Polymerase stuttering

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.

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.

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]

Literature

Anderson, EC; Hunt, SL; Jackson, RJ (Nov 2007). "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. 88 (11): 3043–52. doi:10.1099/vir.0.82463-0.
Mauro, VP; Chappell, SA; Dresios, J (2007). "Analysis of polymerase shunting during translation initiation in eukaryotic mRNAs". Methods Enzymol. 429: 323–54. doi:10.1016/s0076-6879(07)29015-9.
Kurzynska-Kokorniak, A; Jamburuthugoda, VK; Bibillo, A; Eickbush, TH (Nov 2007). "DNA-directed DNA polymerase and strand displacement activity of the reverse transcriptase encoded by the R2 retrotransposon". J Mol Biol. 374 (2): 322–33. doi:10.1016/j.jmb.2007.09.047. PMC 2121658. PMID 17936300.

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[1] Anderson, EC; Hunt, SL; Jackson, RJ (Nov 2007). "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. 88 (11): 3043–52. doi:10.1099/vir.0.82463-0.

[2] Mauro, VP; Chappell, SA; Dresios, J (2007). "Analysis of polymerase shunting during translation initiation in eukaryotic mRNAs". Methods Enzymol. 429: 323–54. doi:10.1016/s0076-6879(07)29015-9.

[3] Kurzynska-Kokorniak, A; Jamburuthugoda, VK; Bibillo, A; Eickbush, TH (Nov 2007). "DNA-directed DNA polymerase and strand displacement activity of the reverse transcriptase encoded by the R2 retrotransposon". J Mol Biol. 374 (2): 322–33. doi:10.1016/j.jmb.2007.09.047. PMC 2121658. PMID 17936300.