A New Architecture for DNA-Templated Synthesis in Which Abasic Sites Protect Reactants from Degradation.

The synthesis of artificial sequence-defined polymers that match and extend the functionality of proteins is an important goal in materials science. One way of achieving this is to program a sequence of chemical reactions between precursor building blocks by means of attached oligonucleotide adapters. However, hydrolysis of the reactive building blocks has so far limited the length and yield of product that can be obtained using DNA-templated reactions. Here, we report an architecture for DNA-templated synthesis in which reactants are tethered at internal abasic sites on opposite strands of a DNA duplex. We show that an abasic site within a DNA duplex can protect a nearby thioester from degradation, significantly increasing the yield of a DNA-templated reaction. This protective effect has the potential to overcome the challenges associated with programmable, sequence-controlled synthesis of long non-natural polymers by extending the lifetime of the reactive building blocks.

Surface Hybridization Chain Reaction of Binary Mixture DNA-PEG Corona Nanostructures Produced by Low-Volume RAFT-Mediated Photopolymerization-Induced Self-Assembly.

DNA-polymer hybrids have been attracting interest as adaptable functional materials by combining the stability of polymers with DNA nanotechnology. Both research fields have in common the capacity to be precise, versatile, and tunable, a prerequisite for creating powerful tools which can be easily tailored and adapted for bio-related applications. However, the conjugation of hydrophilic DNA with hydrophobic polymers remains challenging. In recent years, polymerization-induced self-assembly (PISA) has attracted significant attention for constructing nano-objects of various morphologies owing to the one-step nature of the process, creating a beneficial method for the creation of amphiphilic DNA-polymer nanostructures. This process not only allows pure DNA-polymer-based systems to be produced but also enables the mixture of other polymeric species with DNA conjugates. Here, we present the first report of a DNA-PEG corona nano-object's synthesis without the addition of an external photoinitiator or photocatalyst via photo-PISA. Furthermore, this work shows the use of DNA-macroCTA, which was first synthesized using a solid-support method resulting in high yields, easy upscaling, and no need for HPLC purification. In addition, to the formation of DNA-polymer structures, increasing the nucleic acid loading of assemblies is of great importance. One of the most intriguing phenomena of DNA is the hybridization of single-stranded DNA with a second strand, increasing the nucleic acid content. However, hybridization of DNA in a particle corona may destabilize the nanomaterial due to the electrostatic repulsive force on the DNA corona. Here, we have investigated how changing the DNA volume fraction in hybrid DNA-polymer self-assembled material affects the morphology. Moreover, the effect of the corona composition on the stability of the system during the hybridization was studied. Additionally, the hybridization chain reaction was successfully applied as a new method to increase the amount of DNA on a DNA-based nano-object without disturbing the morphology achieving a fluorescence signal amplification.

Changed reactivity of secondary hydroxy groups in C8-modified adenosine - lessons learned from silylation.

Synthesis of site-specifically modified oligonucleotides has become a major tool for RNA structure and function studies. Reporter groups or specific functional entities are required to be attached at a pre-defined site of the oligomer. An attractive strategy is the incorporation of suitably functionalized building blocks that allow post-synthetic conjugation of the desired moiety. A C8-alkynyl-modified adenosine derivative was synthesized, reviving an old synthetic pathway for iodination of purine nucleobases. Silylation of the C8-alkynyl-modified adenosine revealed unexpected selectivity of the two secondary sugar hydroxy groups, with the 3'-O-isomer being preferentially formed. Optimization of the protection scheme lead to a new and economic route to the desired C8-alkynylated building block and its incorporation in RNA.

Reductive Charge Transfer through an RNA Aptamer.

The transfer of charges through double helical DNA is a very well investigated bioelectric phenomenon. RNA, on the contrary, has been less studied in this regard. The few available data report on charge transfer through RNA duplex structures mainly composed of homonucleotide sequences. In the light of the RNA world scenarios, it is an interesting question, if charge transfer can be coupled with RNA function. Functional RNAs however, contain versatile structural motifs. Therefore, electron transport also through non-Watson-Crick base-paired regions might be required. We here demonstrate distance-dependent reductive charge transfer through RNA duplexes and through the non-Watson-Crick base-paired region of an RNA aptamer.

Preparation and characterization of pyrene modified uridine derivatives as potential electron donors in RNA.

Charge transfer across double stranded DNA was observed for the first time about 20 years ago, and ever since it has been the subject of a large number of studies. RNA has been hardly investigated in this regard, which not least is due to the lack of suitably functionalized ribonucleotide building blocks to serve as electron sources upon incorporation into oligoribonucleotides. We have synthesized two uridine derivatives carrying pyrene or dimethylaminopyrene linked to C5 of the nucleobase. The key to successful synthesis was the adaptation of Suzuki-Miyaura conditions to the coupling of the pyrene moiety with the ribonucleoside. Final decoration of the pyrenylated nucleosides with standard 5'-O- and 2'-O-protecting groups and subsequent 3'-O-phosphitylation delivered the building blocks for incorporation into RNA. Spectroscopic analysis of the two pyrenylated uridines and of the accordingly modified oligonucleotides showed that in particular the dimethyaminopyrene functionalized nucleoside is a promising candidate as an electron source for RNA charge transport studies.

Ribozymes that can be regulated by external stimuli.

Ribozymes have been known for about 30 years, and nowadays are understood well enough to be turned into useful tools for a number of applications in vitro and in vivo. Allosteric ribozymes switch on and off their activity in response to a specific chemical (ligand) or physical (temperature, light) signal. The possibility of controlling ribozyme activity by external stimuli is of particular relevance for applications in different fields, such as environmental and medicinal diagnostics, molecular computing, control of gene expression and others. Herein, we review recent advances and describe selected examples of addressable ribozymes.

Preparation of modified long-mer RNAs and analysis of FMN binding to the ypaA aptamer from B. subtilis.

In recent years, RNA has been shown to fulfil a number of cellular functions. This has led to much interest in elucidation of the structure of functional RNA molecules, and thus, in the preparation of suitably functionalized RNAs. The chemical synthesis of RNAs allows for the site-specific modification; however, is limited to sequences of about 60-70 nucleotides in length. At the example of the flavine mononucleotide (FMN) responsive aptamer of the ypaA riboswitch from B. subtilis, we demonstrate the highly efficient preparation of site-specifically modified long-mer RNAs. Our strategy consists of the chemical synthesis of fragments followed by enzymatic or chemical ligation. Splint ligation with T4 RNA ligase turned out to be most successful among the enyzymatic protocols. Highly efficient chemical ligation was performed by azide-alkyne cycloaddition of suitably modified RNA fragments. Wild-type and 2-aminopurine (2-AP)-modified variants of the ypaA aptamer were prepared. FMN binding to all synthesized ypaA aptamer variants is demonstrated. However, dissociation of FMN from its binding site by reduction of the isoalloxazin unit as demonstrated before for a small-hairpin-derived aptazyme could not be shown. This implies that either FMN is less accessible to reduction when it is bound to its natural aptamer; that reduced FMN remains bound to the aptamer; or that FMN upon reduction indeed is released from its binding site, without the aptamer folding back in the natural ligand-free state. The results of this study are of general interest to the preparation of site-specifically modified RNAs for investigation into structure and function.