iiinova — where your digital self keeps evolving

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

If you made it this far, thanks for reading - we hope you like our paper! For other related work of ours, see myhrvoldlab.com. (26/26)

myhrvoldlab.com

Myhrvold Lab

Myhrvold Lab in the Princeton Molecular Biology Dept.

010

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

A huge thank you to all the co-authors involved (Ofer, Ben, Emily, and AJ (@ajtevelthuis.bsky.social)), and to funding from NIH, the Princeton Catalysis Initiative, and the Branco Weiss Fellowship (to Ofer). Working with such talented people is one of the best parts of my job! (25/26)

111

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

Finally, our IT model is very simple, requiring >1 nonspecific binding patch on the protein surface (which could just be a patch of positive residues), so we think that ITs could be a general mechanism used by RBPs to make them more efficient. (24/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

In future work, we are excited to explore how secondary structure and other factors influence Cas13 search in cells. I am sure there is a lot to discover there! (23/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

In summary, Cas13 uses intersegmental transfers to efficiently find its target RNA, which acts as a length filter, thereby biasing it towards longer RNAs, which are more likely to be of phage origin. (22/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

More broadly, we find that ITs for RNA can dramatically speed up the search relative to 1D sliding or ITs for DNA. This effect is more pronounced at high ratios of non-target to target RNA, which is likely the case for all but the most highly-expressed target RNAs. (21/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

ITs let Cas13 quickly fall off short RNAs and spend more time on long RNAs. Bacteriophage mRNAs tend to be longer than typical bacterial RNAs, so we think that ITs help as a ‘length filter’ to make Cas13 target bacteriophage RNAs more efficiently. (20/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

As one last piece of evidence for ITs, we used biolayer interferometry to show that adding non-target RNA increases the dissociation rate of a Cas13-crRNA-target complex by about a factor of 3. (19/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

However, in scenario 3, we see Cas13 activity is high again! In this case we think that Cas13 can transfer from the longer RNA to the shorter RNA. Such a configuration would not speed up a search based on 1D sliding. (18/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

To test the intersegmental transfer hypothesis directly, we set up an experiment where Cas13 can bind to (1) a long target RNA, (2) a short target, or (3) a complex of a short and long target. As expected, scenario 1 has high activity and scenario 2 has low activity. (17/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

Our modeling work shows that ITs can bias a protein towards binding longer RNA molecules, depending on the ratio of the distance between the sites (l) and the typical length over which RNA is flexible (b). (16/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

Our results are consistent with a model for ITs using parameters relevant to RNA. This is because RNAs are *much* more flexible than DNAs, with a ~50x shorter persistence length. This allows the RNA to reconfigure more easily, and more quickly. (15/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

To test this experimentally, we sonicated a long nontarget RNA, producing many short RNAs. Models assuming 1D sliding or intracoil diffusion predict this should slow down search. However, we saw that sonication increased Cas13 activity! (14/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

During this transient binding, the nucleic acid reconfigures, which allows for the protein to move a long distance along the nucleic acid. However, ITs are relatively inefficient for searching DNA as dsDNA is very stiff. So, does Cas13 use ITs to search for its RNA target? (13/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

We are particularly intrigued by intersegmental transfers (ITs) which were first postulated by von Hippel and colleagues in 1975. ITs involve a protein using multiple non-specific binding patches to ‘monkey bar’ from one part of a nucleic acid to another. books.google.com/books?hl=en&... (12/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

Intracoil diffusion involves the protein dissociating and then rebinding to the same nucleic acid molecule. One study on Argonaute argues that intracoil diffusion plays an important role in its search process. www.sciencedirect.com/science/arti... (11/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

1D sliding involves a protein nonspecifically associating with a nucleic acid and moving along it bidirectionally. In this way, a 3D random walk shifts to 1D, which is more efficient over short distances. TFs, Cas9, and Cas12 all use 1D sliding. www.bmbreports.org/journal/view... (10/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

