Chemistry Reference
In-Depth Information
the crystal (see below and Figure 3.4b). An interesting feature of this G-quadruplex
is the occurrence of two single nucleotide double-chain reversal loops, which were
fi rst found in the case of the
c - myc
promoter G - quadruplex.
44,221,231
The loop in the
middle of the sequence of
c - myc - 2345
contains two nucleotides (GA) while the
other two loops consist of a single T. The topology of a related
c - myc - 1245
sequence
is similar to the structure shown schematically in Figure 3.5a. The difference between
the structures of
c - myc - 1245
and
c - myc - 2345
is in the loop length. In the former,
loops closer to the 5
-ends of the molecule contain a single residue (A or T),
while the central loop contains six residues (T
5
A). Interestingly, the G-quadruplex
adopted by
c - myc - 2345
is more stable by 15 °C. The difference can be attributed to
different loop length and consequently distinct structures. An NMR structure deter-
mination of
c - myc - 2345
mutant (two guanines replaced by thymines) adopted the
topology shown in Figure 3.5a.
216
It is important to note that the three structures
mentioned above improved the insight into the structural details of
c - myc
promoter
by correcting some earlier low-resolution assessments.
46
The recent study focused on the
c - myc
sequence containing fi ve of the six
guanine tracts.
232
The sequence designated as
c - myc - 23456
consisted of the second,
third, fourth, fi fth and sixth guanine tracts of the 27-mer
c - myc
NHE III
1
element.
The topology of the G-quadruplex adopted in the presence of K
+
is shown in Figure
3.5b. The structure consists of three G-quartets. Interestingly, guanines involved in
the G-quartets originate from each of the fi ve tracts (underlined here: 5
′
- and 3
′
′
- dTGA
GGG T GG GGA GGG T GG G GA AG G - 3
). The four strands are in parallel ori-
entations. All guanines are in the
anti
conformation except for the 3
′
- end guanine,
which is a snap-back
syn
nucleotide. The loops are in a double-chain reversal con-
formation, except for the fi nal one, which is a diagonal loop and contributes to the
stability of the structure (Figure 3.5b).
A new G-quadruplex fold was shown to be adopted by the
c - kit
promoter
sequence positioned upstream of the transcription start site (Figure 3.5c).
233
The
c -
kit
promoter encodes for a tyrosine kinase receptor and is therefore involved in a
regulation of signal transduction.
c - kit
kinase is targeted in clinical treatments of
several cancers and by small molecule inhibitors that promote G-quadruplex forma-
tion.
228,229,233 - 235
The
c - kit
sequence that folded into a single structure in the presence
of K
+
ions consists of four GGG tracts. Its structure exhibits an unusual feature
where an isolated guanine is involved in the formation of a G-quartet core, despite
the presence of four G-tracts (guanines involved in the G-quartets are underlined
here: 5
′
).
233
Strands are in parallel
orientation and all guanines are in the
anti
conformation. The structure contains
four loops. Two of them are single-nucleotide loops in a double-chain reversal con-
formation. The two-residue linker connects two edges of the outer G-quartet, while
the longer fi ve-residue loop allows the fi nal two guanines to be inserted into the
G-quartets. The latter loop contributes to the stability of the structure through
Watson - Crick A - T base pairs. The 5
′
- dA GG G A G GG C G CT GGG AGG AG G G - 3
′
-ends are on the opposite sides of the
G-quadruplex (Figure 3.5c), which is potentially of relevance in the context of
longer DNA as it allows for continuation of the sequence. The use of single molecule
fl uorescence resonance energy transfer enabled detection of G-quadruplexes in the
context of extended DNA duplex.
234
′
and 3
′
