Simultaneous Localization of Two High Affinity Divalent Metal Ion Binding Sites in the Tetracycline RNA Aptamer with Mn2+-Based Pulsed Dipolar EPR Spectroscopy

Mg2+ ions play an essential part in stabilizing the tertiary structure of nucleic acids. While the importance of these ions is well documented, their localization and elucidation of their role in the structure and dynamics of nucleic acids are often challenging. In this work, pulsed electron-electron double resonance spectroscopy (PELDOR, also known as DEER) was used to localize two high affinity divalent metal ion binding sites in the tetracycline RNA aptamer with high accuracy. For this purpose, the aptamer was labeled at different positions with a semirigid nitroxide spin label and diamagnetic Mg2+ was replaced with paramagnetic Mn2+, which did not alter the folding process or ligand binding. Out of the several divalent metal ion binding sites that are known from the crystal structure, two binding sites with high affinity were detected: one that is located at the ligand binding center and another at the J1/2 junction of the RNA.

BNB-Doped Phenalenyls: Modular Synthesis, Optoelectronic Properties, and One-Electron Reduction

A highly modular synthesis of BNB- and BOB-doped phenalenyls is presented. Treatment of the 1,8-naphthalenediyl-bridged boronic acid anhydride 1 with LiAlH₄/Me₃SiCl afforded the corresponding 1,8-naphthalenediyl-supported diborane(6) 2, which served as the starting material for all subsequent transformations. Upon addition of MesMgBr/Me₃SiCl, 2 was readily converted to the tetraorganyl diborane(6) 5. The further heteroatoms were finally introduced through the reaction of 2 with (Me₃Si)₂NR' or 5 with H₂NR' or H₂O (R' = H, Me, p-Tol). A helically twisted, fully BNB-embedded PAH 11 was prepared by combining 2 with a dibrominated m-terphenylamine, followed by a Grignard-mediated double ring-closure reaction. All compounds devoid of B-H bonds show favorable optoelectronic properties, such as luminescence and reversible reduction behavior. In the case of the BNB-phenalenyl 7 (BMes, NMe), the radical-anion salt K[7^•] was generated through chemical reduction with K metal and characterized by EPR spectroscopy. K[7^•] is not long-term stable in a THF/c-hexane solution, but abstracts an H atom with formation of the diamagnetic BNB-doped 1H-phenalene K[7H].

Binding of tetracycline to its aptamer determined by 2D-correlated Mn2+ hyperfine spectroscopy

The tetracycline-binding RNA aptamer (TC-aptamer) binds its cognate ligand the antibiotic tetracycline (TC) via a Mg²⁺ or Mn²⁺ ion with high affinity at high divalent metal ion concentrations (K_D=800pM, ⩾10 mM). These concentrations lie above the physiological divalent metal ion concentration of ca. 1 mM and it is known from literature, that the binding affinity decreases upon decreasing the divalent metal ion concentration. This work uses a Mn²⁺ concentration of 1 mM and 1D-hyperfine experiments reveal two pronounced ³¹P couplings from the RNA besides the ¹³C signal of ¹³C-labeled TC. From these 1D-hyperfine data alone, however, no conclusions can be drawn on the binding of TC. Either TC may bind via Mn²⁺ to the aptamer or TC may form a free Mn-TC complex and some Mn²⁺ also binds to the aptamer. In this work, we show using 2D-correlated hyperfine spectroscopy at Q-band frequencies (34 GHz), that the ¹³C and ³¹P signals can be correlated; thus arising from a single species. We use THYCOS (triple hyperfine correlation spectroscopy) and 2D ELDOR-detected NMR (2D electron electron double resonance detected NMR) for this purpose showing that they are suitable techniques to correlate two different nuclear spin species (¹³C and ³¹P) on two different molecules (RNA and TC) to the same electron spin (Mn²⁺). Out of the two observed ³¹P-hyperfine couplings, only one shows a clear correlation to ¹³C. Although THYCOS and 2D EDNMR yield identical results, 2D EDNMR is far more sensitive. THYCOS spectra needed a time factor of ×20 in comparison to 2D EDNMR to achieve a comparable signal-to-noise.

Influence of Mg2+ on the conformational flexibility of a tetracycline aptamer

The tetracycline-binding RNA aptamer (TC-aptamer) is a synthetic riboswitch that binds the antibiotic tetracycline (TC) with exceptionally high affinity. Although a crystal structure exists of the TC-bound state, little is known about the conformational dynamics and changes upon ligand binding. In this study, pulsed electron paramagnetic resonance techniques for measuring distances (PELDOR) in combination with rigid nitroxide spin labels (Çm spin label) were used to investigate the conformational flexibility of the TC-aptamer in the presence and absence of TC at different Mg²⁺ concentrations. TC was found to be the essential factor for stabilizing the tertiary structure at intermediate Mg²⁺ concentrations. At higher Mg²⁺ concentrations, Mg²⁺ alone is sufficient to stabilize the tertiary structure. In addition, the orientation of the two spin-labeled RNA helices with respect to each other was analyzed with orientation-selective PELDOR and compared to the crystal structure. These results demonstrate for the first time the unique value of the Çm spin label in combination with PELDOR to provide information about conformational flexibilities and orientations of secondary structure elements of biologically relevant RNAs.

Noncovalent spin-labeling of RNA: the aptamer approach

In the first example of site-directed spin-labeling of unmodified RNA, a pyrrolidine-nitroxide derivative of tetramethylrosamine (TMR) was shown to bind with high affinity to the malachite green (MG) aptamer, as determined by continuous-wave (CW) electron paramagnetic resonance (EPR), pulsed electron-electron double resonance (PELDOR) and fluorescence spectroscopies.