Alan A. Chen

This study investigates how DNA strand polarity affects base-stacking energetics using single-molecule and computational methods, finding polarity-dependent stability differences in purine-purine and purine-pyrimidine interactions.

This study investigates how miR-34a interacts with its mRNA targets and how AGO2 modulates their binding affinity and structure, revealing structural determinants of repression efficacy.

This study investigates how base-stacking interactions affect the stability of DNA tetrahedra by testing 16 designs, finding that altering a single base stack can change melting temperatures by up to 10°C.

This study investigates how pseudoknot base pairing affects cotranscriptional structural switching in fluoride riboswitches, showing a critical wobble base pair is essential for function across different temperatures.

The paper uses molecular dynamics simulations to study how RNA modifications and magnesium ions affect tRNAPhe conformational dynamics in S. cerevisiae.

The paper shows that mutating two intronic nucleotides alters RNA structure and dynamics, disrupting MBNL1 and RBFOX1 regulation of INSR exon 11 splicing.

This paper uses metadynamics to predict small molecule-RNA binding modes, showing agreement with experimental structures and providing binding pathways for RNA aptamers.