Akanksha Yadav @akankshay58@qoto.org

Neat single-molecule experiments!

Two-component molecular motor driven by a GTPase cycle | Nature Physics
https://www.nature.com/articles/s41567-023-02009-3
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RT @stpalli
The mechanism of this new motor is distinct from conventional ones.

Unlike motors such as Kinesin, it runs on GTP not ATP.

Also, the motor has no "power stroke" motion of one protein domain relative to another, but relies on a sudden change in the stiffness of the en…
https://twitter.com/stpalli/status/1654141624933335048

Tried tracing trends: concept, molecules, methods
(via word search on PubMed)

So very cool!
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RT @CellRaiser_
MinDE circuits produce a unique signal that acts like a “cellular radio”, emitting frequency-barcoded data that can spectrally separate single cells or sub-cellular compartments using digital signal processing tools like FFTs, FIR filters, or wavelets with a single fluorophore.
https://twitter.com/CellRaiser_/status/1592909960157237249

‘The functions of an engineer’ from Nature 1900 issue, an address by Sir William Henry Preece, on being an engineer, printing, engineering/tackling bacteria!
https://www.nature.com/articles/061374b0

#DNAnanotech #preprint
4 DNA origami structures (helix-bundles and ring) used as scaffolds to initiate assembly of CCMV^ (virus) coat protein, takeaways -
- capsid shape, size control
- DNA encapsulation (nuclease resistant)
- tubular origami structure preferred, negative curvature not well tolerated

*imagining 🪆*
^CCMV's reversible assembly process is well characterized, pH/ionic strength control --> formation of hexagonal sheets, tubes

Building on prior work (from the same lab) 2014,
https://pubs.acs.org/doi/abs/10.1021/nl500677j

DNA origami directed virus capsid polymorphism @biorxivpreprint https://biorxiv.org/content/10.1101/2022.11.07.515152v1

Unrelated (or not), also appending an ode to the thought of a connection my brain made while reading the above with the following figure from https://www.nature.com/articles/s41592-020-0869-x
5/n

Steps involved -
- rolling circle amplification of DNA -> concatemers on flowcell
- imaging 🐙 ie 'avidite': a dye labeled polymer with multiple, identical nucleotide attached -> binds multiple nucleotides across DNA copies
- washing with 🐙 intact -> detection
- remove 🐙 (since held by non-covalent interaction)
- extend 1 base with polymerase + unlabeled, blocked nucleotide
- remove block, repeat

Undiscussed but personally curious about 🐙 design.
4/n

Avidity in this context implies the cumulative strength of multiple base pair interactions as opposed to single base pair binding events that SBS relies on.

Stronger interaction means lower substrate concentration needed and longer residence time ➡️ enables imaging without bond formation

Some nice biochemical characterization summarized in the figure below from the paper to crunch kinetic rates from -
3/n