Chemo‐Enzymatic Synthesis of Position‐Specifically Modified RNA for Biophysical Studies including Light Control and NMR Spectroscopy

The investigation of non‐coding RNAs requires RNAs containing modifications at every possible position within the oligonucleotide. Here, we present the chemo‐enzymatic RNA synthesis containing photoactivatable or ¹³C,¹⁵N‐labelled nucleosides. All four ribonucleotides containing ortho‐nitrophenylethyl (NPE) photocages, photoswitchable azobenzene C‐nucleotides and ¹³C,¹⁵N‐labelled nucleotides were incorporated position‐specifically in high yields. We applied this approach for the synthesis of light‐inducible 2′dG‐sensing riboswitch variants and detected ligand‐induced structural reorganization upon irradiation by NMR spectroscopy. This chemo‐enzymatic method opens the possibility to incorporate a wide range of modifications at any desired position of RNAs of any lengths beyond the limits of solid‐phase synthesis.     

Synthesis of Selectively 15N‐Labeled 2′‐O‐{[(Triisopropylsilyl)oxy]methyl}(=tom)‐Protected Ribonucleoside Phosphoramidites and Their Incorporation into a Bistable 32Mer RNA Sequence

We present optimized reaction conditions for the conversion of 2′‐O‐{[(triisopropylsilyl)oxy]methyl}(=tom) protected uridine and adenosine nucleosides into the corresponding protected (3‐¹⁵N)‐labeled uridine and cytidine and (1‐¹⁵N)‐labeled adenosine and guanosine nucleosides 4, 6, 12 , and 18 , respectively (Schemes 1–4). On a DNA synthesizer, the resulting ¹⁵N‐labeled 2′‐O‐tom‐protected phosphoramidite building blocks 19 – 22 were efficiently incorporated into five selected positions of a bistable 32mer RNA sequence 23 (known to adopt two different structures) (Fig. 1). By 2D‐HSQC and HNN‐COSY experiments in H₂O/D₂O 9 : 1, the ¹⁵N‐signals of all base‐paired ¹⁵N‐labeled nucleotides could be identified and attributed to one of the two coexisting structures of 23 .     

Aromatic 19F–13C TROSY—[19F, 13C]‐Pyrimidine Labeling for NMR Spectroscopy of RNA

We present the access to [5‐¹⁹F, 5‐¹³C]‐uridine and ‐cytidine phosphoramidites for the production of site‐specifically modified RNAs up to 65 nucleotides (nts). The amidites were used to introduce [5‐¹⁹F, 5‐¹³C]‐pyrimidine labels into five RNAs—the 30 nt human immunodeficiency virus trans activation response (HIV TAR) 2 RNA, the 61 nt human hepatitis B virus ? (hHBV ?) RNA, the 49 nt SAM VI riboswitch aptamer domain from B. angulatum, the 29 nt apical stem loop of the pre‐microRNA (miRNA) 21 and the 59 nt full length pre‐miRNA 21. The main stimulus to introduce the aromatic ¹⁹F–¹³C‐spin topology into RNA comes from a work of Boeszoermenyi et al., in which the dipole‐dipole interaction and the chemical shift anisotropy relaxation mechanisms cancel each other leading to advantageous TROSY properties shown for aromatic protein sidechains. This aromatic ¹³C–¹⁹F labeling scheme is now transferred to RNA. We provide a protocol for the resonance assignment by solid phase synthesis based on diluted [5‐¹⁹F, 5‐¹³C]/[5‐¹⁹F] pyrimidine labeling. For the 61 nt hHBV ? we find a beneficial ¹⁹F–¹³C TROSY enhancement, which should be even more pronounced in larger RNAs and will facilitate the NMR studies of larger RNAs. The [¹⁹F, ¹³C]‐labeling of the SAM VI aptamer domain and the pre‐miRNA 21 further opens the possibility to use the biorthogonal stable isotope reporter nuclei in in vivo NMR to observe ligand binding and microRNA processing in a biological relevant setting.     

