Redox-active metal-containing nucleotides: synthesis, tunability, and enzymatic incorporation into DNA

Hydrogen-bond self-assembly of DNA-analogues into hexameric rosettes

The self-assembly of a DNA-analogue hexameric rosette from triaminopyrimidine and cyanuric acid-based nucleosides, and its subsequent aggregation into rod-like morphologies is reported.

Template-directed assembly and characterization of metallosalen-DNA conjugates

Nucleic acid template-directed synthesis represents a powerful method for the encoded synthesis of new bioconjugates. Our laboratory previously reported a strategy for the synthesis of a new metal-DNA hybrid, metallosalen-DNA, by the DNA or RNA template-directed cross-linking of two salicylaldehyde-modified DNA oligonucleotides. The current manuscript describes the optimal assembly requirements and biophysical characterization of metallosalen-DNA conjugates containing nickel and manganese ions. Competitive assembly reactions demonstrated the template-directed nature of metallosalen-DNA formation. A single metallosalen-DNA conjugate was assembled selectively in the presence of two pairs of salicylaldehyde precursor strands and a single DNA template. Assembly reactions were sensitive to base pair mismatches in the pairing arms. Single base mismatches resulted in a loss of metallosalen-DNA conjugate yield. Metallosalen-DNA assembly yields depended on the identity and length of the template spacer, the reaction pH, and the type of metal and diamine utilized in the assembly reaction. Metallosalen-DNA conjugates were stable to a variety of conditions, including extended incubation at 50 degrees C. Nickel metallosalen-DNA remained unchanged after incubation at 80 degrees C for 24 h, while decomposition of manganese metallosalen-DNA was observed under the same conditions. Circular dichroism (CD) spectroscopy indicated that DNA duplexes containing internal metallosalen moieties adopted B-form double helices. UV thermal denaturation analysis demonstrated that 32-nucleotide duplexes containing internal metallosalen modifications displayed melting temperatures approximately 5 degrees C less than unmodified DNA duplexes.

Polymer-DNA hybrids as electrochemical probes for the detection of DNA

The syntheses of several norbornene block copolymers containing oligonucleotide and ferrocenyl side chains and their use in the electrochemical detection of DNA are described. Two kinds of DNA-containing block copolymers with either ferrocenyl or dibromoferrocenyl groups were prepared via ring-opening metathesis polymerization (ROMP). Based on these two distinct ferrocene derivatives, a triblock copolymer labeling strategy was developed. With this strategy, the identity of DNA target can be determined by the E1/2s of the ferrocenyl moieties and the ratio of peak currents. These polymers exhibit predictable and tailorable electrochemical properties, high DNA duplex stability, and unusually sharp melting transitions, which are highly desirable characteristics for DNA detection applications. Significantly, single-base mismatches could be easily detected using two distinct block copolymers as dual-channel detection probes in an electrochemical DNA detection format.

Proximity extension of circular DNA aptamers with real-time protein detection

Multivalent circular aptamers or 'captamers' have recently been introduced through the merger of aptameric recognition functions with the basic principles of DNA nanotechnology. Aptamers have strong utility as protein-binding motifs for diagnostic applications, where their ease of discovery, thermal stability and low cost make them ideal components for incorporation into targeted protein assays. Here we report upon a property specific to circular DNA aptamers: their intrinsic compatibility with a highly sensitive protein detection method termed the 'proximity extension' assay. The circular DNA architecture facilitates the integration of multiple functional elements into a single molecule: aptameric target recognition, nucleic acid hybridization specificity and rolling circle amplification. Successful exploitation of these properties is demonstrated for the molecular analysis of thrombin, with the assay delivering a detection limit nearly three orders of magnitude below the dissociation constants of the two contributing aptamer-thrombin interactions. Real-time signal amplification and detection under isothermal conditions points towards potential clinical applications, with both fluorescent and bioelectronic methods of detection achieved. This application elaborates the pleiotropic properties of circular DNA aptamers beyond the stability, potency and multitargeting characteristics described earlier.

Proofreading genotyping assays and electrochemical detection of SNPs

The use of proofreading DNA polymerases in genotyping assays offers the prospect of improved performance. To this end, we have recently used compatible DNA polymerases, protected primers, and substrates to implement proofreading single base extension (P-SBE) and proofreading allele-specific extension (PRASE) assays. Key aspects of the P-SBE and related proofreading assay formats are described here. For transduction of genotyping reactions into physical signals, electrochemical SBE implementations may offer simple, inexpensive assays in electrode array or electrophoretic formats. We have developed electrochemically-labeled nucleotides and electrode detection methods with a view to these applications. Detection of electrochemically-labeled SBE products on an oligonucleotide-modified gold electrode surface is demonstrated.

Multipotential electrochemical detection of primer extension reactions on DNA self-assembled monolayers

Electroactive nucleoside triphosphates ("electrotides") have been incorporated into primers by DNA polymerase and detected on oligonucleotide surface-assembled monolayers. Four electrotides bearing three different electroactive moieties-ferrocene, vinylferrocene, and anthraquinone-are detected in four alternative formats.

