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

2002 ◽  
Vol 106 (38) ◽  
pp. 9945-9950 ◽  
Author(s):  
Dionisios Rentzeperis ◽  
Ronald Shikiya ◽  
Souvik Maiti ◽  
James Ho ◽  
Luis A. Marky
Keyword(s):  
Dna Hairpin ◽  
Hairpin Loops

Asymmetric structure of five and six membered DNA hairpin loops

1996 ◽  
Vol 22 (1) ◽  
pp. 25-31 ◽  
Author(s):  
Ulrich Baumann ◽  
Sherwood Chang
Keyword(s):  
Asymmetric Structure ◽  
Dna Hairpin ◽  
Hairpin Loops

scholarly journals Quantitative Binding of Divalent Metal Ions to DNA Hairpin Loops

2019 ◽  
Vol 116 (3) ◽  
pp. 285a
Author(s):  
Harrison Russell ◽  
William Gunderson ◽  
Julie Gunderson
Keyword(s):  
Metal Ions ◽  
Divalent Metal ◽  
Divalent Metal Ions ◽  
Dna Hairpin ◽  
Hairpin Loops

scholarly journals The Role of DNA-PKcs and Artemis in Opening Viral DNA Hairpin Termini in Various Tissues in Mice

2007 ◽  
Vol 81 (20) ◽  
pp. 11304-11321 ◽  
Author(s):  
Katsuya Inagaki ◽  
Congrong Ma ◽  
Theresa A. Storm ◽  
Mark A. Kay ◽  
Hiroyuki Nakai
Keyword(s):  
Dna Repair ◽  
Inverted Terminal Repeat ◽  
Dependent Manner ◽  
Dna Hairpin ◽  
Dna Hairpins ◽  
Alternative Pathways ◽  
Hairpin Loops ◽  
Dependent Protein ◽  
Significant Pathway ◽  
Cellular Dna

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.

scholarly journals Targeting DNA Hairpin Loops with their Partially Complementary Strands

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

scholarly journals An extended APOBEC3A mutation signature in cancer

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.

scholarly journals Kinetics of conformational fluctuations in DNA hairpin-loops

1998 ◽  
Vol 95 (15) ◽  
pp. 8602-8606 ◽  
Author(s):  
G. Bonnet ◽  
O. Krichevsky ◽  
A. Libchaber
Keyword(s):  
Dna Hairpin ◽  
Hairpin Loops ◽  
Kinetics Of

scholarly journals Kinetics of conformational fluctuations in DNA hairpin-loops in crowded fluids

2013 ◽  
Vol 15 (11) ◽  
pp. 113010 ◽  
Author(s):  
Olivia Stiehl ◽  
Kathrin Weidner-Hertrampf ◽  
Matthias Weiss
Keyword(s):  
Dna Hairpin ◽  
Hairpin Loops ◽  
Kinetics Of

scholarly journals Effect of DNA Hairpin Loops on the Twist of Planar DNA Origami Tiles

Langmuir ◽  
2011 ◽  
Vol 28 (4) ◽  
pp. 1959-1965 ◽  
Author(s):  
Zhe Li ◽  
Lei Wang ◽  
Hao Yan ◽  
Yan Liu
Keyword(s):  
Dna Origami ◽  
Dna Hairpin ◽  
Hairpin Loops

scholarly journals Polycytosine regions contained in DNA hairpin loops interact via a four-stranded, parallel structure similar to the i-motif

1994 ◽  
Vol 22 (22) ◽  
pp. 4653-4659 ◽  
Author(s):  
Jan Rohozinski ◽  
John M. Hancock ◽  
Max A. Keniry
Keyword(s):  
Parallel Structure ◽  
Dna Hairpin ◽  
Hairpin Loops

scholarly journals DNA hairpin loops in solution. Correlation between primary structure, thermostability and reactivity with single-strand-specific nuclease from mung bean

1991 ◽  
Vol 19 (7) ◽  
pp. 1505-1511 ◽  
Author(s):  
Luigi E. Xodo ◽  
Giorgio Manzini ◽  
Franco Quadrifoglio ◽  
Gijs van der Marel ◽  
Jacques van Boom
Keyword(s):  
Primary Structure ◽  
Mung Bean ◽  
Single Strand ◽  
Dna Hairpin ◽  
Hairpin Loops
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