Structure of the human telomere in Na+ solution: an antiparallel (2+2) G-quadruplex scaffold reveals additional diversity

Abstract

Single-stranded DNA overhangs at the ends of human telomeric repeats are capable of adopting four-stranded G-quadruplex structures, which could serve as potential anticancer targets. Out of the five reported intramolecular human telomeric G-quadruplex structures, four were formed in the presence of K+ ions and only one in the presence of Na+ ions, leading often to a perception that this structural polymorphism occurs exclusively in the presence of K+ but not Na+. Here we present the structure of a new antiparallel (2+2) G-quadruplex formed by a derivative of a 27-nt human telomeric sequence in Na+ solution, which comprises a novel core arrangement distinct from the known topologies. This structure complements the previously elucidated basket-type human telomeric G-quadruplex to serve as reference structures in Na+-containing environment. These structures, together with the coexistence of other conformations in Na+ solution as observed by nuclear magnetic resonance spectroscopy, establish the polymorphic nature of human telomeric repeats beyond the influence of K+ ions.

Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations

“…Note that the structures A and B, and E and F have the same topology but differ in some structural details. We did not include the recently discovered antiparallel quadruplex with middle propeller loop (PDB: 2JMB) [27], as the resulting triplexes would have topologies identical to our models G and H. The three-triad triplex relevant for the two-quartet 2KF8 structure (strands 2e4) would be topologically equivalent to the structure C, though the upper triad has one syn to anti flip due to other specific interactions. Our study thus includes all possible three-triad triplexes relevant for a folding of all currently known human telomeric G-DNA folds.…”

“…Polymorphism of folded G-quadruplex structures in the thermodynamics equilibrium is well established [12e18, 21,25,27]. However, diversity of the structures occurring during folding processes may be much larger.…”

“…Any Gquadruplex forming strand can in principle adopt altogether 26 distinct G-quadruplex topologies, differing in strand directionality and type of the loops [22,30]. Although not all of them are energetically feasible, at least five three-quartet (and in addition one two-quartet) topologies have already been observed for the human telomeric quadruplex (see above) as dominant equilibrium structures in various atomistic experiments [12e16, 27,29,35,36,49,63]. Further, the G-rich sequence can potentially form quadruplexes with incomplete number of tetrads, including structures with a slipped strand (actually, the two-quartet quadruplex PDB: 2KF8 [12] falls into this category).…”

A direct view of the complex multi-pathway folding of telomeric G-quadruplexes

“…The prevalence of one particular conformation in solution is dictated by factors such as counter-ion type and concentration, solvent composition, as well as the length of the DNA sequence and the type of terminal flanking nucleotides (15). Depending on these factors several stable folded G4 structures have been identified for the human telomeric sequence (16–20). This multifactorial nature of G4s makes their folding highly complex, possibly involving a number of stable intermediate states and misfolded species and is beyond a simple two-state approximation (21).…”

Diverse effects of naturally occurring base lesions on the structure and stability of the human telomere DNA quadruplex

“…The same CD spectrum has been recently observed in Na þ solution with a htel 27mer and its derivative substituted by 8-bromoguanine in position 22 (corresponding to G20 in our 21mer). The structure was interpreted by NMR as a novel antiparallel (2 þ 2) quadruplex with edgewisepropeller-edgewise loops [52]. The loss of adenine in apA19 affected quadruplex thermostability less than with apA7 and apA13 [40] (Fig.…”