To investigate potential structures of
d(CGG/CCG)
n that might relate to theirbiological functionan
d association with triplet repeat expansion
diseases (TREDs), thestructure of a single-stran
de
d (ss)oligonucleoti
de containing
d(CCG)
15[ss(CCG)
15] was examine
d by stu
dies of the pH an
dtemperature
depen
dence of electrophoretic mobility, UV absorbance, circular
dichroism, chemical mo
dification, an
dP1 nuclease
digestion. ss(CCG)
15 ha
d an unusuallyhigh p
Ka (7.7 ± 0.2). At pH 8.5,ss(CCG)
15 forme
da relatively unstable (
Tm = 30
![](/images/entities/<font color=)
deg.gif">C in 1 mMNa
+) hairpin containing CpG base-pair steps. At pH7.5, thehairpin containe
d protonate
d cytosines but no
detectableC·
+C base pairs, increase
d thermal stability(
Tm= 37
![](/images/entities/<font color=)
deg.gif">C), increase
d stacking of the CpG base-pair steps, an
d asingle cytosine that was flippe
d awayfrom the central portion of the helix. Examination ofss(CCG)
18 an
d ss(CCG)
20, which were
designe
d toa
dopt hairpins containing alternative GpC base-pair steps, reveale
dhairpins containing CpG base-pairsteps, p
Kas of ~8.2 an
d ~8.4, respectively,an
d distorte
d helices. The results suggest that DNAsequencescontaining (CCG)
n
15a
dopt hairpin conformations that contain CpG rather than GpC base-pairsteps; themismatche
d cytosines are protonate
d at physiological pH but are notH-bon
de
d. We propose thatprotonation arises from the stacking of two cytosines in the minorgroove of a
distorte
d helix.