Specifically designed dimeric, planar trimeric, tetrameric, pentameric, and 3D hexameric assemblies of Au nanoparticles were constructed from self-assembling DNA modules that contain disulfide groups, for attachment to the nanoparticles, and covalently linked 2,5-bis(2-thienyl)pyrrole (SNS) monomers. Treatment of these arrays with horseradish peroxidase and H2O2 (HRP/H2O2) results in bond formation between the SNS monomers that cross-links or ligates the DNA modules making the assemblies permanent (“fixed”).

A series of linear and cyclic, sequence controlled, DNA-conjoined copolymers of aniline (ANi) and 2,5-bis(2-thienyl)pyrrole (SNS) were synthesized. In one approach, linear copolymers were prepared from complementary DNA oligomers containing covalently attached SNS and ANi monomers. Hybridization of the oligomers aligns the monomers in the major groove of the DNA. Treatment of the SNS- and ANi-containing duplexes with horseradish peroxidase (HRP) and H2O2 causes rapid and efficient polymerization. In this way, linear copolymers (SNS)4(ANi)6 and (ANi)2(SNS)2(ANi)2(SNS)2(ANi)2 were prepared and analyzed. A second approach to the preparation of linear and cyclic copolymers of ANi and SNS employed a DNA encoded module strategy. In this approach, single-stranded DNA oligomers composed of a central region containing (SNS)6 or (ANi)5 covalently attached monomer blocks and flanking 5′- and 3′-single-strand DNA recognition sequences were combined in buffer solution. Self-assembly of these oligomers by Watson–Crick base pairing of the recognition sequences creates linear or cyclic arrays of SNS and ANi monomer blocks. Treatment of these arrays with HRP/H2O2 causes rapid and efficient polymerization to form copolymers having patterns such as cyclic BBA and linear ABA, where B stands for an (SNS)6 block and A stands for an (ANi)5 block. These DNA-conjoined copolymers were characterized by melting temperature analysis, circular dichroism spectroscopy, native and denaturing polyacrylamide gel electrophoresis, and UV–visible–near-IR optical spectroscopy. The optical spectra of these copolymers are typical of those of conducting polymers and are uniquely dependent on the specific order of monomers in the copolymer.

One-electron oxidation of A/T-rich DNA leads to mutations at thymine. Experimental investigation of DNA containing methyl-deuterated thymine reveals a large isotope effect establishing that cleavage of this carbon–hydrogen bond is involved in the rate-determining step of the reaction. First-principles quantum calculations reveal that the radical cation (electron hole) generated by DNA oxidation, initially located on adenines, localizes on thymine as the proton is lost from the methyl group, demonstrating the role of proton-coupled electron transfer (PCET) in thymine oxidation. Proton transport by structural diffusion along a segmented “water-wire” culminates in proton solvation in the hydration environment, serving as an entropic reservoir that inhibits reversal of the PCET process. These findings provide insight into mutations in A/T-rich DNA such as replication fork stalling that is implicated in early stage carcinogenesis.

Ordered 2,5-bis(2-thienyl)pyrrole (SNS) zipper arrays are formed by hybridization of complementary DNA oligomers each containing covalently bound SNS monomers. Upon oxidation with HRP/H2O2, these SNS arrays are converted to oligomers having specific lengths and conformation. As a consequence of this reaction the two SNS-containing strands are permanently crosslinked.

Oxidatively generated damage to DNA has been implicated as causing mutations that lead to aging and disease. The one-electron oxidation of normal DNA leads to formation of a nucleobase radical cation that hops through the DNA until it is trapped irreversibly, primarily by reaction at guanine. It has been observed that 5-methylcytosine (Cm) is a mutational “hot-spot”. However, Cm in a Watson–Crick base pair with G is not especially susceptible to oxidatively induced damage. Radical cation hopping is inhibited in duplexes that contain C–A or C–T mispairs, but no reaction is detected at cytosine. In contrast, we find that the one-electron oxidation of DNA that contains Cm–A or Cm–T mispairs results primarily in reaction at Cm even in the presence of GG steps. The reaction at Cm is attributed to proton coupled electron transfer, which provides a relatively low activation barrier path for reaction at 5-methylcytosine. This enhanced reactivity of Cm in mispairs may contribute to the formation of mutational hot spots at Cm.

