Structural Features of Intra- and Intermolecular G-Quadruplexes Derived from Telomeric Repeats

Abstract

The 3' strand of telomeres is composed of tandem repeats of short G-rich sequences which protrude as single-stranded DNA overhangs. These repeats are G(3)T(2)A in humans and G(4)T(2) and G(4)T(4) in the ciliates Tetrahymena and Oxytricha, respectively. We analyzed different quadruplex-forming sequences derived from telomeric sequences, G(3+k)(T(n+k)G(3+k))(3) and G(3+k)(T(2)AG(3+k))(3), in the presence of Li(+), Na(+), and K(+) through the use of circular dichroism, UV spectroscopy, and electrophoresis, where k = 0 or 1 and n = 1-3. Results obtained under the given conditions can provide more detailed information about the quadruplex structure. The major findings are as follows. (i) G-Repeats in solution form a mix of topologically different structures; only G(3)(T(2)G(3))(3) and G(3)(TG(3))(3) repeats preferentially form the parallel interstrand structure. (ii) The Tetrahymena repeat can form at least two intramolecular conformers with different strand orientations and levels of stability. (iii) G-Quadruplex conformation and molecularity strongly depend on the type and concentration of ions used in the solution. The formation of intramolecular quadruplexes is governed by the length of the loops connecting G-runs. Intermolecular G-quadruplex forms are more likely to form in a higher concentration of ions for sequences where G-runs are separated by only one or two nucleotides.

The folding of 5′-UTR human G-quadruplexes possessing a long central loop

“…This feature determines the variability in the number of stacked G-quartets and connecting loops. The presence of multiple G-quadruplex species in solution is one of the major problems complicating data evaluation in many biophysical approaches, including circular dichroism, NMR, and UV melting, where the resulting data often represent a mixture of different DNA G-quadruplex structures (Viglasky et al 2010). This report demonstrates that additional G-tracks located either in the loops or the regions flanking the predicted PG4s readily fold into a mixture of different G-quadruplex structures (see the candidates BAG1, HIRA, and CTGLF6) (Figs.…”

The circular dichroism and differential scanning calorimetry study of the properties of DNA aptamer dimers

“…DNA oligomers were visualized with stains-all after the electrophoresis, and the electrophoretic record was photographed with an Olympus Camedia 3000 camera. The same temperaturegradient gel electrophoresis (TGGE) equipment has been used as described previously [19].…”

The Human Telomere Sequence, (TTAGGG)4, in the Absence and Presence of Cosolutes: A Spectroscopic Investigation

“…Of particular interest recently are the conformations available to G-rich DNAs which are designated as G-quadruplexes. DNA sequences that have islands of G 2-4 separated by 1 to 4 A and/or T bases can form a rich library of secondary structures with different molecularities, strand orientations, and guanine base conformation (i.e., syn or anti) [3][4][5][6][7][8][9][10][11][12][13][14]. The conformations and their stabilities are highly dependent upon the sequence context and buffer conditions [15][16][17][18][19][20][21].…”

“…A model was presented for the quadruplex to random coil transition, via formation of an unknown intramolecular intermediate, with exclusion of K + during each transition. Review of the literature reveals that different investigators have used slight variations of the sequence (TTAGGG) 4 for their investigations and have drawn conclusions based upon their data [3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21]. We recently reported however that changing just one base in just one loop of the folded quadruplex influences both conformation and stability [20].…”