Construction and characterization of metal ion-containing DNA nanowires for synthetic biology and nanotechnology

Abstract

DNA is an attractive candidate for integration into nanoelectronics as a biological nanowire due to its linear geometry, definable base sequence, easy, inexpensive and non-toxic replication and self-assembling properties. Recently we discovered that by intercalating Ag + in polycytosine-mismatch oligonucleotides, the resulting C-Ag + -C duplexes are able to conduct charge efficiently. To map the functionality and biostability of this system, we built and characterized internally-functionalized DNA nanowires through non-canonical, Ag + -mediated base pairing in duplexes containing cytosine-cytosine mismatches. We assessed the thermal and chemical stability of ion-coordinated duplexes in aqueous solutions and conclude that the C-Ag + -C bond forms DNA duplexes with replicable geometry, predictable thermodynamics, and tunable length. We demonstrated continuous ion chain formation in oligonucleotides of 11–50 nucleotides (nt), and enzyme ligation of mixed strands up to six times that length. This construction is feasible without detectable silver nanocluster contaminants. Functional gene parts for the synthesis of DNA- and RNA-based, C-Ag + -C duplexes in a cell-free system have been constructed in an Escherichia coli expression plasmid and added to the open-source BioBrick Registry, paving the way to realizing the promise of inexpensive industrial production. With appropriate design constraints, this conductive variant of DNA demonstrates promise for use in synthetic biological constructs as a dynamic nucleic acid component and contributes molecular electronic functionality to DNA that is not already found in nature. We propose a viable route to fabricating stable DNA nanowires in cell-free and synthetic biological systems for the production of self-assembling nanoelectronic architectures.

Minimal DNA Electron Transfer Catalysts Switched by a Chaotropic Ion

“…A range of techniques have been employed, including microbial systems, protein-directed assembly of metal clusters, metallated base pairs, and biopolymer-directed assembly of nanoparticles. [7][8][9][10][11] With 0.34 nm spacing between nucleobases and exquisite, atomic-precision selfassembly directed by nucleobase hydrogen bonding, nucleic acids are an especially attractive means by which to pursue further miniaturization of electronics. The phosphoramidite synthesis method by which the overwhelming majority of synthetic DNA is produced today allows for inclusion of essentially any chemical functionality, including redox-active side chains and alternative base pairs.…”

“…A range of techniques have been employed, including microbial systems, protein-directed assembly of metal clusters, metallated base pairs, biopolymer-directed assembly of nanoparticles, and minimal peptides. [1][2][3][4][5][6] With 0.34 nm spacing between nucleobases and exquisite, atomic-precision selfassembly directed by nucleobase hydrogen bonding, nucleic acids are an especially attractive means by which to develop programmable electron transfer catalysts. DNA possesses inherent conductivity; a hole generated by a single-electron oxidation can propagate through a double helix.…”

Enzymatic Formation of an Artificial Base Pair Using a Modified Adenine Nucleoside Triphosphate

“…Nucleic acids containing metal base pairs have found applications in numerous fields including the construction of logic gate devices and the development of novel nanomaterials. [55][56][57][58] The enzymatic construction of artificial metal base pairs represents an alluring alternative method that alleviates the synthetic burden and size limitation impaired to traditional approaches involving solidphase synthesis. Here, we demonstrate that the two synthetic analogues dIm C and dPur P can be used for the enzymatic synthesis of Ag + -mediated base pairs.…”

Enzymatic Formation of an Artificial Base Pair Using a Modified Purine Nucleoside Triphosphate

“…Nucleic acids containing metal base pairs have found applications in numerous fields including the construction of logic gate devices and the development of novel nanomaterials. [65][66][67][68] The enzymatic construction of artificial metal base pairs represents an alluring alternative method that alleviates the synthetic burden and size limitation impaired to traditional approaches involving solid-phase synthesis.…”