Once we established that Cas13 uses facilitated diffusion, we next asked which mechanism (1D sliding, intracoil diffusion, or intersegmental transfers) Cas13 uses. Each mechanism makes quantitatively different predictions about how target length affects search. (9/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

We tested this hypothesis experimentally and saw that lower [NaCl] actually *increased* Cas13 activity, implying that facilitated diffusion is involved. For more on this, see von Hippel and Berg (1989): www.sciencedirect.com/science/arti... (8/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

Then, we asked how salt concentration ([NaCl]) affects Cas13 activity. Nucleic acids have negative charge, and Cas13 has positive charge, so in the absence of facilitated diffusion lower [NaCl] should monotonically decrease Cas13 activity due to longer dwell times. (7/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

Next, we measured Cas13 activity when targeting RNA of different lengths. If Cas13 uses 3D diffusion alone, we would expect that longer targets would slow down the search (as there are more off-target sites to bind to), but in fact we saw the opposite! (6/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

First, we measured Cas13 activity in the presence of varying concentrations of “background RNAs” that do not contain the protospacer. Background RNA slowed down Cas13 substantially. (5/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

We use Cas13 as a model RBP as it must function quickly to combat bacteriophage infection, and it is easy to measure Cas13 activity in high throughput using a quenched fluorescent RNA reporter. (4/26)

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

Previous work on transcription factors (TFs) has shown that they can operate faster than the 3D diffusion limit, typically by performing 1D sliding along DNA. Some RNA-binding proteins (RNase E, Hfq, Argonaute) also use 1D sliding. www.sciencedirect.com/science/arti... (3/26)

sciencedirect.com

How do proteins locate specific targets in DNA?

Many aspects of biology depend on the ability of DNA-binding proteins to locate specific binding sites within the genome. Interest in this target sear…

100

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

RNA is more challenging to search through than DNA as there are so many RNA molecules in a cell. Also, RNAs are very heterogeneous in length, flexible, and structured. So we wondered: how can RBPs efficiently find their targets amid a sea of other RNAs? www.biorxiv.org/content/10.6... (2/26)

biorxiv.org

Intersegmental transfers drive target search in an RNA-targeting CRISPR system

Sequence-specific RNA-binding proteins (RBPs) must efficiently locate their targets among a multitude of cellular RNAs. Cas13, an RNA-guided CRISPR protein, represents an ideal model system in which t...

131

Cameron Myhrvold @cambearon.bsky.social · 19/06/2026

Over the past 50 years, we have learned much about how transcription factors and other DNA-binding proteins search for their targets, but we know much less about how sequence-specific RNA-binding proteins (RBPs) search for their targets. 🧵⤵️ (1/26)

184

Cameron Myhrvold @cambearon.bsky.social · 15/08/2025

My lab has developed mSHINE, allowing for both highly multiplexed and portable nucleic acid detection. Very exciting work led by the talented @sijbren-kramer.bsky.social, who is off to do a PhD at Stanford at the end of the month!

041

Reposted by Cameron Myhrvold

Sijbren Kramer @sijbren-kramer.bsky.social · 15/08/2025

Multiplexed nucleic acid detection is critical for the surveillance of pathogens and mutations, but existing technologies either require extensive lab equipment or have low multiplexing. We built a portable microfluidic manifold for massively multiplexed CRISPR-based detection. (1/12)

biorxiv.org

A handheld microfluidic manifold for massively multiplexed CRISPR-based nucleic acid detection

Multiplexed methods for nucleic acid detection are immensely challenging to deploy outside of laboratory settings. Conversely, field-deployable methods are limited to low levels of multiplexing. Durin...

112

Cameron Myhrvold @cambearon.bsky.social · 07/08/2025

Our latest paper using SHINE for TB detection directly from sputum just came out in Science Advances! See the thread from co-first author Alex Bell for more details...

000

Cameron Myhrvold @cambearon.bsky.social · 24/06/2025

NYC is not a stretch: Rockefeller, Columbia, NYU, Weill Cornell...

020

Cameron Myhrvold @cambearon.bsky.social · 29/05/2025

Well, meese are not very good drivers, so what did you expect?

020