Polymerase stuttering
From Wikipedia, the free encyclopedia
Polymerase stuttering is the process by which a polymerase transcribes a nucleotide several times without progressing further on the mRNA chain. It is often used in addition of poly A tails or capping mRNA chains by less complex organisms such as viruses.
[edit] Process
A polymerase may undergo stuttering as a probability controlled event, hence it is not explicitly controlled by any mechanisms in the translation process. Generally, it is a result of many short repeated frameshifts on a slippery sequence of nucleotides on the mRNA strand[1]. However, the frameshift is restricted to one (in some cases two[2]) nucleotides with a pseudoknot or choke points on both sides of the sequence.
An example of the process is denoted below, with P representing a polymerase:
Step 1
--->P ATCGTAGCAAATCGTAA } Original strand ATCGT } Growing new strand
Step 2
--------------->P ATCGTAGCAAATCGTAA } Original strand ATCGTAGCAAATCGTAA } Growing new strand
Step 3
P<- } Polymerase slips back one ATCGTAGCAAATCGTAA } Original strand ATCGTAGCAAATCGTAA } Growing new strand
Step 4
->P } Transcribes another A ATCGTAGCAAATCGTAA } Original strand ATCGTAGCAAATCGTAAA } Growing new strand
Note: Step 3 & 4 is repeated and new nucleotides are added to the 3' end.
[edit] Examples
A polymerase that exhibits this behavior is RNA-dependent RNA polymerase, present in many RNA viruses. Reverse transcriptase has also been observed to undergo this polymerase stuttering[3].
[edit] Literature
- ^ Anderson EC, Hunt SL, Jackson RJ. "Internal initiation of translation from the human rhinovirus-2 internal ribosome entry site requires the binding of Unr to two distinct sites on the 5' untranslated region." J Gen Virol. 2007 Nov;88(Pt 11):3043-52.
- ^ Mauro VP, Chappell SA, Dresios J. "Analysis of polymerase shunting during translation initiation in eukaryotic mRNAs." Methods Enzymol. 2007;429:323-54.
- ^ Kurzynska-Kokorniak A, Jamburuthugoda VK, Bibillo A, Eickbush TH. "DNA-directed DNA polymerase and strand displacement activity of the reverse transcriptase encoded by the R2 retrotransposon." J Mol Biol. 2007 Nov 23;374(2):322-33. Epub 2007 Sep 20.