Effect of G-Tract Length on the Topology and Stability of Intramolecular DNA Quadruplexes

Abstract

G-Rich sequences are known to form four-stranded structures that are based on stacks of G-quartets, and sequences with the potential to adopt these structures are common in eukaryotic genomes. However, there are few rules for predicting the relative stability of folded complexes that are adopted by sequences with different-length G-tracts or variable-length linkers between them. We have used thermal melting, circular dichroism, and gel electrophoresis to examine the topology and stability of intramolecular G-quadruplexes that are formed by sequences of the type d(GnT)4 and d(GnT2)4 (n = 3-7) in the presence of varying concentrations of sodium and potassium. In the presence of potassium or sodium, d(GnT)4 sequences form intramolecular parallel complexes with the following order of stability: n = 3 > n = 7 > n = 6 > n = 5 > n = 4. d(G3T)4 is anomalously stable. In contrast, the stability of d(GnT2)4 increases with the length of the G-tract (n = 7 > n = 6 > n = 5 > n = 4 > n = 3). The CD spectra for d(GnT)4 in the presence of potassium exhibit positive peaks around 260 nm, consistent with the formation of parallel topologies. These peaks are retained in sodium-containing buffers, but when n = 4, 5, or 6, CD maxima are observed around 290 nm, suggesting that these sequences [especially d(G5T)4] have some antiparallel characteristics. d(G3T2)4 adopts a parallel conformation in the presence of both sodium and potassium, while all the other d(GnT2)4 complexes exhibit predominantly antiparallel features. The properties of these complexes are also affected by the rate of annealing, and faster rates favor parallel complexes.

Translational Repression of the Disintegrin and Metalloprotease ADAM10 by a Stable G-quadruplex Secondary Structure in Its 5′-Untranslated Region

“…1). Moreover, determination of the thermodynamic parameters ⌬G vH ϭ Ϫ10.6 Ϯ 0.8 kJ/mol, ⌬H vH ϭ Ϫ151.5 Ϯ 13.2 kJ/mol, and ⌬S vH ϭ Ϫ0.45 Ϯ 0.04 kJ/mol K, in the presence of 1 mM KCl are comparable with known DNA and RNA G-quadruplexes (37,54,55). In a recent study, the dependence of the stability of RNA G-quadruplexes on the loop length between the G-quadruplex forming G-tetrads was determined (53).…”

The Effect of DNA Sequence Directionality on G‐Quadruplex Folding

“…[15,18,19,16,21] Second, anti-anti and syn-anti steps contribute to higher stability in comparison to anti-syn and syn-syn steps. [22] Third, syn conformation at the 5'-end of oligonucleotide is preferred.…”

A Metal‐Mediated Conformational Switch Controls G‐Quadruplex Binding Affinity

“…[10] A quadruplex with a "parallel" structure (all its glycosidic angles in the anti conformation) is generally characterized by ellipticity (V) maxima at 264 (positive) and 240 nm (negative). [10] In contrast, the "antiparallel" structure (a combination of syn and anti angles, Scheme 1 A, right) has maxima at 295 (positive) and 264 nm (negative), and the "mixedhybrid" structure (a different combination of the syn and anti angles, Scheme 1 A, center) has two positive maxima at 295 and 268 nm. [10] The characteristic spectra originate in the guanine glycosidic torsion angles [11] or in the interplay between the polarity of the neighboring quartets.…”

“…[10] In contrast, the "antiparallel" structure (a combination of syn and anti angles, Scheme 1 A, right) has maxima at 295 (positive) and 264 nm (negative), and the "mixedhybrid" structure (a different combination of the syn and anti angles, Scheme 1 A, center) has two positive maxima at 295 and 268 nm. [10] The characteristic spectra originate in the guanine glycosidic torsion angles [11] or in the interplay between the polarity of the neighboring quartets. [12] Great caution must be exercised in CD interpretation; assignments used herein are based on recent bibliographic consensus.…”