Thread: DNA Domains

Hi, since RNA is synthesised initially from DNA which amongst the process RNA splicing occurs. The exons are stitched together leaving the free introns which are later removed from the nucleus to be degraded. These introns at some point had been synthesised from DNA so I was wondering if it was plausible that these introns in the nucleus could correspond and bind with the bases in the DNA to establish domains?

Chromosomal DNA is double-stranded and the intron is single-stranded RNA, while the nucleotide base-sequence would be complementary to the opposite strand from which it was transcribed from, it would not be able to base pair with it as the DNA nucleotide's are double-stranded and already paired. I also imagine that the introns are removed from the nucleus by RNA-binding proteins that transport it through the nuclear pore and into the cytoplasm, perhaps the same proteins that transport the mRNA into the cytoplasm; i.e., they wouldn't be left to freely float around the nucleus.

yes that is true, but a domain is created by a unspecified molecule that bonds between a base pair from a double stranded helicase of DNA to another basepair further along that helicase creating a looped domain. So if by initially basepairing in a double stranded DNA helicase ,which I think would mean thats it is the primary structure of the DNA, creates complete non-polarity or nuetralization (whichever one) therefore it would never be able to form domain loops or secondary structures or tertiary structure, like compact chromosomes. you are right though, the introns that have been cleaved from the exons during RNA splicing and are later removed/ transported from the nucleus to a lysozome to be degraded to mono-subunits or something like that.

Sorry, I'm having difficulties understanding your terminology. A helicase is an enzyme that unwinds double-stranded DNA. Are you referring to the secondary structure of RNA molecules? Compact chromosomes are formed by an interaction between the DNA and histone proteins.

Sorry I ment helice not helicase. No I was refering to the sec-/ tert- of DNA. I was saying that if the double stranded helice of DNA is completely non-polar/ non-reactive by the base pairing between the two DNA strands that form the double stranded helice then how would there ever be looped domains in the strand/ helice. Since looped domains are created by an unspecifide molecule which bonds between one base pair on the strand to another base pair further along that strand creating a loop. So the helix which is a double stranded helice or chain that twists. The histones do shape the chromosomes but they don't form the domain. you basically have a helix with loops in it which I think is the secondary structure of DNA but don't hold me to it, the primary structure of DNA is a simple double helice chain and a chromosome is the tertiary or quaternary structure of DNA which is the looped domained DNA chain which are then formed as part of the chromatin which is DNA and protein (histone), the chromatin fibre is in a condensed/compact structure which is a chromosome. You will have to excuse my writting as I'm very tired because it is 1:50 am over here. Back to the main point of all this though. I was unfortunately having a good think about this while I was trying to sleep. The single stranded short segement of RNA (intron), becuase its not based with another strand its polar charge would be higher/stronger then the direct area in which the domain is formed. So for it to be an intron, the intron would have to be basepaired with another intron to have an equal strength of charge but of opposites of course to the DNA point where the domain is formed. This interaction of two introns base pairing seems unlikely and even if it occured the segements are too short and the hydrogen bonds are too weak for it to maintain this before it can attach to the DNA. Therefore even if this was to occur the introns would too quickly unzip and by that time a transport protein would be in close enough range to attach to the intron which would then be exported. Surely though the unspecified molecule would have to be some sort of molecule that is already known, since the nucleus is highly selective of what goes in and what goes out, and that there has be numerous research on the import and export through the nucleur pores. I don't understand why the cell would evolve over billions of years to include something as splicing, it seems like such a pointless waste. But then again the cell always keeps genes even after the species has evolved to the point of not needing them becuase it is easier to store the genes rather then continue to sort through and discard unneeded ones. Maybe this is why there are introns I don't know.

Hi Awals,

I'm afraid I don't understand much of what you have included in this post, which may be due my own ignorance. Please excuse me for this, but I will comment on the parts that are more familiar. As spoonman has pointed out, it seems very unlikely that a bit (excuse the pun) of intronic RNA would interact with DNA of the double helix, since the DNA is already base-paired.

I don't understand why the cell would evolve over billions of years to include something as splicing, it seems like such a pointless waste.

It effectively allows multiple mRNAs to be encoded by a single stretch of DNA.
I was unfortunately having a good think about this while I was trying to sleep.

Hope this helps,

Tridimity.

It effectively allows multiple mRNAs to be encoded by a single stretch of DNA

Well that makes a lot sence, thankyou for the help.

I still feel as though its not because the DNA is already base paired because if this was the case then there would no such thing as a domain. A domain is created by a molecule bonding to a base pair in a DNA chain to another base pair in that same DNA chain which forms a loop. If DNA wasn't looped by that molecule thereby forming domains then the protien histone would be less effective in compacting the DNA into the chromosome structure that is known. I feel as though the intron would be implausable to use in creating a domain simply because the charge of an intron would be completely inappropriate. Because the DNA is already base paired, defies how a domain is created therefore the problem is not with the DNA strand at all, its with the intron.

Oh I see the problem here, in my initial statement I had confused prokaryotic domain loops with eukaryotic domain loops. Prokaryotic DNA is most commonly circular and its domains are formed by an unspecified molecule. Where eukaryotic DNA is linear (chain) and its domains are formed by nonhistone proteins bonded at the DNAs base.