Selective Enzymatic Demethylation of N2,N2‐Dimethylguanosine in RNA and Its Application in High‐Throughput tRNA Sequencing

The abundant Watson–Crick face methylations in biological RNAs such as N¹‐methyladenosine (m¹A), N¹‐methylguanosine (m¹G), N³‐methylcytosine (m³C), and N²,N²‐dimethylguanosine (m²₂G) cause significant obstacles for high‐throughput RNA sequencing by impairing cDNA synthesis. One strategy to overcome this obstacle is to remove the methyl group on these modified bases prior to cDNA synthesis using enzymes. The wild‐type E. coli AlkB and its D135S mutant can remove most of m¹A, m¹G, m³C modifications in transfer RNA (tRNA), but they work poorly on m²₂G. Here we report the design and evaluation of a series of AlkB mutants against m²₂G‐containing model RNA substrates that we synthesize using an improved synthetic method. We show that the AlkB D135S/L118V mutant efficiently and selectively converts m²₂G modification to N²‐methylguanosine (m²G). We also show that this new enzyme improves the efficiency of tRNA sequencing.     

NMR “Crystallography” for Uniformly (13C, 15N)‐Labeled Oriented Membrane Proteins

In oriented‐sample (OS) solid‐state NMR of membrane proteins, the angular‐dependent dipolar couplings and chemical shifts provide a direct input for structure calculations. However, so far only ¹H–¹⁵N dipolar couplings and ¹⁵N chemical shifts have been routinely assessed in oriented ¹⁵N‐labeled samples. The main obstacle for extending this technique to membrane proteins of arbitrary topology has remained in the lack of additional experimental restraints. We have developed a new experimental triple‐resonance NMR technique, which was applied to uniformly doubly (¹⁵N, ¹³C)‐labeled Pf1 coat protein in magnetically aligned DMPC/DHPC bicelles. The previously inaccessible ¹H_α–¹³C_α dipolar couplings have been measured, which make it possible to determine the torsion angles between the peptide planes without assuming α‐helical structure a priori. The fitting of three angular restraints per peptide plane and filtering by Rosetta scoring functions has yielded a consensus α‐helical transmembrane structure for Pf1 protein.     

Efficient Access to Peptidyl‐RNA Conjugates for Picomolar Inhibition of Non‐ribosomal FemXWv Aminoacyl Transferase

Peptidyl–RNA conjugates have various applications in studying the ribosome and enzymes participating in tRNA‐dependent pathways such as Fem transferases in peptidoglycan synthesis. Herein a convergent synthesis of peptidyl–RNAs based on Huisgen–Sharpless cycloaddition for the final ligation step is developed. Azides and alkynes are introduced into tRNA and UDP‐MurNAc‐pentapeptide, respectively. Synthesis of 2′‐azido RNA helix starts from 2′‐azido‐2′‐deoxyadenosine that is coupled to deoxycytidine by phosphoramidite chemistry. The resulting dinucleotide is deprotected and ligated to a 22‐nt RNA helix mimicking the acceptor arm of Ala‐tRNA^Ala by T4 RNA ligase. For alkyne UDP‐MurNAc‐pentapeptide, meso‐cystine is enzymatically incorporated into the peptidoglycan precursor and reduced, and L ‐Cys is converted to dehydroalanine with O‐(mesitylenesulfonyl)hydroxylamine. Reaction of but‐3‐yne‐1‐thiol with dehydroalanine affords the alkyne‐containing UDP‐MurNAc‐pentapeptide. The Cu^I‐catalyzed azide alkyne cycloaddition reaction in the presence of tris[(1‐hydroxypropyl‐1H‐1,2,3‐triazol‐4‐yl)methyl]amine provided the peptidyl‐RNA conjugate, which was tested as an inhibitor of non‐ribosomal FemX_Wv aminoacyl transferase. The bi‐substrate analogue was found to inhibit FemX_Wv with an IC₅₀ of (89±9) pM , as both moieties of the peptidyl–RNA conjugate contribute to high‐affinity binding.     

Characterization of G‐Quadruplex/Hairpin Transitions of RNAs by 19F NMR Spectroscopy

2′‐O‐[(4‐Trifluoromethyl‐triazol‐1‐yl)methyl] reporter groups have been incorporated into guanosine‐rich RNA models (including a known bistable Qd/Hp RNA and two G‐rich regions of mRNA of human prion protein, PrP) and applied for the ¹⁹F NMR spectroscopic characterization of plausible G‐quadruplex/hairpin (Qd/Hp) transitions in these RNA structures. For the synthesis of the CF₃‐labeled RNAs, phosphoramidite building blocks of 2′‐O‐[(4‐CF₃‐triazol‐1‐yl)methyl] nucleosides (cytidine, adenosine, and guanosine) were prepared and used as an integral part of the standard solid‐phase RNA synthesis. The obtained ¹⁹F NMR spectra supported the usual characterization data (obtained by UV‐ and CD‐melting profiles and by ¹H NMR spectra of the imino regions) and additionally gave more detailed information on the Qd/Hp transitions. The molar fractions of the secondary structural species (Qd, Hp) upon thermal denaturation and under varying ionic conditions could be determined from the intensities and shifts of the ¹⁹F NMR signals. For a well‐behaved Qd/Hp transition, thermodynamic parameters could be extracted.     

