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A hybrid G-quadruplex structure formed between RNA and DNA explains the extraordinary stability of the mitochondrial R-loop

Journal article
Authors Paulina Wanrooij
Jay Uhler
Yonghong Shi
Fredrik Westerlund
Maria Falkenberg
Claes M Gustafsson
Published in Nucleic Acids Research
Volume 40
Issue 20
Pages 10334-10344
ISSN 0305-1048
Publication year 2012
Published at Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology
Pages 10334-10344
Language en
Keywords human pif1 helicase, binding protein, transcription termination, primer, formation, strand origin, in-vitro, replication, polymerase, sequence, twinkle
Subject categories Cell and molecular biology


In human mitochondria the transcription machinery generates the RNA primers needed for initiation of DNA replication. A critical feature of the leading-strand origin of mitochondrial DNA replication is a CG-rich element denoted conserved sequence block II (CSB II). During transcription of CSB II, a G-quadruplex structure forms in the nascent RNA, which stimulates transcription termination and primer formation. Previous studies have shown that the newly synthesized primers form a stable and persistent RNA-DNA hybrid, a R-loop, near the leading-strand origin of DNA replication. We here demonstrate that the unusual behavior of the RNA primer is explained by the formation of a stable G-quadruplex structure, involving the CSB II region in both the nascent RNA and the non-template DNA strand. Based on our data, we suggest that G-quadruplex formation between nascent RNA and the non-template DNA strand may be a regulated event, which decides the fate of RNA primers and ultimately the rate of initiation of DNA synthesis in human mitochondria.

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