Vertebrate telomere repeat DNAs favor external loop propeller quadruplex structures in the presence of high concentrations of potassium

Abstract

The circular dichroism, CD, spectra of the telomere repeats of vertebrates, d(TTAGGG), indicate that parallel type quadruplex structures or disordered single-stranded structures are formed in low salt. Anti-parallel quadruplex structures are favored in the presence of high concentrations, 140 mM, of sodium. External loop, also known as propeller, parallel type structures are favored in the presence of high concentrations, 100 mM, of potassium in the presence of either 5 or 140 mM sodium. The cation dependence of the CD spectra of the vertebrate telomere repeat DNAs is distinctly different from that of the telomere repeats of Tetrahymena and Oxytricha as well as that of the thrombin binding aptamer. These results indicate that the external loop structures may be present in vertebrate telomeres under the conditions of high potassium and low sodium concentration found in nuclei.

A single base permutation in any loop of a folded intramolecular quadruplex influences its structure and stability

“…Note the designations of Loops 1 through 3 all of which have the sequence of -(TTA)-as well as the 5'-Tail. Loop 1 is described as a propeller loop while Loops 2 and 3 are lateral loops [17].…”

Polymorphism of human telomeric quadruplex structures

“…Because the K + structure is considered to be biologically more relevant due to the higher intracellular concentration of K + , it has been the subject of intense investigation [32][33][34][35][36][37][38][39][40][41][42][43][44][45], although the Na + structure was reported more than a decade ago [46]. In 2002, a crystal structure of the parallel-stranded G-quadruplex was reported using a 22-nt human telomeric sequence in the presence of K + [47].…”

An important functional group, benzo[1,3]dioxole, of alkaloids induces the formation of the human telomeric DNA G-quadruplex

“…Melting curves of the antiparallel G-quadruplexes were obtained by recording the CD intensity at 292 nm. The heating rate was 1.0 °C min CD measurement has been extensively applied to study secondary structures of DNA [11][12][13]. The CD spectral features allow the approximate, but convenient, recognition of different DNA motifs.…”