Chemistry Reference
In-Depth Information
small ligands and metal ions (Figure 10.1b), which may generate many isomers from a set
of different ligands and metal ions. A solution to this problem is offered by a strategy for
creating homo- and heterometallic molecules based on the use of ligand-containing
nucleic acid oligomers synthesized by only one, very high yield reaction between back-
bone linkers to which various ligands are attached (Figure 10.1c). Using this strategy,
oligomers with different ligands arranged in any sequence can be obtained in high yield.
The difficulty that remains in the case of oligomers composed exclusively of ligand-con-
taining monomers is the presence of multiple, different coordination sites that may have
comparable affinity for metal ions and thus, upon metal coordination, it can lead to sev-
eral super molecules with different arrangements of the oligomers. This problem can be
alleviated or avoided if the oligomers contain besides ligands another recognition site that
drives the assembly of oligomers in a unique way independent of the metal ion(s) (Figure
10.1d). Ligand-modified nucleic acid duplexes such as those generically represented in
Figure 10.1d are possible outcomes of this strategy. The formation of the duplex is driven
by the information stored in the sequence of nucleobases of the two strands that interact
through Watson-Crick base pairing. Subsequent to the duplex hybridization, metal coor-
dination takes place at the ligand sites rather than at the nucleobases because, under a
wide range of conditions, these sites have higher affinity for the metal ions than the nucle-
obases. Conversely, it is also possible to first self-assemble the ligand-modified nucleic
acid oligomers through metal coordination and then create the conditions for Watson-
Crick hybridization, for example by a change in temperature or by the addition of a com-
plementary oligomer.
The use of ligand-modified nucleic acids to create hybrid inorganic-nucleic acid struc-
tures ensures that the metal binding is site specific rather than uniform, as is the case when
the metal ions bind to either the backbone or the nucleobases of the non-modified nucleic
acid. In DNA, the G-N7 and A-N7 positions are the most common coordination sites for
transition metal ions, with the G-N7 being preferred over the A-N7 site [1]. The factors
that affect metal binding to DNA include: (a) the nucleophilicity of the phosphates and
nucleobases and their hard and soft Lewis base character, respectively, (b) the accessibil-
ity of these groups to metal ions, (c) the molecular electrostatic potential of DNA, (d) the
ability of the groups neighboring the metal coordination site to form hydrogen bonds with
the water molecules coordinated to the metal, and, (e) in the case of binding of multiple
metal ions to the same DNA duplex, the changes in the secondary structure of the DNA
and in the nucleophilicity of the phosphate and nucleobases induced by the first metal ions
that bind to the DNA [2].
Although not site specific, metal binding to non-modified DNA was successfully
exploited to create nano-size, hybrid inorganic-nucleic acid structures with interesting
conduction or charge transfer properties. For example, a conductive silver wire was
obtained by treatment of a DNA scaffold with Ag
þ
,followedbyreductionofAg
þ
to
metallic silver, and subsequent uniform deposition of Ag or Au on the initial Ag clusters
formed on DNA [3,4]. Sequence specificity of the Ag deposition has been achieved by
using RecA proteins for sequence-specific protection of the DNA [5]. While this strategy
offered sequence specificity, the metal ion localization was with cluster/nanometer resolu-
tion rather than atom/angstrom resolution, respectively. A different strategy for the syn-
thesis of hybrid inorganic-nucleic acid structures in which the metal ions are uniformly
distributed on DNA was to coordinate 3d transition metal ions to non-modified DNA at
Search WWH ::
Custom Search