Rigid, conjugated, fluoresceinated thymidine triphosphates: syntheses and polymerase mediated incorporation into DNA analogues

Syntheses of a unique set of energy transfer dye labeled nucleoside triphosphates, compounds 1-3, are described. Attempts to prepare these compounds were only successful if the triphosphorylation reaction was performed before coupling the dye to the nucleobase, and not the other way around. Compounds were prepared as both the 2'-deoxy (a) and 2',3'-dideoxy- (b) forms. They feature progressively longer rigid conjugated linkers connecting the nucleobase and the hydroxyxanthone moiety. UV spectra of the parent nucleosides 12-14 show that as the length of the linker increases so does the absorption of the donor in the 320-330 nm region, but with relatively little red-shift of the maxima. Fluorescence spectra of the same compounds show that radiation in the 320-330 nm region results in predominant emission from the fluorescein. When the linker is irradiated at 320 nm, the only significant emission observed corresponds to the hydroxyxanthone part of the molecules at 520 nm; this corresponds to an effective Stokes' shift of 200 nm. As the absorption at 320-330 nm by the linker increases with length, so does the intensity of the fluorescein emission. A gel assay was used to gauge relative incorporation efficiencies of compounds 1-3, dTTP, ddTTP, and 6-TAMRA-ddTTP. Throughout, the thermostable polymerase TaqFS was used, as it is the one most widely applied in high throughput DNA sequencing. This assay showed that only compounds 3 were incorporated efficiently; these have the longest linkers. Of these, the 2'-deoxy nucleoside 3 a was incorporated and did not prevent the polymerase from extending the chain further. The 2',3'-dideoxy nucleoside 3 b was incorporated only about 430 times less efficiently than ddTTP under the same conditions, and caused chain termination. The implications of these studies on modified sequencing protocols are discussed.

2',5'-linked DNA is a template for polymerase-directed DNA synthesis

Genomes are composed of nucleic acids bearing 3',5'-phosphodiester-linked sugars. The 2',5'-phosphodiester linkage is a fundamental alternative to the natural linkage and is the predominant product of most nontemplate, nonenzymatic oligomerizations of nucleotide monomers. This fact suggests a chemical bias for the formation of 2',5'-phosphodiester bonds, an important consideration in the context of molecular evolution on Earth or elsewhere. Although 2',5'-linked RNA occurs naturally, it is evidently not used to encode genetic information. Nevertheless, the capacity of the 2',5'-phosphodiester linkage to serve as a genetic material has been probed in laboratory experiments. Initial studies examined both self-pairing and pairing with natural nucleic acids. These studies showed that, while 2',5'-linked DNA and RNA form double and triple helices with themselves, their interactions with natural nucleic acids are asymmetric-pairing is seen with 3',5'-linked RNA but not DNA. Although the ability to form a stable structure (such as a helix) is likely a necessary condition for nonenzymatic information transfer, in the case of enzymatic reactions this precondition may be expected to be lifted in cases where the enzyme can serve as a "template for the template" and make up for structural deficiencies that would be fatal to its abiotic counterpart. In support of this suggestion, we demonstrate that 2',5'-linked DNA is a template for enzymatic synthesis of natural DNA with a variety of DNA polymerases and reverse transcriptases directing the incorporation of all four natural nucleotides with fidelity.

A massively parallel electrochemical approach to the miniaturization of organic micro- and nanostructures on surfaces

This paper describes a simple and convenient strategy for reducing the dimensions of organic micro-and nanostructures on metal surfaces. By varying electrochemical desorption conditions, features patterned by dip-pen nanolithography or micro contact printing and made of linear alkanethiols or selenols can be gradually desorbed in a controlled fashion. The process is referred to as electrochemical whittling because the adsorbate desorption is initiated at the exterior of the feature and moves inward as a function of time. The whittling process and adsorbate desorption were studied as a function of substrate morphology, adsorbate head and tail groups, and electrolyte solvent and salt. Importantly, one can independently address different nanostructures made of different adsorbates and effect their miniaturization based upon ajudicious selection of adsorbate, applied potential, and supporting electrolyte. Some of the physical and chemical origins of these observations have been elucidated.

Oligonucleotides with strongly fluorescent groups pi-conjugated to a nucleobase: syntheses, melting temperatures, and conformation

Phosphoramidite 1 was prepared, incorporated into oligonucleotides, and these were studied via thermal denaturation and circular dichroism.

Single base extension (SBE) with proofreading polymerases and phosphorothioate primers: improved fidelity in single-substrate assays

Model single base extension (SBE) genotyping reactions with individual deoxy-, dideoxy- and acyclonucleoside triphosphates are monitored by MALDI-TOF mass spectrometry. Three non-proofreading DNA polymerases display remarkably high misincorporation (up to 64% of correct incorporation) when extending primers with single substrates at saturating concentrations. Introduction of one phosphorothioate (PS) linkage into the primer 3' terminus reduces misincorporation by these enzymes an average 1.4-fold (range 0- to 3.5-fold) versus correct incorporation. Combined use of 3'-PS primers with strongly proofreading DNA polymerases yields order of magnitude improvements in SBE fidelity over those produced by the equivalent non-proofreading enzymes. Errors are reduced to below MALDI-TOF detectable levels in almost all cases. The Sp diastereomer of the 3'-PS primer, which can be prepared in situ by incubation with proofreading polymerase, is stable to 3'-exonuclease activity over periods longer than 16 h. Products of correct extension by T7 DNAP are retained over 30-60 min during idling turnover at a dNTP concentration of 2.5 micro M, indicating that the assay can be applied over a broad range of substrate concentrations. These results suggest that the use of PS primers and proofreading polymerases will offer a simple and cost-effective means to improve fidelity in a range of single-substrate SBE assay formats.