Asymmetric structure of five and six membered DNA hairpin loops

ABSTRACT A subset of cellular DNA hairpins at double-strand breaks is processed by DNA-dependent protein kinase catalytic subunit (DNA-PKcs)- and Artemis-associated endonuclease. DNA hairpin termini of adeno-associated virus (AAV) are processed by DNA repair machinery; however, how and what cellular factors are involved in the process remain elusive. Here, we show that DNA-PKcs and Artemis open AAV inverted terminal repeat (ITR) hairpin loops in a tissue-dependent manner. We investigated recombinant AAV (rAAV) genome metabolism in various tissues of DNA-PKcs- or Artemis-proficient or -deficient mice. In the absence of either factor, ITR hairpin opening was impaired, resulting in accumulation of double-stranded linear rAAV genomes capped with covalently closed hairpins at termini. The 5′ end of 3-base hairpin loops of the ITR was the primary target for DNA-PKcs- and Artemis-mediated cleavage. In the muscle, heart, and kidney, DNA-PKcs- and Artemis-dependent hairpin opening constituted a significant pathway, while in the liver, undefined alternative pathways effectively processed hairpins. In addition, our study revealed a Holliday junction resolvase-like activity in the liver that cleaved T-shaped ITR hairpin shoulders by making nicks at diametrically opposed sites. Thus, our approach furthers our understanding of not only rAAV biology but also fundamental DNA repair systems in various tissues of living animals.

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Folding of Intramolecular DNA Hairpin Loops: Enthalpy−Entropy Compensations and Hydration Contributions

The Journal of Physical Chemistry B ◽

10.1021/jp0260853 ◽

2002 ◽

Vol 106 (38) ◽

pp. 9945-9950 ◽

Cited By ~ 15

Author(s):

Dionisios Rentzeperis ◽

Ronald Shikiya ◽

Souvik Maiti ◽

James Ho ◽

Luis A. Marky

Keyword(s):

Dna Hairpin ◽

Hairpin Loops

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Targeting DNA Hairpin Loops with their Partially Complementary Strands

Biophysical Journal ◽

10.1016/j.bpj.2009.12.3600 ◽

2010 ◽

Vol 98 (3) ◽

pp. 656a

Author(s):

Hui-Ting Lee ◽

Carolyn Carr ◽

Hollie Siebler ◽

Irine Khutsishvilli ◽

Luis A. Marky

Keyword(s):

Dna Hairpin ◽

Hairpin Loops

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An extended APOBEC3A mutation signature in cancer

Nature Communications ◽

10.1038/s41467-021-21891-0 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Adam Langenbucher ◽

Danae Bowen ◽

Ramin Sakhtemani ◽

Elodie Bournique ◽

Jillian F. Wise ◽

...

Keyword(s):

Secondary Structure ◽

The Other ◽

Twin Paradox ◽

Cancer Evolution ◽

Dna Hairpin ◽

Sequence Preference ◽

Mutational Hotspots ◽

Hairpin Loops ◽

Cancer Genomes ◽

Driver Event

AbstractAPOBEC mutagenesis, a major driver of cancer evolution, is known for targeting TpC sites in DNA. Recently, we showed that APOBEC3A (A3A) targets DNA hairpin loops. Here, we show that DNA secondary structure is in fact an orthogonal influence on A3A substrate optimality and, surprisingly, can override the TpC sequence preference. VpC (non-TpC) sites in optimal hairpins can outperform TpC sites as mutational hotspots. This expanded understanding of APOBEC mutagenesis illuminates the genomic Twin Paradox, a puzzling pattern of closely spaced mutation hotspots in cancer genomes, in which one is a canonical TpC site but the other is a VpC site, and double mutants are seen only in trans, suggesting a two-hit driver event. Our results clarify this paradox, revealing that both hotspots in these twins are optimal A3A substrates. Our findings reshape the notion of a mutation signature, highlighting the additive roles played by DNA sequence and DNA structure.

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