[HTML][HTML] DNA and RNA quadruplex-binding proteins

V Brázda, L Hároníková, JCC Liao, M Fojta - International journal of …, 2014 - mdpi.com
Four-stranded DNA structures were structurally characterized in vitro by NMR, X-ray and
Circular Dichroism spectroscopy in detail. Among the different types of quadruplexes (i …

Predicting thermal adaptation by looking into populations' genomic past

AJ Cortés, F López-Hernández… - Frontiers in …, 2020 - frontiersin.org
Molecular evolution offers an insightful theory to interpret the genomic consequences of
thermal adaptation to previous events of climate change beyond range shifts. However …

The complete sequence of a human Y chromosome

A Rhie, S Nurk, M Cechova, SJ Hoyt, DJ Taylor… - Nature, 2023 - nature.com
The human Y chromosome has been notoriously difficult to sequence and assemble
because of its complex repeat structure that includes long palindromes, tandem repeats and …

Impact of alternative DNA structures on DNA damage, DNA repair, and genetic instability

G Wang, KM Vasquez - DNA repair, 2014 - Elsevier
Repetitive genomic sequences can adopt a number of alternative DNA structures that differ
from the canonical B-form duplex (ie non-B DNA). These non-B DNA-forming sequences …

Non-B DB v2. 0: a database of predicted non-B DNA-forming motifs and its associated tools

RZ Cer, DE Donohue, US Mudunuri… - Nucleic acids …, 2012 - academic.oup.com
The non-B DB, available at http://nonb. abcc. ncifcrf. gov, catalogs predicted non-B DNA-
forming sequence motifs, including Z-DNA, G-quadruplex, A-phased repeats, inverted …

The amino acid composition of quadruplex binding proteins reveals a shared motif and predicts new potential quadruplex interactors

V Brázda, J Červeň, M Bartas, N Mikysková, J Coufal… - Molecules, 2018 - mdpi.com
The importance of local DNA structures in the regulation of basic cellular processes is an
emerging field of research. Amongst local non-B DNA structures, G-quadruplexes are …

Palindrome analyser–a new web-based server for predicting and evaluating inverted repeats in nucleotide sequences

V Brázda, J Kolomazník, J Lýsek, L Hároníková… - Biochemical and …, 2016 - Elsevier
DNA cruciform structures play an important role in the regulation of natural processes
including gene replication and expression, as well as nucleosome structure and …

Mutational impact of APOBEC3A and APOBEC3B in a human cell line and comparisons to breast cancer

MA Carpenter, NA Temiz, MA Ibrahim, MC Jarvis… - PLoS …, 2023 - journals.plos.org
A prominent source of mutation in cancer is single-stranded DNA cytosine deamination by
cellular APOBEC3 enzymes, which results in signature C-to-T and C-to-G mutations in TCA …

Structural genomic variation and behavioral interactions underpin a balanced sexual mimicry polymorphism

TO Dodge, BY Kim, JJ Baczenas, SM Banerjee… - Current Biology, 2024 - cell.com
How phenotypic diversity originates and persists within populations are classic puzzles in
evolutionary biology. While balanced polymorphisms segregate within many species, it …

Deep statistical modelling of nanopore sequencing translocation times reveals latent non-B DNA structures

M Hosseini, A Palmer, W Manka, PGS Grady… - …, 2023 - academic.oup.com
Motivation Non-canonical (or non-B) DNA are genomic regions whose three-dimensional
conformation deviates from the canonical double helix. Non-B DNA play an important role in …