Giardia Telomeric Sequence d(TAGGG)₄ Forms Two Intramolecular G-Quadruplexes in K⁺ Solution: Effect of Loop Length and Sequence on the Folding Topology

Abstract

Recently, it has been shown that in K(+) solution the human telomeric sequence d[TAGGG(TTAGGG)(3)] forms a (3 + 1) intramolecular G-quadruplex, while the Bombyx mori telomeric sequence d[TAGG(TTAGG)(3)], which differs from the human counterpart only by one G deletion in each repeat, forms a chair-type intramolecular G-quadruplex, indicating an effect of G-tract length on the folding topology of G-quadruplexes. To explore the effect of loop length and sequence on the folding topology of G-quadruplexes, here we examine the structure of the four-repeat Giardia telomeric sequence d[TAGGG(TAGGG)(3)], which differs from the human counterpart only by one T deletion within the non-G linker in each repeat. We show by NMR that this sequence forms two different intramolecular G-quadruplexes in K(+) solution. The first one is a novel basket-type antiparallel-stranded G-quadruplex containing two G-tetrads, a G x (A-G) triad, and two A x T base pairs; the three loops are consecutively edgewise-diagonal-edgewise. The second one is a propeller-type parallel-stranded G-quadruplex involving three G-tetrads; the three loops are all double-chain-reversal. Recurrence of several structural elements in the observed structures suggests a "cut and paste" principle for the design and prediction of G-quadruplex topologies, for which different elements could be extracted from one G-quadruplex and inserted into another.

NMR spectroscopy of G-quadruplexes

“…Replacement of a particular guanine by a thymine can abolish the ability of this residue to participate in the formation of the G-tetrad core [40,41]. Differing from a guanine by only one amino group substitution, an inosine creates a milder effect as compared to a thymine in disrupting the participation of a residue in the G-tetrad core [42][43][44][45]. G-to-I substitutions have been used to selectively isolate either one of two naturally co-existing hTERT G-quadruplex structures ( Fig.…”

“…In one study, spin-down approach was used to purify a slowly formed interlocked dimeric G-quadruplex adopted by the c-kit2 sequence [59]. Other experimental conditions, such as DNA concentration, nature and concentration of salt, temperature, and pH can also affect the relative population and NMR spectra of G-quadruplexes [22,35,39,45,46,53,59]. For example, the population of parallelstranded G-quadruplex was found to be increased at higher temperatures as opposed to anti-parallel counterparts [39,45,46].…”

“…Other experimental conditions, such as DNA concentration, nature and concentration of salt, temperature, and pH can also affect the relative population and NMR spectra of G-quadruplexes [22,35,39,45,46,53,59]. For example, the population of parallelstranded G-quadruplex was found to be increased at higher temperatures as opposed to anti-parallel counterparts [39,45,46]. Furthermore, molecular crowding conditions, simulated by addition of co-solutes such as polyethylene glycol (PEG), ethanol, acetonitrile, ficoll or DMSO into solution, have been shown to induce parallelstranded G-quadruplexes [46,[54][55][56][57].…”

DNA quadruplex folding formalism – A tutorial on quadruplex topologies

“…A greater number of stacking possibilities have been experimentally determined in this group: (a) (ÀlÀlÀl) as a two-stacked topology [23], (b) (+l+l+l) as the two-stacked 2KM3 [41] and 148D [42], (c) (Àld+l) as the four-stacked 201D [22], the three-stacked 143D [16] and the two-stacked 2KF8 [20] and 2KKA [21], and (d) (+ldÀl) as the twostacked 2KOW [43].…”

Is the G-Quadruplex an Effective Nanoconductor for Ions?

“…As a matter of fact, the sole simulation of the problem was published in 2012. 19 Akhshi et al investigated ion mobility in a parallel-stranded d[TG 4 T] 4 Gquadruplex by computing the potential of mean force (PMF) profiles for Na + , K + , and NH 4 + ions along the central pore. 19 We summarize their findings here for reference, and we comment in the Final Remarks how we add relevant knowledge.…”