Controlled Nucleation of DNA Metallization

Abstract

The outstanding self-recognition properties of DNA have been exploited in the use of this biomolecule as a template for the construction of nanoscale assemblies [1] and hybrid structures. [2,3] To further expand the utility of DNA for other applications, research is currently aimed at increasing its intrinsically low electric conductivity.[4] The selective coating of DNA with a thin layer of a conductive element, such as Ag, [5] Pd, [6] Pt, [7] Cu, [8] or Co, [9] has emerged as a promising avenue. Most coating procedures involve the reduction of electrostatically bound metal ions on the DNA by an exogeneous reductant to give small metal clusters attached to the DNA. In a second, development step, known from black-andwhite photography, these metal clusters function as nucleation sites for the reductive deposition of metal atoms until a continuous conductive coating is formed. Novel procedures aimed at increasing the selectivity of the metallization process are the decoration of DNA with functional groups to control the spatial distribution of the nucleation sites, [10] the photochemical deposition of silver on DNA strands, [11] and the formation of DNA-Pt II adducts as precursors for metal deposition on DNA.[12] The most critical step in the whole metallization process is the initial nucleation step. The uniformity and the distribution of the metal clusters define the homogeneity of the development step and hence the result of the metallization process. Unfortunately, nucleation in chemical reactions is still a poorly understood process and is therefore difficult to control.To coat DNA with silver, small silver clusters Ag n (n = 2, 4, 6…) that are able to undergo a development process need to be deposited on the DNA. These clusters can be formed in a redox reaction between Ag + in solution and aldehyde groups present on the DNA (Tollens reaction). Owing to the stoichiometry of the redox process, one aldehyde group can reduce two silver ions to form an Ag 2 cluster. Dialdehyde groups should be able to form an Ag 4 cluster (Scheme 1). It is suspected that these Ag 4 clusters, as a result of their electronic structure, are the smallest stable, developable (magic-size) silver clusters.[13] If this hypothesis is correct, the controlled formation of Ag 4 clusters on DNA should enable more reliable DNA metallization.To construct DNA with dialdehyde moieties, we functionalized DNA with cis-3,4-dihydroxypyrrolidine units, which Scheme 1. Transformation of diol-modified DNA-1 and DNA-3 into aldehyde-and dialdehyde-modified DNA-2 and DNA-4, followed by metallization steps.

Direct Polymerase Synthesis of Reactive Aldehyde‐Functionalized DNA and Its Conjugation and Staining with Hydrazines

“…When using 287 nt template, Pwo polymerase did not work, while Vent(exo À ) gave only weak amplification. Only the use of KOD XL polymerase [7] gave efficient amplification with this template (Figure 1 c). Therefore, the KOD XL polymerase was then used for successful PCR amplification of a long 1162 nt template (Figure 1 d).…”

“…The syntheses of the nucleoside/nucleotide monomers were laborious multistep procedures and additional post-synthetic steps were required to release the aldehyde function in DNA. [7,8] Metallization [7] or interstrand cross-linking [8] were demonstrated to be very useful applications of aldehyde-modified oligonucleotides (ONs) or DNA. Therefore we decided to develop a simple and efficient direct protocol for construction of aldehyde-modified DNA by application of our two-step (cross-coupling polymerase incorporation) method.…”

“…However, it was considered too reactive and fragile to be incorporated directly (chemically or enzymatically) [6] and the few successful examples were prepared indirectly by a click reaction with azide derivatives of reducing sugars, [3] or by introduction of 2,3-dihydroxypropyl or 3,4-dihydroxypyrrolidine moieties [7,8] and subsequent oxidative cleavage of the vicinal diols to (di)aldehydes. The syntheses of the nucleoside/nucleotide monomers were laborious multistep procedures and additional post-synthetic steps were required to release the aldehyde function in DNA.…”

Metallic Nanostructures Based on DNA Nanoshapes

“…They found that a negatively-charged silicon oxide surface itself could act as a reducing agent. Wirges et al [67] introduced an alternative pathway to form linear, pearl necklace-shaped nanowires, by binding two- and four-ion silver clusters onto DNA. This protocol utilized the well-known reaction of monoaldehyde and dialdehyde molecules and the Tollens solution, where the silver clusters act as nucleation centers for the following growth process.…”

Nucleotides and nucleic acids; oligo- and polynucleotides

“…These dicarboxylic acid derivatives have then been used to lay down silver ion clusters on the surface of the duplex DNA to give metalized DNA structures. 176 Various hydrophobic 5-vinyl-dU analogues have been examined in a template-directed photoligation reaction with either cytosine or 5-methylcytosine. It was shown that more hydrophobic groups, such as 5-heptenyl, showed a ligation-selectivity with 5-methyl-dC up to five times greater than for dC.…”