very brief historical introduction to each method. The main optical genome mapping approaches are introduced in the same manner, although only a subset of these are or have ever been commercially available. The review comes with a deck of slides containing all of the figures for ease of access and consultation.

Single-molecule mechanical study of an autonomous artificial translational molecular motor beyond bridge-burning design

A key capability of molecular motors is sustainable force generation by a single motor copy. Direct force characterization at the single-motor level is still missing for artificial molecular motors, though long reported for their biological counterparts. Here we report single-molecule detection of sustained force-generating motility for an artificial track-walking molecular motor capable of autonomous chemically fueled operation. A single motor plus its track (both made of deoxyribonucleic acids or DNA) is assembled, operated and detected under magnetic tweezers by a method designed to overcome difficulty from the motor's soft double-stranded track. The motor shows self-directed walking by ∼16 nm steps up to a distance of 120 nm (covering the entire track), yielding a stall force of ∼2-3 pN. These results imply a reasonably efficient chemomechanical conversion of the motor compared to a high-efficiency biomotor. The stall force is near the level of translational biomotors powering human muscles and allows similar force-demanding applications by their artificial counterparts. This single-motor study reveals fast subsecond steps, suggesting big room for improvement in the speed of DNA motors in general. Besides, the established single-molecule method is applicable to force measurements of many other DNA motors with soft tracks.

Screening substrate-binding positions by rolling circle amplification suggesting a binding model of Nt.BstNBI

Nicking endonucleases (NEs) become increasingly attractive for their promising applications in isothermal amplification. Unfortunately, in comparison with their applications, their catalytic mechanism studies have relatively lagged behind due to a paucity of crystal structure information. Nt.BstNBI is one of those widely used NEs. However, many aspects of its catalytic mechanism still remained to be explored. Herein, we employed only rolling circle amplification (RCA) assay as a major analytic tool and succeeded in identifying the potential binding positions and regions of the DNA substrate based on locked nucleic acid modification, DNA duplex length of substrate, and substrate mismatch designs. Based on these data, we, for the first time, revealed that Nt.BstNBI was likely to recognize six adjacent positions of the recognition sequence (G1rt, A2rt, G3rt, A2rb, C3rb, and T4rb) in the major groove and hold three positions of the cleavage sequence (N3ct, N4ct, and N7cb) in the minor groove of DNA duplex for nicking. Moreover, this work also demonstrated the unexpected efficiency of RCA to study the macromolecular interaction for certain kind of nucleases in an easy and high-throughput way.

Screening oligonucleotide sequences for silver staining and d-galactose visual detection using RCA silver staining in a tube

Oligonucleotides were screened for strongly silver-stained repetitive sequences. An 'AG'-clustered purine sequence showed strong staining, and the staining density can be compromised by disrupting the continuity of the 'AG'-clustered sequence. The staining-favored sequence was then employed in rolling circle amplification (RCA) for its product detection. A tube-staining method was developed for convenient and visual RCA assay. Moreover, by introducing GalR into RCA, d-galactose was detected by RCA tube-staining with naked eyes without any equipment. About 10 mM d-galactose can be easily identified, and the detection of d-galactose was specific in comparison with that of several other monosaccharides.