Nanometer-scale arrays of conducting polymers were prepared on scaffolds of self-assembling DNA modules. A series of DNA oligomers was prepared, each containing six 2,5-bis(2-thienyl)pyrrole (SNS) monomer units linked covalently to N4 atoms of alternating cytosines placed between leading and trailing 12-nucleobase recognition sequences. These DNA modules were encoded so the recognition sequences would uniquely associate through Watson–Crick assembly to form closed-cycle or linear arrays of aligned SNS monomers. The melting behavior and electrophoretic migration of these assemblies showed cooperative formation of multicomponent arrays containing two to five DNA modules (i.e., 12–30 SNS monomers). The treatment of these arrays with horseradish peroxidase and H2O2 resulted in oxidative polymerization of the SNS monomers with concomitant ligation of the DNA modules. The resulting cyclic and linear arrays exhibited chemical and optical properties typical of conducting thiophene-like polymers, with a red-end absorption beyond 1250 nm. AFM images of the cyclic array containing 18 SNS units revealed highly regular 10 nm diameter objects.

The feature article is a review of the reaction of thymine in the one-electron oxidation of duplex DNA. Oxidation of DNA causes chemical reactions that result in remote damage (mutation) to a nucleobase. Normally this reaction occurs at guanine, but in oligonucleotides that lack guanines, or when the DNA contains a thymine–thymine mispair, reaction occurs primarily at thymine notwithstanding its high oxidation potential. Selective substitution of uracil for thymine in TT sequences indicates the operation of a tandem reaction mechanism at adjacent thymines. Analysis of the reaction products suggests that proton-coupled electron transfer generates the 5-thymidyl methyl radical, which is trapped by molecular oxygen to give eventually 5-formyl-2′-deoxyuridine and 5-(hydroxymethyl)-2′-deoxyuridine. In a second process, water adds to the 5,6-double bond of the oxidized thymine giving eventually the cis- and trans-diastereomers of 5,6-dihydroxy-5,6-dihydrothymidine.

Specifically designed conducting polymers were prepared from monomers that are covalently linked to duplex DNA. These materials combine the self-assembly properties of DNA with those of conducting polymers and may be valuable in the development of self-directing molecular nanowires. Single-strand DNA oligomers having 2,5-bis(2-thienyl)pyrroles (SNS monomers) covalently linked at every other nucleobase along one strand form stable duplexes with their complementary strands. The duplex DNA serves as a scaffold that aligns the SNS monomers within its major groove. The reaction of these SNS-containing duplexes with horseradish peroxidase and H2O2 (an oxidant) results in the conversion of the SNS monomers to a conjoined (covalently linked) polymer having the optical properties of a conducting polymer. Examination of radiolabeled oligomers confirms bond formation between SNS monomers, and that conclusion is supported by AFM images. The conjoined polymers have structures that are determined and controlled by the DNA template.

Thymine−thymine mispairs are barriers to long-distance radical cation migration and are high reactivity sites in duplex DNA oligomers. A DNA oligomer was prepared that contains only A/T base pairs, arranged into a regularly repeating series of TT steps, and a covalently linked anthraquinone photosensitizer. Its UV irradiation causes the one-electron oxidation of the DNA introducing a radical cation that reacts predominantly at the TT steps as revealed by subsequent strand cleavage. When a remote GG step is introduced into the DNA oligomer, there is little reaction at any of the TT steps and strand cleavage is detected almost exclusively at the GG step. However, when a TT step contains a thymine−thymine mispair, one electron oxidation of the oligomer results in strand cleavage at the mispair and at TT steps preceding it with little reaction at the remote GG step. Experiments in which a thymine in the mispair is replaced by uracil show that the mispair is both a highly reactive site and a barrier to radical cation hopping. These effects of the thymine−thymine mispairs may be associated with its wobble base pair structure.

Ordered 2,5-bis(2-thienyl)pyrrole (SNS) zipper arrays are formed by hybridization of complementary DNA oligomers each containing covalently bound SNS monomers. Upon oxidation with HRP/H2O2, these SNS arrays are converted to oligomers having specific lengths and conformation. As a consequence of this reaction the two SNS-containing strands are permanently crosslinked.

The feature article is a review of the reaction of thymine in the one-electron oxidation of duplex DNA. Oxidation of DNA causes chemical reactions that result in remote damage (mutation) to a nucleobase. Normally this reaction occurs at guanine, but in oligonucleotides that lack guanines, or when the DNA contains a thymine–thymine mispair, reaction occurs primarily at thymine notwithstanding its high oxidation potential. Selective substitution of uracil for thymine in TT sequences indicates the operation of a tandem reaction mechanism at adjacent thymines. Analysis of the reaction products suggests that proton-coupled electron transfer generates the 5-thymidyl methyl radical, which is trapped by molecular oxygen to give eventually 5-formyl-2′-deoxyuridine and 5-(hydroxymethyl)-2′-deoxyuridine. In a second process, water adds to the 5,6-double bond of the oxidized thymine giving eventually the cis- and trans-diastereomers of 5,6-dihydroxy-5,6-dihydrothymidine.