The effects of monovalent metal ions on the conformation of human telomere DNA using analytical ultracentrifugation

Abstract

A human telomere DNA segment (HT-DNA) can fold into a G-quadruplex in the presence of some monovalent cations. These cations can interact with the phosphate groups of the DNA segment and/or with the O6 oxygen atom of guanines, which are called non-specific interactions and specific interactions, respectively. However, until now how these two interactions affect the structure of HT-DNA has not been well understood. In this study, a combination of analytical ultracentrifugation (AUC) and circular dichroism (CD) was used to explore the effects of these two interactions on the structure of a 22-mer single-stranded DNA with a sequence of 5'-AGGG(TTAGGG)3-3'. The results showed that the standard sedimentation coefficient (s20,w) of HT-DNA starts to increase when the concentration of potassium ions (CK(+)) is higher than 10.0 µM due to the formation of a G-quadruplex through specific interactions. Whereas, for a control DNA, a higher CK(+) value of 1.0 mM was needed for increasing s20,w due to non-specific interactions. Moreover, potassium ions could promote the formation of the G-quadruplex much more easily than lithium, sodium and cesium ions, presumably due to its appropriate size in the dehydrated state and easier dehydration. The molar mass of DNA at different cation concentrations was nearly a constant and close to the theoretical value of the molar mass of monomeric HT-DNA, indicating that what we observed is the structural change of individual DNA chains.

Sedimentation velocity analysis of TMPyP4-induced dimer formation of human telomeric G-quadruplex

“…24 The titrations of NaCl into the Tel22-ligand mixture solution ( Fig. S4 †) show the CD signal at 295 nm still increases when C NaCl is larger than the minimum concentration (100 mM) to fully induce the formation of G-quadruplex without the addition of TMPyP4, as reported in our previous study, 43 reecting the negative inuence of TMPyP4 on the stability of G-quadruplex.…”

“…The concentration of DNA was determined by measuring the absorbance at 260 nm using a UV-vis spectrophotometer (UV-2802PCS, UNICO, Shanghai) with a molar extinction coefficient of 228.5 mM À1 cm À1 . 19,43 TMPyP4 in the form of a tetra-o-tosylate salt was purchased from Tokyo Chemical Industry (TCI) and used as received. The solid sample was dissolved in 10 mM Tris-HCl buffer solution (pH ¼ 7.5) to obtain a stock solution with a concentration of $1.0 mM.…”

“…S1(a), † the sedimentation coefficients (s) of Tel22 in the presence of 100 mM NaCl and KCl are 1.90 S and 2.02 S, respectively, which are in good agreement with earlier reports on G-quadruplex structures. 43,50 Fig. S1(b) † shows that Tel22 presents a positive peak at 295 nm and a negative peak at 265 nm in the presence of 100 mM NaCl, and has a positive peak at 290 nm with a shoulder at around 270 nm and a negative peak around 235 nm with the addition of 100 mM KCl, indicating the formation of basket-type and hybrid structures in these two salt solutions, respectively.…”

“…A unimodal distribution with s ¼ 1.90 S of Tel22 in an aqueous solution containing 100 mM NaCl and without the addition of TMPyP4 indicates an intramolecular basket-type Gquadruplex (M). 43,50 With the addition of 8.0 mM TMPyP4, a second peak (D) with a sedimentation coefficient of 2.7 S appears, presumably due to the formation of a dimer between Tel22-TMPyP4 complexes. Moreover, Fig.…”

Characterization of mixed solutions of hyperbranched and linear polystyrenes by a combination of size‐exclusion chromatography and analytical ultracentrifugation

“…[18] In addition to liquid chromatography, analytical ultracentrifugation (AUC) is also a good tool for separation of solutes based on the molar mass and the size of the solutes in solutions. [19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35] It has been widely used to characterize polymers and nanoparticles, [19][20][21][22][23][24][25][26] proteins, [27][28][29][30] and DNA. [31][32][33][34][35] However, only a few research studies have been done to characterize polymers by a combination of SEC and AUC.…”