Dimeric structures of DNA ATTTC repeats promoted by divalent cations

Abstract

Structural studies of repetitive DNA sequences may provide insights why and how certain repeat instabilities in their number and nucleotide sequence are managed or even required for normal cell physiology, while genomic variability associated with repeat expansions may also be disease-causing. The pentanucleotide ATTTC repeats occur in hundreds of genes important for various cellular processes, while their insertion and expansion in noncoding regions are associated with neurodegeneration, particularly with subtypes of spinocerebellar ataxia and familial adult myoclonic epilepsy. We describe a new striking domain-swapped DNA–DNA interaction triggered by the addition of divalent cations, including Mg2+ and Ca2+. The results of NMR characterization of d(ATTTC)3 in solution show that the oligonucleotide folds into a novel 3D architecture with two central C:C+ base pairs sandwiched between a couple of T:T base pairs. This structural element, referred to here as the TCCTzip, is characterized by intercalative hydrogen-bonding, while the nucleobase moieties are poorly stacked. The 5′- and 3′-ends of TCCTzip motif are connected by stem-loop segments characterized by A:T base pairs and stacking interactions. Insights embodied in the non-canonical DNA structure are expected to advance our understanding of why only certain pyrimidine-rich DNA repeats appear to be pathogenic, while others can occur in the human genome without any harmful consequences.

Nanopore-Based Single-Molecule Investigation of Cation Effect on the i-Motif Structure

“…Previous reports have indicated that i-DNA can fold into an i-motif structure under weakly acidic conditions and low concentrations of divalent cations can stabilize the DNA secondary structure. 50 Here, we observed that the unfolding of all i-DNA into a single strand is aided by a mildly acidic solution with a high concentration of divalent cation electrolytes. Therefore, we deduce that the concentration of divalent cations may potentially affect the unfolding and folding of the i-motif.…”