Polymorphism of human telomeric quadruplex structures

Abstract

Human telomeric DNA consists of tandem repeats of the sequence d(TTAGGG). Compounds that can stabilize the intramolecular DNA G-quadruplexes formed in the human telomeric sequence have been shown to inhibit the activity of telomerase and telomere maintenance, thus the telomeric DNA G-quadruplex has been considered as an attractive target for cancer therapeutic intervention. Knowledge of intramolecular human telomeric G-quadruplex structure(s) formed under physiological conditions is important for structure-based rational drug design and thus has been the subject of intense investigation. This review will give an overview of recent progress on the intramolecular human telomeric G-quadruplex structures formed in K+ solution. It will also give insight into the structure polymorphism of human telomeric sequences and its implications for drug targeting.

Figure 1

A schematic drawing of an intramolecular G-quadruplex (right) that is composed of three G-tetrads. A G-tetrad with H1-H1 and H1-H8 connectivity patterns detectable in NOESY experiments is also shown (left).

Figure 2

(A) Schematic drawing of the folding topologies of the Hybrid-1 (major conformation in Tel26) and Hybrid-2 (major conformation in wtTel26) intramolecular telomeric G-quadruplexes in K⁺ solution. Yellow box = (anti) guanine, red box = (syn) guanine; red ball = guanine, green ball = adenine, blue ball = thymine. (B) Folding topology of the basket-type intramolecular G-quadruplex formed by wtTel22 in Na⁺ solution as determined by NMR. (C) Folding topology of the propeller-type parallel-stranded intramolecular G-quadruplex formed by wtTel22 in the presence of K⁺ in crystalline state. The numbering system is based on wtTel26.

Figure 3

(A) Four-G-tract native human telomeric sequences with different flanking sequences. The numbering system is shown above wtTel27. (B) Four-G-tract human telomeric DNA sequences that have been used for structure determination. The numbering system is shown above wtTel26.

Figure 4

The imino proton region of the 1D ¹H NMR of wtTel22 (A), wtTel26 with assignment (B), and Tel26 with assignment (C) in K⁺ solution. The imino proton region of the 1D ¹H NMR of the 1hr (D) and overnight (E) K⁺ solution samples of Tel26 is also shown.

Figure 5

(A) Stereo view of the representative model of the NMR-refined structure of the hybrid-1 type telomeric G-quadruplex formed by Tel26 in K⁺ solution. (B) Stereo view of the representative model of the NMR-refined structure of the hybrid-2 type telomeric G-quadruplex formed by wtTel26 in K⁺ solution. (C) The top view of the adenine triple (red) capping the top G-tetrad (cyan). (D) The bottom view of the T:A:T triple capping the bottom G-tetrad (blue), with the potential hydrogen-bonds shown in dashed lines. The loop adenines are in red, and the loop thymines are in green. The top G-tetrad (as in Figure 2A) is in cyan, the middle G-tetrad is in magenta, and the bottom G-tetrad is in blue.

Figure 6

Comparison of G-quadruplex-forming sequences. Loops colored in red have been shown to adopt parallel-stranded double-chain-reversal side loops (see text for more details).

Figure 7

A model of DNA secondary structure composed of compact-stacking multimers of hybrid-type G-quadruplexes in human telomeres, with an equilibrium between hybrid-1 and hybrid-2 forms in K⁺ solution. The hybrid-1 and hybrid-2 telomeric G-quadruplexes have distinct molecular structures, as shown by the representative NMR structures (guanine = yellow, adenine = red, thymine = blue).

Figure 8

(A) CD spectra of wtTel26, Tel26, and wtTel22 in 100 mM Na⁺ or K⁺ solution at 25 °C. Similar CD signatures are observed for wtTel26 and Tel26 in K⁺ solution, while similarly distinct CD signatures are observed for wtTel26, Tel26, and wtTel22 in Na⁺ solution. (B) Titration experiments of K⁺ in the presence of 150 mM Na⁺ for Tel26, and (C) titration experiments of Na⁺ in the presence of 100 mM K⁺ for Tel26, monitored by CD spectroscopy.

Figure 9

Schematic diagram of a possible mechanism of the interconversions between the basket type (Na⁺) and the hybrid-type (K⁺) forms of telomeric G-quadruplexes. The hybrid-1 structure is used for illustration. The hybrid-type G-quadruplex structure is the most stable and thus the predominant form in the presence of K⁺, regardless of the presence or absence of Na⁺. The interconversion rate is much slower for the extended four repeat telomeric sequence Tel26 (A) than for the truncated four repeat telomeric sequence wtTel22 (B).