Difference between the 2 bases pairs

[scope]

hi,

i wonder if there is any clear chemical difference between the bases pairs CG and AT? is one more reactive than the other one for example? is there any chemical difference that is used? i would be very grateful for any reply!

thanks!

 

[Jack the Stri]

G and C form three hydrogen bonds, A and T form two, and they both differ in the display of (partially) charged groups in the grooves.

 

[scope]

wonderful, and what are the chemical consequences for this? more stability for one ? can you tell me anything like this? this seems so fascinating!

 

[Jack the Stri]

GC pairs are indeed more stable, and the difference in groove display allows specific enzymes to recognise specific DNA sequences, very useful for controlling gene expression.

There are also chemical consequences of the order of the base pairs, e.g. GC repetitions can cause 'slipping' of the DNA replication machinery and thus cause the size of the repetition to vary in subsequent divisions.

 

[scope]

wonderful. but then if they are most stable, maybe CG is more abundant than AT? since stability is related to abundance?

 

[Jack the Stri]

Well, you must take into account that DNA has to be able to open its strands in order to replicate or produce an mRNA molecule. Therefore, too high stability is detrimental. In organisms living at higher temperatures, there is a bias towards G/C instead of A/T in certain parts of the genetic code.

 

[scope]

wonderful! does the same occur for RNA if we compare CG and AU?

 

[bobze]

wonderful! does the same occur for RNA if we compare CG and AU?

RNA is more complicated because it normally is "single" stranded. However, it can fold back on itself providing more stability through base-pairing. This can increase the shelf-life of mRNAs or adds the functionality to functional RNAs.

I reckon, if you were to look, you'd find a higher GC content to functional RNAs or mRNAs (particularly in the 5' and 3' NCRs) with long shelf lives. Its also compounded by proteins which bind RNA can increase their longevity.

 

[Jack the Stri]

This is also valid for RNA/DNA hybrids, as seen in polyA tracts at the end of mRNA molecules. Since these are thermodynamically less stable, the mRNA strand can more easily release from the DNA template. Of course, this has evolved to exert multiple functions throughout time, but it's unofficially generally accepted that this was the original reason for the terminating polyA sequence.

 

[mishrashubham]

Helicases, which are a class of enzymes,start splitting the DNA apart during replication at places rich in A-T pairs because they form 2 hydrogen bonds compared to 3 of G-C bonds. Therefore they are easier to break and require less energy.