Tag: dna

DNA memory

When stored on most conventional storage devices—USB pens, DVDs, or magnetic tapes—data starts to degrade after 50 years or so. DNA could hold data error-free for millennia, thanks to the inherent stability of its double helix and Reed-Solomon codes. If kept in the clement European air outside their laboratory in Zurich, they estimate a ballpark figure of around 2000 years. But place these glass beads in the dark at -18C, the conditions of the Svalbard Global Seed Bank on the Norwegian island of Spitsbergen, and you could save your photos, music, and eBooks for 2M.

and using CRISPR to store movies:

We use the CRISPR–Cas system to encode the pixel values of black and white images and a short movie into the genomes of a population of living bacteria. In doing so, we push the technical limits of this information storage system and optimize strategies to minimize those limitations. They also uncover underlying principles of the CRISPR–Cas adaptation system, including sequence determinants of spacer acquisition that are relevant for understanding both the basic biology of bacterial adaptation and its technological applications. This work demonstrates that this system can capture and stably store practical amounts of real data within the genomes of populations of living cells.

another approach:

Roswell is bringing the $100 genome that can scale rapidly and also deliver Exabyte data storage.

DNA rewriting for memory

We used to think that once a cell reaches full maturation, its DNA is totally stable, including the molecular tags attached to it to control its genes and maintain the cell’s identity. Some cells actually alter their DNA all the time, just to perform everyday functions

2021-08-30: DNA breaks for memory consolidation

When the team mapped genes undergoing double-strand breaks in the prefrontal cortex and hippocampus of mice that had been shocked, they found breaks occurring near 100s of genes, many of which were involved in synaptic processes related to memory. DNA breakage might be a regulatory mechanism in many other cell types. But even if breaking DNA is a particularly fast way to induce crucial gene expression, whether for memory consolidation or for other cellular functions, it’s also risky. If the double-strand breaks occur at the same locations over and over again and aren’t properly repaired, genetic information could be lost. Moreover, “this type of gene regulation could render neurons vulnerable to genomic lesions, especially during aging and under neurotoxic conditions. It is interesting that it’s used so intensively in the brain, and that the cells can get away with it without incurring damage that’s devastating.”

Centromeres are tricky

The scientists decided to return to the human genome and search for K111. They isolated DNA from their HIV patients, as well as from healthy people. Remarkably, the scientists didn’t find just 1 copy of K111 in each of their subject’s genomes, as is the case in chimps. The more the scientists looked, the more variants they found. Some K111 viruses were fairly intact, while others were vestiges. The scientists found over 100 copies of the virus in the human genome, scattered across 15 chromosomes.
This finding suggests that between 6 ma and 800 ka ago, K111 was duplicated a few times at a fairly slow pace. It’s possible that Markowitz and his colleagues missed some other copies because the reconstruction of those ancient genomes wasn’t quite accurate enough for their search. But even if we generously assumed that Neanderthals and Denisovans had 20 K111 viruses apiece, that’s still a small fraction of the 100 or more copies of K111 the scientists found in the human genome. It was only later, in the past 800 ka, that K111 started proliferating at a faster pace.

1 reason that K111 has gone overlooked till now is that it found a good place to hide–the center of chromosomes. This region, called the centromere, is a genomic Bermuda Triangle. It’s loaded with lots of short, repetitive stretches of DNA. When scientists reconstruct the sequence of a genome, they break DNA down into many overlapping segments, which they then try to rebuild based on overlapping similarities. Centromere DNA is so similar to itself that it’s easy to line up fragments in many different arrangements. As a result, centromeres make up much of the last 5% of the human genome that has yet to be mapped.

DNA bricks

A research team team used their “DNA–brick self–assembly” method, which was first unveiled in a 2012 Science publication when they created more than 100 3D complex nanostructures about the size of viruses. The newly–achieved periodic crystal structures are more than 1000x larger than those discrete DNA brick structures, sizing up closer to a speck of dust, which is actually quite large in the world of DNA nanotechnology.