Transcription and RNA Processing

ID #2351

Could someone please explain intrastrand base pairing in each RNA- tRNA, mRNA and rRNA?

Single-stranded nucleic acids (like all types of RNA) have a phosphodiester backbone and exposed bases. These exposed bases are still hydrogen bond donors or acceptors that have no binding partners. When presented with the possibility of forming a base pair, the bases on single stranded nucleic acid molecule will do that. Nucleotides in single-stranded RNAs have the ability to form hydrogen bonds either with bases within the same strand (like tRNA) or with bases within another strand (like an anticodon binding to a codon). 
The same rules of base-pairing apply: The nucleotides must be complimentary (A binds U and G binds C) and the strands are running anti-parallel to each other. A perfect example of this is the "3-leaf clover" structure of tRNA. If you trace along from the 5' end of the tRNA molecule you will come across a stem where some of the bases have base paired with other bases. If you just label the directionality of the two components of the stem, you will see that they are the reverse compliment and that they do run antiparallel to each other. 
Intrastrand base pairing occurs in RNA all the time. It is more energetically favorable for RNA to "fold" into these stem-loop (or hairpin) structures than to float around in its single stranded form. Examples that we have seen in class specifically are the Rho-independent termination region in mRNA and tRNA. rRNA also exhibits this type of intrastrand base pairing and it tends to be very complex. 

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