Can gene structure determine its "strength"?

[icakeov]

Are certain DNA (genetic) strands structurally better build for survival than others?
If yes, is there a term for this?

For example, is there a specific order of nucleotides that is harder to destroy than another?
Or if there is a specific order/combination of nucleotides that would have higher potency to replicate than some other? Or for example, that it would be easier to replicate a specific DNA into vast number of replicas, all purely because of its structure.

Hope that was a clear question, I tried googling this and didn't find an answer that specifically addresses this issue.

Thanks!

 

[Calaver]

Well, I'm not an expert on this subject, but since no one else has replied, I'll give it a shot.

If you are asking about whether some genes are better built for survival in their expression, then yes, that's called survival of the fittest.

But it sounds like you're asking about the structural component of DNA survival specifically. To be honest, I don't know. But, it seems that such effects would be quite negligible when compared to, say, damage from UV radiation. Nonetheless, there are several errors that can happen during replication. Upon further research, I found that these shifts seem to be called tautomeric shifts, and these shifts seem to be affected by whether there is an acid or a base present. So possibly, based upon the abundance of a certain molecule within a strand of DNA, the DNA might have a higher percent of it that becomes mutated if a certain acid or base was with a higher abundance of the right molecule in the strand. So it seems that the structural survival of DNA would depend more on ratio of the kinds of molecules present, instead of the order of the molecules.

This is just my hypothesis, and I'm not sure of it's validity, so take it as a grain of salt until someone with more knowledge replies.

 

[jim mcnamara]

I think you are asking: is there a sequence of nucleotides that is more resistant to environmental damage than another sequence? Or asked another way: A-A-A-A and A-T-A-T are two nucleotide sequences. Is one more stable in a living cell than another?

Yes? No?
There is a LOT of data on environmental damage to living DNA. We call it variously mutation rate, mutagenesis, teratogensis, carcinogenesis. I do not know if the differences you mention play that much of a role since random mutations mostly just kill outright modern living cells in culture. The survivors are the ones with slightly more resistant DNA sequences from your point of view. Survival because of random chance is more likely in this cell culture context.

Here is a maybe-why-answer :

Life on Earth persists - and in horrible extremes from a mammalian worldview. Extremophiles - beasties that live by oxidizing metals on the surface of rocks. Or in ice, in solid rock deep in the crust, in undersea volcanic vents, and in pH ranges that would kill humans quickly. These little guys have nucleotides like us. They apparently have been around literally since the early emergence of life on Earth. Their nucleotide sequences are stable enough to have endured multiple billion years of otherwise awful conditions. Human mitochondrial nucleotide sequences are similar to theirs. You have "vestigial" DNA in your mitochondria originally derived from Procaryotes a billion years ago. Or more. It even looks like bacterial DNA - it is a plasmid (a ring shape not a chromosome). Some early cells grew better in the company of other different cells - maybe the way lichens "work" now - fungus like cells mixed with algae.

One day the progenitors of Eukaryotes merged together literally and became cells well adapted to the rising oxygen levels in the atmosphere. 2 billion years ago? Don't know.

We are living examples of those little beasties exemplified as colonial organisms. Mitochondria are a feature of Eukaryotes - which have been around for a billion+ years. So your very own mitochondrial DNA could answer your question - if you could figure out how it has evolved from more than 1+ billion years ago.

So I do not know how useful/meaningful the answer you are seeking really is. I would say that Natural Selection had already severely tested that - probably 3+ billion years ago. Our mitochondia give sort of an answer. This is closer to @Ygggdrasil 's home turf. Maybe we can get a definitive answer there.

 

[Ygggdrasil]

Well, I may not be able to provide a definitive answer, but I'll try to address the question as best I can. There are a couple of different potential questions here:
1) DNA sequences that are beneficial to the survival of an organism will persist through natural selection. There are no general means to predict how a specific DNA sequence will affect the fitness of an organism.
2) Are there DNA sequences that are more prone to damage than others? Certain mutational processes affect certain sequences more often than others. For example, CpG sequences are especially prone to mutations in many vertebrate species (https://en.wikipedia.org/wiki/CpG_site#Frequency_in_vertebrates) because the cytosine residues in CpG dinucleotides get methylated and a common form of DNA damage (deamination) will turn a methyl-C into a T residue. There may be other such examples of sequences prone to mutation.
3) Are there specific sequences that can promote their own self-propagation? Yes. These elements are sometimes referred to as selfish genetic elements or transposable elements and comprise things such as endogenous retroviruses, transposons, and repetitive elements. These are quite common in many genomes and make up ~ 50% of the human genome (many plants, like maize can have up to 90% of their genomes consisting of such elements). Using newly developed CRISPR technologies, scientists have also engineered synthetic selfish genetic elements called gene drives.

 

[Calaver]

Well, I may not be able to provide a definitive answer, but I'll try to address the question as best I can. There are a couple of different potential questions here:
1) DNA sequences that are beneficial to the survival of an organism will persist through natural selection. There are no general means to predict how a specific DNA sequence will affect the fitness of an organism.
2) Are there DNA sequences that are more prone to damage than others? Certain mutational processes affect certain sequences more often than others. For example, CpG sequences are especially prone to mutations in many vertebrate species (https://en.wikipedia.org/wiki/CpG_site#Frequency_in_vertebrates) because the cytosine residues in CpG dinucleotides get methylated and a common form of DNA damage (deamination) will turn a methyl-C into a T residue. There may be other such examples of sequences prone to mutation.
3) Are there specific sequences that can promote their own self-propagation? Yes. These elements are sometimes referred to as selfish genetic elements or transposable elements and comprise things such as endogenous retroviruses, transposons, and repetitive elements. These are quite common in many genomes and make up ~ 50% of the human genome (many plants, like maize can have up to 90% of their genomes consisting of such elements). Using newly developed CRISPR technologies, scientists have also engineered synthetic selfish genetic elements called gene drives.

Very interesting! I thought 2 could be a possibility but couldn't find anything to verify it, and I've never heard much about the concept in 3! Thanks for posting this info with the links!

 

[icakeov]

Thank you so much for all your answers everyone, amazing feedback!
@Ygggdrasil yes that you hit it on the dot, especially point 2 and then 3 to follow up.