A. Reymer

Mechanistic Insights into ASO-RNA Complexation: Advancing Antisense Oligonucleotide Design Strategies.

This study uses molecular dynamics simulations to show that ASO-mRNA complex stability depends on ASO length, triple base pairs, and hairpin loop accessibility, offering insights for ASO design.

Decoding the Dual Recognition Mechanism of Glucocorticoid Receptor for DNA and RNA: Sequence vs. Shape.

This study investigates how the glucocorticoid receptor (GR) recognizes DNA and RNA through structural and sequence-based mechanisms, showing distinct binding preferences for DNA versus RNA hairpin motifs.

Methylation in NDUFA13 gene promoter disrupts communication between collaborative transcription factors - potential mechanism for onset of breast cancer.

The paper investigates how methylation in the NDUFA13 gene promoter disrupts transcription factor binding, leading to gene downregulation and potentially contributing to breast cancer.

Homologous BHLH transcription factors induce distinct deformations of torsionally-stressed DNA: a potential transcription regulation mechanism.

This study shows homologous BHLH transcription factors induce distinct DNA deformations under torsional stress, potentially modulating their transcriptional specificity.

Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors

The paper uses molecular dynamics simulations to show that AP-1 factors like Yap1 use sequence-specific DNA dynamics and flanking nucleotides to form stable protein-DNA complexes, influencing gene expression.

BZIP Transcription Factors Modulate DNA Supercoiling Transitions

This study investigates how MafB, a BZIP transcription factor, modulates DNA supercoiling transitions under torsional stress using molecular dynamics simulations.