Pincing vescicles with DNA

Welcome to Plenty of Room!

This week there are quite a few of new subscribers: welcome! And a huge thank you for being here.

Plenty of Room is your guide to the cutting-edge news related to molecular machines. New here? Just go ahead and subscribe! Already subscribed? Help a friend or a colleague save some time and share this with them!

Let’s get into it now.

Pinching vesicles with DNA

We all know that proteins are cool: they're essential to life, with an incredible diversity of functions, structures and roles. On the other hand, proteins are complicated: scientists have tried to develop simpler, synthetic equivalents for a while. And what better way to do this than to use DNA, a much easier material to use?

Today’s paper focuses on the interactions between DNA origami and synthetic cells, specifically giant vesicles, mimicking how proteins interact with membranes in well, biological cells. The researchers designed DNA origami pinchers: nanopyramids consisting of three interlinked DNA bundles that can adjust their angles with the help of specific DNA strands. These structures are dynamic and can multitask on the vesicle surfaces.

But what can they actually do? Let’s break it down:

• Morphology control: The pinchers can dynamically adjust their pinching angles while on the vesicles. When this angle is reduced, the nanostructure creates a force on the lipid membrane, reshaping the vesicles and reducing their roundness, similar to how proteins can manipulate cell membranes. This ability can be adjusted stepwise, allowing quite precise control of the shape and morphology of the vesicles.

• Oligomerization and cage formation: The nanopinchers can join together on the membrane surface to create cage-like structures. These cages can capture fragments of the lipid bilayer from the vesicles, creating smaller compartments from the vesicles.

• Membrane disruption: Last but not least, the oligomerization of the structures has a side effect: creating transient pores in the membranes. These pores, typically less than 10 nm in size, allow molecules to move in and out of the vesicles, allowing cargo to move across the membrane.

So, in short, this study shows how DNA origami can be used to manipulate synthetic cells at the nanoscale, just like proteins do, but with far less complexity. The versatility of these structures is what really sets them apart from previous efforts: I think it is particularly interesting to see if similar structures are combined with proteins or aptamers to create smart materials that respond to environmental changes.

Read the whole story here!

In other news:

• Tuning triangular pores: Nanopores are all the rage these days. In this paper, the team presents a tunable triangular DNA nanopore, that can switch between two conformations. They also showed that the nanopore could provide low-noise, repeatable readouts and control the transport of macromolecules across membranes-.

• A prime look into genome editing: I love structural biology papers, because they have the best images. This paper adds to that an explanation for how prime editor systems work and why they can make mistakes when editing. Definitely worth a read!

• Language models explained: Are you, just like me, trying to figure out exactly what language models could mean for biology? Well, then maybe this primer will be of help! It’s high in the list of my next reads for sure.

• Not yet a subscriber to Plenty of Room? Sign up today — it’s free!

• You think a friend or a colleague might enjoy reading this? Don’t hesitate to share it with them!

• Have a tip or story idea you want to share? Email me — I’d love to hear from you!

• You have something you would love me to cover? Just reach out here or on my social!