Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing

J Tao, DE Bauer, R Chiarle - Nature Communications, 2023 - nature.com
CRISPR-Cas gene editing has revolutionized experimental molecular biology over the past
decade and holds great promise for the treatment of human genetic diseases. Here we …

A guide to computational methods for G-quadruplex prediction

E Puig Lombardi, A Londoño-Vallejo - Nucleic acids research, 2020 - academic.oup.com
Guanine-rich nucleic acids can fold into the non-B DNA or RNA structures called G-
quadruplexes (G4). Recent methodological developments have allowed the characterization …

Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites

A Promonet, I Padioleau, Y Liu, L Sanz… - Nature …, 2020 - nature.com
R-loops have both positive and negative impacts on chromosome functions. To identify toxic
R-loops in the human genome, here, we map RNA: DNA hybrids, replication stress markers …

[HTML][HTML] Chemical insights into oxidative and nitrative modifications of DNA

CMC Andrés, JMP Lastra, CA Juan, FJ Plou… - International Journal of …, 2023 - mdpi.com
This review focuses on DNA damage caused by a variety of oxidizing, alkylating, and
nitrating species, and it may play an important role in the pathophysiology of inflammation …

Studying DNA double-strand break repair: an ever-growing toolbox

AC Vítor, P Huertas, G Legube… - Frontiers in molecular …, 2020 - frontiersin.org
To ward off against the catastrophic consequences of persistent DNA double-strand breaks
(DSBs), eukaryotic cells have developed a set of complex signaling networks that detect …

[HTML][HTML] Ionizing radiation and complex DNA damage: from prediction to detection challenges and biological significance

IV Mavragani, Z Nikitaki, SA Kalospyros… - Cancers, 2019 - mdpi.com
Biological responses to ionizing radiation (IR) have been studied for many years, generally
showing the dependence of these responses on the quality of radiation, ie, the radiation …

Off-target analysis in gene editing and applications for clinical translation of CRISPR/Cas9 in HIV-1 therapy

A Atkins, CH Chung, AG Allen, W Dampier… - Frontiers in genome …, 2021 - frontiersin.org
As genome-editing nucleases move toward broader clinical applications, the need to define
the limits of their specificity and efficiency increases. A variety of approaches for nuclease …

Non-canonical DNA/RNA structures during transcription-coupled double-strand break repair: roadblocks or bona fide repair intermediates?

N Puget, KM Miller, G Legube - DNA repair, 2019 - Elsevier
Although long overlooked, it is now well understood that DNA does not systematically
assemble into a canonical double helix, known as B-DNA, throughout the entire genome but …

In vivo dynamics and regulation of DNA G-quadruplex structures in mammals

ZH Zhang, SH Qian, D Wei, ZX Chen - Cell & Bioscience, 2023 - Springer
Abstract G-quadruplex (G4) is a four-stranded helical DNA secondary structure formed by
guanine-rich sequence folding, and G4 has been computationally predicted to exist in a …

Endogenous DNA double-strand breaks during DNA transactions: emerging insights and methods for genome-wide profiling

BAM Bouwman, N Crosetto - Genes, 2018 - mdpi.com
DNA double-strand breaks (DSBs) jeopardize genome integrity and can—when repaired
unfaithfully—give rise to structural rearrangements associated with cancer. Exogenous …