Interaction of proteins with inverted repeats and cruciform structures in nucleic acids

RP Bowater, N Bohálová, V Brázda - International Journal of Molecular …, 2022 - mdpi.com
Cruciforms occur when inverted repeat sequences in double-stranded DNA adopt intra-
strand hairpins on opposing strands. Biophysical and molecular studies of these structures …

Mutation bias and adaptation in bacteria

JS Horton, TB Taylor - Microbiology, 2023 - microbiologyresearch.org
Genetic mutation, which provides the raw material for evolutionary adaptation, is largely a
stochastic force. However, there is ample evidence showing that mutations can also exhibit …

Origin, evolution, and maintenance of gene-strand bias in bacteria

M Atre, B Joshi, J Babu, S Sawant… - Nucleic Acids …, 2024 - academic.oup.com
Gene-strand bias is a characteristic feature of bacterial genome organization wherein genes
are preferentially encoded on the leading strand of replication, promoting co-orientation of …

Challenging the importance of plastid genome structure conservation: new insights from euglenophytes

K Maciszewski, A Fells… - Molecular Biology and …, 2022 - academic.oup.com
Plastids, similar to mitochondria, are organelles of endosymbiotic origin, which retained their
vestigial genomes (ptDNA). Their unique architecture, commonly referred to as the …

[HTML][HTML] Short and long-read ultra-deep sequencing profiles emerging heterogeneity across five platform Escherichia coli strains

P Rugbjerg, ASB Dyerberg, S Quainoo, C Munck… - Metabolic …, 2021 - Elsevier
Reprogramming organisms for large-scale bioproduction counters their evolutionary
objectives of fast growth and often leads to mutational collapse of the engineered production …

SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci

P Goswami, M Bartas, M Lexa… - Briefings in …, 2021 - academic.oup.com
SARS-CoV-2 is an intensively investigated virus from the order Nidovirales (Coronaviridae
family) that causes COVID-19 disease in humans. Through enormous scientific effort …

Maxicircle architecture and evolutionary insights into Trypanosoma cruzi complex

L Berná, G Greif, S Pita, P Faral-Tello… - PLoS neglected …, 2021 - journals.plos.org
We sequenced maxicircles from T. cruzi strains representative of the species evolutionary
diversity by using long-read sequencing, which allowed us to uncollapse their repetitive …

IRfold: An RNA Secondary Structure Prediction Approach

D Hurst, CS Iliopoulos, Z Lim, I Moraru - IFIP International Conference on …, 2024 - Springer
Ribonucleic acid (RNA) sequences can be viewed as an ordered list of symbols
representing the component nucleobases of the RNA sequence also known as its primary …

Coding palindromes in mitochondrial genes of Nematomorpha

KV Mikhailov, BD Efeykin, AY Panchin… - Nucleic Acids …, 2019 - academic.oup.com
Inverted repeats are common DNA elements, but they rarely overlap with protein-coding
sequences due to the ensuing conflict with the structure and function of the encoded protein …

Protein innovation through template switching in the Saccharomyces cerevisiae lineage

M Abraham, E Hazkani-Covo - Scientific Reports, 2021 - nature.com
DNA polymerase template switching between short, non-identical inverted repeats (IRs) is a
genetic mechanism that leads to the homogenization of IR arms and to IR spacer inversion …