Dispersion‐Force‐Assisted Disproportionation: A Stable Two‐Coordinate Copper(II) Complex

The synthesis of the first linear coordinated Cu^II complex Cu{N(SiMe₃)Dipp}₂ ( 1 Dipp=C₆H₅‐2,6Prⁱ₂) and its Cu^I counterpart [Cu{N(SiMe₃)Dipp}₂]^? ( 2 ) is described. The formation of 1 proceeds through a dispersion force‐driven disproportionation, and is the reaction product of a Cu^I halide and LiN(SiMe₃)Dipp in a non‐donor solvent. The synthesis of 2 is accomplished by preventing the disproportionation into 1 by using the complexing agent 15‐crown‐5. EPR spectroscopy of 1 provides the first detailed study of a two‐coordinate transition‐metal complex indicating strong covalency in the Cu?N bonds.     

Template‐ and Metal‐Free Synthesis of Nitrogen‐Rich Nanoporous “Noble” Carbon Materials by Direct Pyrolysis of a Preorganized Hexaazatriphenylene Precursor

The targeted thermal condensation of a hexaazatriphenylene‐based precursor leads to porous and oxidation‐resistant (“noble”) carbons. Simple condensation of the pre‐aligned molecular precursor produces nitrogen‐rich carbons with C₂N‐type stoichiometry. Despite the absence of any porogen and metal species involved in the synthesis, the specific surface areas of the molecular carbons reach up to 1000 m² g^?1 due to the significant microporosity of the materials. The content and type of nitrogen species is controllable by the carbonization temperature whilst porosity remains largely unaffected at the same time. The resulting noble carbons are distinguished by a highly polarizable micropore structure and have thus high adsorption affinity towards molecules such as H₂O and CO₂. This molecular precursor approach opens new possibilities for the synthesis of porous noble carbons under molecular control, providing access to the special physical properties of the C₂N structure and extending the known spectrum of classical porous carbons.     

1,5‐Diamino‐4‐methyltetrazolium 5‐Nitrotetrazolate – Synthesis,Testing and Scale‐up

1,5‐Diamino‐4‐methyltetrazolium 5‐nitrotetrazolate ( 2b ) was synthesized in high yield from 1,5‐diamino‐4‐methyltetrazolium iodide ( 2a ) and highly sensitive silver 5‐nitrotetrazolate (AgNT). A safer synthesis, suitable for scale‐up, is introduced involving reaction of the previously unreported 1‐amino‐5‐imino‐4‐methyltetrazole free base ( 2 ) with ammonium 5‐nitrotetrazolate. Both new compounds ( 2 and 2b ) were fully characterized using vibrational (IR and Raman) and multinuclear NMR spectroscopy (¹H, ¹³C, ¹⁴N, ¹⁵N), elemental analysis and single crystal X‐ray diffraction. The hydrogen‐bonding networks of both materials are described in terms of their graph‐sets. Compound 2b is hydrolytically stable with a high melting point and concomitant decomposition at 160 °C. The sensitivity of the energetic salt 2b towards impact (>30 J) and friction (>360 N) was tested. The constant volume energy of combustion (Δ_cU) of 2b was measured experimentally using bomb calorimetry. In addition, the detonation parameters (detonation pressure and velocity) of the nitrotetrazolate salt were calculated from the energy of formation, the crystal density and the molecular formula using the EXPLO5 computer code (P = 15.5·GPa, D = 6749 m s^?1) and are similar to that of TNT and nitroguanidine making 2b of prospective interest in propellant charge formulations or, in combination with a suitable oxidizer, as a solid propellant.     

