In biology, nucleic acids are carriers of molecular information: DNA’s base sequence stores and imparts genetic instructions, while RNA’s sequence plays the role of a messenger and a regulator of gene expression. As biopolymers, nucleic acids also have exciting physicochemical properties, which can be rationally influenced by the base sequence in myriad ways. Consequently, in recent years nucleic acids have also become important building blocks for bottom-up nanotechnology: as molecules for the self-assembly of molecular nanostructures and also as a material for building machinelike nanodevices. In this Review we will cover the most important developments in this growing field of nucleic acid nanodevices. We also provide an overview of the biochemical and biophysical background of this field and the major “historical” influences that shaped its development. Particular emphasis is laid on DNA molecular motors, molecular robotics, molecular information processing, and applications of nucleic acid nanodevices in biology.

Nucleic acid based molecular devices.

Nucleic acids and analogues are suitable building blocks for reliable self-assembly of nanometer-sized two- or three-dimensional materials. In order to mimic or approach nature with respect to size and function, Angstrom-scale chemical engineering is emerging as pivotal for future developments. Efforts within nucleic acid nanotechnology will be focussed on generating rigid and stable low nanometer-sized structures carrying functionalities with predictable spatial positioning allowing, by encoded self-assembly, functional nucleic acid architectures to be built towards applications within the biological and material sciences.

Nucleic acid nanotechnology-towards Angstrom-scale engineering.

Structures, physicochemical properties, and applications of T–HgII–T, C–AgI–C, and other metallo-base-pairs

In this review several types of interactions between metal ions and DNA are given, starting from basic binding to the use of metal complexes in cancer treatment and diagnostics. Metal cations help to neutralize the negative charge of DNA and thus enable the normal functions of DNA but many other interactions are also possible and are discussed in this paper. Various consequences of such interactions can be reversible (e. g. conformational changes) or irreversible (e. g. cleavage). It is known that some metal ions can also damage DNA which can provoke mutations and in some cases leads to cancer. It is clear that we know a lot about metal-DNA interactions but much more information is needed to understand the role of metal ions completely and to use this knowledge successfully.

Interactions of metal ions with DNA, its constituents and derivatives, which may be relevant for anticancer research

Using in vitro transcription to construct scaffolds for one-dimensional arrays of mercuric ions.

Metal-DNA (M-DNA) is a complex formed between duplex DNA and divalent metal ions which facilitates electron transfer. In this study, 90 base-pair DNA Y-branched junctions were prepared with the ele...

Signal transduction through dye-labeled M-DNA Y-branched junctions: Switching modulated by chemical reduction of anthraquinone

Organic circuit elements and methods are disclosed. An organic circuit element includes a plurality of members, each of which includes an oligonucleotide duplex. The plurality of members includes at least one donor member for receiving conduction electrons from an electron donor, at least one acceptor member for communicating with an electron acceptor to provide a region of attraction for the conduction electrons, and at least one regulator member intersecting with at least one of the plurality of members to define at least one electric field regulation junction, for cooperating with an electric field regulator to regulate an electric field at the junction. A method of regulating an electronic signal between first and second locations in a conductive nucleic acid material includes varying an electrostatic potential at a third location in the nucleic acid material interposed between the first and second locations. The third location may include the regulation junction.

Nucleic acid circuit elements and methods

Organic circuit elements and organic conductors are disclosed, together with electron acceptors and donors that may be chemically modified to alter the conductivity of the circuit or organic conductor. An organic circuit element includes a plurality of members, each of which includes an oligonucleotide duplex. The plurality of members includes at least one donor member for receiving conduction electrons from an electron donor, at least one acceptor member for communicating with an electron acceptor to provide a region of attraction for the conduction electrons, and at least one regulator member intersecting with at least one of the plurality of members to define at least one electric field regulation junction, for cooperating with an electric field regulator to regulate an electric field at the junction. A method of regulating an electronic signal between first and second locations in a conductive nucleic acid material includes chemically modifying an electron acceptor or an electron donor that is coupled to the conductive nucleic acid material.

Chemical switching of nucleic acid circuit elements

M-DNA is an engineered duplex DNA that is synthesized from high doping of transition metal ions (Ni 2+ , Co 2+ and Zn 2+ ) into B-DNA at high pH. X-ray Absorption Near Edge Structure (XANES) of the Nitrogen K-edge shows remarkable differences between the doped and undoped DNA. A metal ion induced conduction band in the M-DNA is used to explain the XANES results.

Local structure of M-DNA at the Nitrogen K-edge: evidence towards a metal ion induced conduction band in DNA.

M-DNA is a complex formed between duplex DNA and divalent metal ions at approximately pH 8.5. 30 base pair linear duplexes were prepared with fluorescein attached to one end, and various electron acceptors at the other. Quenching of the fluorescence emission from fluorescein by the acceptor molecules was observed under conditions corresponding to M-DNA, but not for B-DNA. For the case of anthraquinone as the acceptor, the quenching, which is ascribed to an electron transfer process, was blocked by chemical reduction (NaBH4) of anthraquinone to the dihydroanthraquinone which is not an electron acceptor. Upon the reoxidation of the dihydroanthraquinone by exposure to oxygen the quenching was restored. Quenching of fluorescein fluorescence was also observed in a 90 base pair Y-branched duplex in which rhodamine or anthraquinone were attached to one or two of the remaining arms. Thus the electron transfer process is not impeded by the presence of a junction in the duplex, contrary to results previously reported for B-DNA samples. Again the fluorescein fluorescence could be modulated by reduction of the anthraquinone group in the Y-branched duplexes, mimicking a simple chemical switch. A number of molecular logic functions are demonstrated in M-DNA by considering various chemical inputs, with the level of observed quenching serving as the observed output. Therefore M-DNA may have extraordinary potential for the development of nano-electronic devices.

Chemical Switching and Molecular Logic in Fluorescent-Labeled M-DNA

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