Скачать или смотреть Cameron Mackereth: Unusual DNA architecture in a dopamine-bound aptamer complex

CASP Nucleic Acid SIG #34 Dr. Cameron Mackereth
"Unusual DNA architecture in a dopamine-bound aptamer complex"

Abstract: DNA-based aptamers specific for small molecules provide scaffolds toward diagnostic and therapeutic applications. Despite a growing diversity of the small molecule-binding DNA aptamers, there remains limited molecular knowledge of their binding mechanisms as few have been characterized at the atomic level. We have used NMR spectroscopy to obtain structural details of RKEC1, a shortened version of a DNA aptamer previously reported to bind dopamine. We find that upon binding dopamine, RKEC1 forms a compact structure that surprisingly lacks any Watson-Crick duplex or G-quadruplex regions. Instead, the large variety of base-pairs observed in the DNA structure necessitated the use of base-pair annotation established for the unusually more diverse RNA structures. Despite the unusual architecture, the fold is stabilized by numerous intramolecular hydrogen bonds throughout the complex, as well as intermolecular contacts to the bound dopamine. Ligand binding details were further probed by a series of dopamine analogues, and the structure of the ligand-bound aptamer enabled us to optimize the design for an electronic aptamer-based biosensor using RKEC1. In a broader sense, the unexpected DNA structure highlights the need for more aptamer structures to better understand the mechanism used by DNA aptamers to bind small molecules. The unexpected complexity possible for DNA folds also emphasizes the need for the determination of additional DNA structures to help in structure predictions.