How long is too long? Effects of loop size on G-quadruplex stability.
We compared here 80 different sequences containing four tracts of three guanines with loops of variable length (between 1 and 15 bases for unmodified sequences, up to 30 for fluorescently labeled oligonucleotides). All sequences were capable of forming stable quadruplexes, with T(m) above physiological temperature in most cases. Unsurprisingly, the melting temperature was systematically lower in sodium than in potassium but the difference between both ionic conditions varied between 1 and >39°C (average difference: 18.3°C). Depending on the sequence context, and especially for G4 sequences involving two very short loops, the third one may be very long without compromising the stability of the quadruplex. A strong inverse correlation between total loop length and T(m) was found in K(+): each added base leads to a 2°C drop in T(m) or ∼0.3 kcal/mol loss in ΔG°. The trend was less clear in Na(+), with a longer than expected optimal loop length (up to 5 nt). This study will therefore extend the sequence repertoire of quadruplex-prone sequences, arguing for a modification of the widely used consensus (maximal loop size of 7 bases).
Guédin
Aurore
A
INSERM, U869, European Institute of Chemistry and Biology, Bordeaux 2 University, 2 rue Robert Escarpit, Pessac F-33607, France.
Gros
Julien
J
Alberti
Patrizia
P
Mergny
Jean-Louis
JL
D001483:Base Sequence; D002942:Circular Dichroism; D031541:Fluorescence Resonance Energy Transfer; D054856:G-Quadruplexes; D009691:Nucleic Acid Denaturation; D011188:Potassium / Q000737:chemistry; D012964:Sodium / Q000737:chemistry; D013696:Temperature; D013941:Thymine / Q000737:chemistry
D012964:Sodium; D013941:Thymine; D011188:Potassium