Chemistry Reference
In-Depth Information
genes (1kb upstream of the transcription start site) are signifi cantly enriched in
potential G-quadruplex motifs relative to the rest of the genome.
21,211,212
Further-
more, the regions of the human genome that are both nuclease hypersensitive and
within promoters show a remarkable 230-fold enrichment of G-quadruplex ele-
ments, compared to the rest of the genome.
21
Sequences that have been studied for
potential to form G-quadruplexes are
c - myc
,
46,79,213 - 218
bcl2
,
219 - 222
VEGF,
223
KRAS,
224,225
RET,
226
HIF - 1 a
227
and
c - kit
.
228 - 230
Structures adopted by these sequences, which are
often composed of more than four G-tracts, are affected by their occurrence in the
context of double-stranded DNA. The number of possible G-quadruplex structures
is increased due to the fact that each of the G-tracts contains unequal number of
guanines and that G-tracts are separated by different numbers of nucleotides.
The
c - myc
gene and the respective protein are implicated in many cancers. The
nuclease hypersensitivity element III
1
controls up to 90% of total
c - myc
transcrip-
tion. The guanine-rich sequence of this element contains six G-tracts, which result
in multiple G-quadruplex folds that cannot be characterized individually by NMR.
Early efforts in structure determination focused on the G-quadruplex that was
formed by four of the six guanine tracts. Extensive search for suitable sequences
afforded two sequences that exhibited suffi ciently resolved NMR spectra, which
corresponded to a single structure that enabled structure determination.
231
One of
the sequences named
c - myc - 2345
involved the second, third, fourth and fi fth guanine
tracts. The high-resolution structure of
c - myc - 2345
oligonucleotide in the presence
of K
+
ions has been determined by NMR (Figure 3.5a).
231
This G - quadruplex rep-
resents an intramolecular propeller-type structure with all the strands in the parallel
orientation. All guanines are in
anti
conformation. The structure consists of three
G-quartets which are oriented in the same direction. All three loops are of double-
chain reversal type. The structure resembles a parallel G-quadruplex with three
double-chain reversal loops that was observed for the human telomere repeats in
Figure 3.5
(Plate 3)
Representative structures of gene promoter regions: (a) G-quadruplex
fold formed by guanine tracts of
c-myc-2345
and
c-myc-1245
sequences originating from the
c-myc
promoter, determined by NMR;
231
(b) topology adopted by the
c-myc-23456
sequence
containing fi ve of the six guanine tracts of the
c-myc
promoter region;
232
(c) NMR structure
of unprecedented intramolecular G-quadruplex formed by a G-rich sequence in the
c-kit
promoter in K
+
solution
233
(See colour plate section)
