Stability of intramolecular quadruplexes: sequence effects in the central loop

Abstract

Hundreds of thousands of putative quadruplex sequences have been found in the human genome. It is important to understand the rules that govern the stability of these intramolecular structures. In this report, we analysed sequence effects in a 3-base-long central loop, keeping the rest of the quadruplex unchanged. A first series of 36 different sequences were compared; they correspond to the general formula GGGTTTGGGHNHGGGTTTGGG. One clear rule emerged from the comparison of all sequence motifs: the presence of an adenine at the first position of the loop was significantly detrimental to stability. In contrast, adenines have no detrimental effect when present at the second or third position of the loop. Cytosines may either have a stabilizing or destabilizing effect depending on their position. In general, the correlation between the Tm or ΔG° in sodium and potassium was weak. To determine if these sequence effects could be generalized to different quadruplexes, specific loops were tested in different sequence contexts. Analysis of 26 extra sequences confirmed the general destabilizing effect of adenine as the first base of the loop(s). Finally, analysis of some of the sequences by microcalorimetry (DSC) confirmed the differences found between the sequence motifs.

Influence of pH, temperature and the cationic porphyrin TMPyP4 on the stability of the i-motif formed by the 5′-(C3TA2)4-3′ sequence of the human telomere

“…It is clear from the present and previous studies that the presence of adenine bases at the potential loops affects the stability of the i-motif structure, as already observed for several topologies of G-quadruplex structures [40]. The greater stability shown by C3TT2 than by C3TA2 was observed previously by Mergny et al when studying the sequences 5 -(C 3 TA 2 ) 3 CCC-3 and 5 -(C 3 TT 2 ) 3 CCC-3 [28].…”

The Effect of DNA Sequence Directionality on G‐Quadruplex Folding

“…[18,19] Them elting temperature (T m )v alues for the six oligonucleotides were between 45 and 60 8 8Cinthe presence of K + and between 36 and 48 8 8Ci nt he presence of Na + (Table 1). No hysteresis in the melting curves was observed.…”

“…[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.…”

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

“…Considerable effort has been spent trying to understand the principles which govern the folding of G-quadruplexes (Hardin et al 2000;Xue et al 2011;Karsisiotis et al 2013). Numerous articles have explored the contributions of the composition and length of the loops on the formation and topology of both DNA and RNA G-quadruplexes (Hazel et al 2004;Risitano and Fox 2004;Rachwal et al 2007;Guedin et al 2009Guedin et al , 2010Olsen et al 2009;Zhang et al 2011;Koirala et al 2013;Kwok et al 2013;Pandey et al 2013), and some general conclusions regarding the loops have emerged. Firstly, in contrast to DNA, the topology of RNA G-quadruplexes is always parallel and independent of the loop length and sequence (Zhang et al 2011;Pandey et al 2013).…”