Biomedical Engineering Reference
In-Depth Information
a
b
nucleoprotein filament
+
RecA
+
AgNO
3
Ag aggregates
aldehyde-derivatized dsDNA
c
exposed DNA
Au wire
Fig. 5.4
Main processes in sequence-specific molecular lithography: (
a
) binding of a nucleopro-
tein filament on aldehyde-derivatized dsDNA, (
b
) formation of Ag aggregates by an incubation
of the resulting structure in (
a
) a AgNO
3
solution, (
c
) formation of a metallization gap in regions
protected by RecA
It should be mentioned that DNA metallization can be achieved not only by using
DNA as a template but also by replacing each imino proton of each base pair with
a metal ion. The resulting conducting DNA is called M-DNA. A 15
m-long
M-DNA molecule that uses phage œ-DNA has been reported in
Rakitin et al.
(
2001
),
the substituting Zn
2C
metal ion being spaced at about 4 A irrespective of the base
sequence. This conductive wire has sticky ends to attach to electrodes. Imino proton
substitution occurs at a pH of 9.0, and, as a consequence, the DNA molecule
acquired metallic-like conduction, characterized by a finite zero bias conductance.
Metal ions can also be introduced into proteins, more precisely into natural or
synthetic polypeptide sequences that fold into three-dimensional structures and able
to bind a metal ion (
Lu et al. 2009
). We do not refer further to this metallization
procedure.
It is often desirable that not all, but only a part of a molecular wire is met-
allized, task accomplished by the sequence-specific molecular lithography (
Keren
et al. 2002
). In this process, schematically represented in Fig.
5.4
, a nucleoprotein
filament is first formed by polymerizing RecA proteins from the
Escherichia coli
bacteria on an ssDNA probe molecule, the filament binding in a subsequent process
at a 2,027-base-pair (bp)-long homologous sequence on an aldehyde-derivatized
dsDNA substrate that contains 48,502 bp. In the homologous recombination, two
DNA molecules (a long dsDNA that acts as scaffold and a short ssDNA) with
sequence homology cross over at equivalent sites. In the following step, after
incubation in a solution of AgNO
3
, Ag aggregates form on the substrate except
at regions protected by RecA. These aggregates act then as catalysts for electroless
Au deposition, such that the unprotected regions are transformed into conductive
metal wires. The high-resolution lithography, which has as a result continuous gold
wires interrupted by gaps at specific locations, is guided by DNA substrate and probe
molecules, while RecA proteins act as a resist, protecting the covered DNA segment
against metallization, and incentive for the homologous recombination. The size
and location of the insulating gap is controlled by the length and base sequence
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