Anchoring for DNA: A lipophilic oligonucleotide consisting of 21 thymidine units and two lipophilic nucleotides L was synthesized and bound to vesicular surfaces (see fluorescence image). The membrane‐bound oligonucleotide binds complementary DNA strands by formation of Watson–Crick base pairs. The lipid‐anchored oligonucleotide is preferentially enriched in liquid‐disordered membrane domains.

RNA aptamers are in vitro-selected binding domains that recognize their respective ligand with high affinity and specificity. They are characterized by complex three-dimensional conformations providing preformed binding pockets that undergo conformational changes upon ligand binding. Small molecule-binding aptamers have been exploited as synthetic riboswitches for conditional gene expression in various organisms. In the present study, double electron-electron resonance (DEER) spectroscopy combined with site-directed spin labeling was used to elucidate the conformational transition of a tetracycline aptamer upon ligand binding. Different sites were selected for post-synthetic introduction of either the (1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl) methanethiosulfonate by reaction with a 4-thiouridine modified RNA or of 4-isocyanato-2,6-tetramethylpiperidyl-N-oxid spin label by reaction with 29-aminouridine modified RNA. The results of the DEER experiments indicate the presence of a thermodynamic equilibrium between two aptamer conformations in the free state and capture of one conformation upon tetracycline binding.

Allosteric regulation is a fundamental principle in nature. Most enzymes working in metabolic pathways are regulated by interaction with other molecules acting as allosteric cofactors. Over the past decade, RNA conformation has been shown to respond to external stimuli. A number of ligand-specific molecular switches that are composed of aptamers attached to ribozyme structures have been developed.[1] Binding of a specific ligand to the aptamer domain either stabilizes or destabilizes the active conformation of the catalytic domain and results in an increase or decrease in catalytic activity. Riboswitches have also been discovered in nature; the mRNA conformation is changed upon interaction with a specific ligand and this results in inhibition/disruption of transcription or translation.[2] Although natural riboswitches can run through many cycles of switching, artificial riboswitches do not work in a reversible mode: the activity is either switched on or off in response to the addition of the allosteric cofactor. We set out to develop a system that has the potential to be regulated in a reversible manner. To this end, we have designed a hairpin ribozyme variant whose catalytic properties are dependent on flavine mononucleotide (FMN). Herein we show that ribozyme activity is switched on in the presence of FMN in the oxidized state, whereas under reducing conditions, FMN is released from its binding site and a clear decline in activity results.To construct hairpin ribozyme variants that can be regulated in an allosteric way, we decided to replace helix 4 of the wild-type hairpin ribozyme [3] (Figure 1) with a specific sequence. This sequence acts as a communication module and connects the ribozyme moiety with the FMN-specific aptamer, which was previously identified by in vitro selection. [4] The 11-nucleotide bulge segment (nucleotides 8-13 and 24-28 in Figure 1 b) has been used before for the construction of FMN-dependent hammerhead aptazymes [5] and for competitive regulation of modular allosteric aptazymes by a small molecule and an oligonucleotide effector.[6] Furthermore, a natural RNA fold within mRNA has been discovered that specifically interacts with FMN to regulate the expression of bacterial genes involved in the biosynthesis and transport of riboflavin and FMN. [7] We have engineered two variants of hairpin aptazymes, HPAR2 and HPAR5 (Figure 1). In the absence of FMN, we expected the conformation of loop B to be less stable. Binding of FMN to the aptamer domain should trigger a conformational change within the bridge that in turn should cause a structural rearrangement of the adjoining ribozyme, thus dictating its activity. The communication module used in HPAR2 was developed by in vitro selection

Nowadays, RNA synthesis has become an essential tool not only in the field of molecular biology and medicine, but also in areas like molecular diagnostics and material sciences. Beyond synthetic RNAs for antisense, aptamer, ribozyme, and siRNA technologies, oligoribonucleotides carrying site-specific modifications for structure and function studies are needed. This often requires labeling of the RNA with a suitable spectroscopic reporter group. Herein, we describe the synthesis of functionalized monomer building blocks that upon incorporation in RNA allow for selective reaction with a specific reporter or functional entity. In particular, we report on the synthesis of 5′-O-dimethoxytrityl-2′-O-tert-butyldimethylsilyl protected 3′-O-phosphoramidites of nucleosides that carry amino linkers of different lengths and flexibility at the heterocyclic base, their incorporation in a variety of RNAs, and postsynthetic conjugation with fluorescent dyes and nitroxide spin labels. Further, we show the synthesis of a flavine mononucleotide-N-hydroxy-succinimidyl ester and its conjugation to amino functionalized RNA.