Chemistry Reference
In-Depth Information
of aptamer clones have been used to scrutinize their ability to bind NMM. As a result
among both P and PS families, the aptamers able to bind NMM contain guanine-rich
regions. The selected aptamers used to study the binding affinities were able to bind
NMM with sub-micromolar affinity, but the discrimination capability between
NMM and MPIX, despite the lower affinity toward the latter, is not very high in
the used experimental conditions. The binding sites of NMM involve the guanine N7
nitrogens in hydrogen bonding or metal binding. Iron (III) porphyrins, in the
presence of strong oxidizing agents, are able to promote strand DNA cleavage,
thus suggesting the capability of hemin (or meso-hemin) bound to aptamers to define
binding domains as in situ footprints.
To summarize, for the small aptamers (PS2) DMS and hemin/KO
2
, footprinting
data indicated that the guanine-rich domains are responsible for binding porphyrins.
The DNase I digestion data suggested that, for PS2, the conformation changes and
the enzyme accessibility can extend well beyond the domains defined by the other
two footprinting techniques.
Mutually consistent data referred to aptamers and short nucleotide oligomer
indicate that NMM didn't bind to a preexisting higher-order structure formed by
G-rich motif, but, more likely, induce distinctive folding patterns for the binding
motif, thus influencing the overall folded structure of a number of aptamers.
UV absorption spectroscopy and CD spectroscopy investigated the mode of
binding of NMM to folded aptamers. The UV data show a strong hypochromic
effect (~10%), in the NMM (1
ʼ
M) Soret region, in the presence of an excess
(5
M) of PS2. No significant shift (~1 nm) is observed. As to the CD data, the short
oligonucleotide did not give any CD signal in the absence of NMM while a more
structured signal is observed in the presence of NMM, thus pointing to an overall
nonhelical content of this small DNA molecule. PS2 gives the expected B-DNA CD
spectrum that remains almost unvaried in the presence of NMM. No porphyrin
CD-induced signal is observed in the porphyrin Soret region.
In the present study, the guanine quartets (G-quartets) might be responsible for
NMM binding. The formation of G-G Hoogsteen hydrogen bonds can be responsi-
ble for the methylation protection observed for some of the studied aptamers even
in the absence of NMM.
The interaction of NMM with folded DNA structures that possibly contain one
or more G-quartets cannot be promoted by a classic intercalation mechanism as
suggested by UV and CD measurements. In fact, the interaction of DNA-binding
drugs with G-quartets through classical intercalation mechanism between adjacent
G-quartets is accompanied by significant red shift and about 20% hypochromicity
of the visible (ethidium) adsorption band.
Lauceri et al. [
167
] investigated the interactions of carboranylated porphyrin
with DNA (Fig.
18
). Water-soluble anionic nido-carboranyl-containing porphyrins
have been proposed as boron delivery drugs in boron neutron capture therapy
(BNCT) of tumors [
168
-
171
].
They highlight the importance of porphyrin inner core protonation. In fact,
p-H
2
TCP
4
has a high p
K
a (7.4), thus resulting to be fully protonated at pH 7.
Spectral UV evidence (small red shift ~2 nm) and hypochromicity (~10%),
ʼ