Rare examples of base pairing via a protonated pyridine N atom in two salts of N2,N6‐bis(1,3‐dimethylimidazolin‐2‐ylidene)pyridine‐2,6‐diamine

The title compounds, namely 2,6‐bis[(1,3‐dimethylimidazolin‐2‐ylidene)amino]pyridinium perchlorate, C₁₅H₂₄N₇⁺·ClO₄⁻, (I), and bis{2,6‐bis[(1,3‐dimethylimidazolin‐2‐ylidene)amino]pyridinium} μ‐oxido‐bis[trichloridoiron(III)], (C₁₅H₂₄N₇)₂[Fe₂Cl₆O], (II), are structurally unusual examples of the organization of molecular units via base pairing. The cations in salts (I) and (II) are derived from the bisguanidine N²,N⁶‐bis(1,3‐dimethylimidazolin‐2‐ylidene)pyridine‐2,6‐diamine, which associates in centrosymmetric pairs via two N—H...N hydrogen‐bond interactions. N—H...N bridges are formed between the protonated pyridine N atom and one of the nonprotonated guanidine N atoms, with N...H distances of 2.01 (1)–2.10 (1) Å. Compound (I) contains two crystallographically independent cations and anions per asymmetric unit. One of the perchlorate anions is disordered, while the [Fe₂Cl₆O]²⁻ anion lies on an inversion centre.     

Synthesis and Pairing Properties of Oligodeoxynucleotides Containing N7‐(Purin‐2‐amine Deoxynucleosides)

A general synthesis of the four isomeric N⁷‐α‐D ‐, N⁷‐β‐D ‐, N⁹‐α‐D ‐, and N⁹‐β‐D ‐(purin‐2‐amine deoxynucleoside phosphoramidite) building blocks for DNA synthesis is described (Scheme). The syntheses start with methyl 3′,5′‐di‐O‐acetyl‐2′‐deoxy‐D ‐ribofuranoside ( 2 ) as the sugar component and the N²‐acetyl‐protected 6‐chloropurin‐2‐amine 1 as the base precursor. N⁷‐Selectivity was achieved by kinetic control, and N⁹‐selectivity by thermodynamic control of the nucleosidation reaction. The two N⁷‐(purin‐2‐amine deoxynucleosides) were introduced into the center of a decamer DNA duplex, and their pairing preferences were analyzed by UV‐melting curves. Both the N⁷‐α‐D ‐ and N⁷‐β‐D ‐(purin‐2‐amine nucleotide) units preferentially pair with a guanine base within the Watson‐Crick pairing regime, with ΔT_ms of −6.7 and −8.7 K, respectively, relative to a C⋅G base pair (Fig. 3 and Table 1). Molecular modeling suggests that, in the former base pair, the purinamine base is rotated into the syn‐arrangement and is able to form three H‐bonds with O(6), N(1), and NH₂ of guanine, whereas in the latter base pair, both bases are in the anti‐arrangement with two H‐bonds between the N(3) and NH₂ of guanine, and NH₂ and N(1) of the purin‐2‐amine base (Fig. 4).     

Novel Fluoride‐Labile Nucleobase‐Protecting Groups for the Synthesis of 3′(2′)‐O‐Aminoacylated RNA Sequences

With the aim to develop a general approach to a total synthesis of aminoacylated t‐RNAs and analogues, we describe the synthesis of stabilized, aminoacylated RNA fragments, which, upon ligation, could lead to aminoacylated t‐RNA structures. Novel RNA phosphoramidites with fluoride‐labile 2′‐O‐[(triisopropylsilyl)oxy]methyl (=tom) sugar‐protecting and N‐{{2‐[(triisopropylsilyl)oxy]benzyl}oxy}carbonyl (=tboc) base‐protecting groups were prepared (Schemes 4 and 5), as well as a solid support containing an immobilized N⁶‐tboc‐protected adenosine with an orthogonal (photolabile) 2′‐O‐[(S)‐1‐(2‐nitrophenyl)ethoxy]methyl (=(S)‐npeom) group (Scheme 6). From these building blocks, a hexameric oligoribonucleotide was prepared by automated synthesis under standard conditions (Scheme 7). After the detachment from the solid support, the resulting fully protected sequence 34 was aminoacylated with L ‐phenylalanine derivatives carrying photolabile N‐protecting groups (→ 42 and 43 ; Scheme 9). Upon removal of the fluoride‐labile sugar‐ and nucleobase‐protecting groups, the still stabilized, partially with the photolabile group protected precursors 44 and 45 , respectively, of an aminoacylated RNA sequence were obtained (Scheme 9 and Fig. 3). Photolysis of 45 under mild conditions resulted in the efficient formation of the 3′(2′)‐O‐aminoacylated RNA sequence 46 (Fig. 4). Additionally, we carried out model investigations concerning the stability of ester bonds of aminoacylated ribonucleotide derivatives under acidic conditions (Table) and established conditions for the purification and handling of 3′(2′)‐O‐aminoacylated RNA sequences and their stabilized precursors.     

Metal‐Catalyzed “On‐Demand” Production of Carbonyl Sulfide from Carbon Monoxide and Elemental Sulfur

The group 6 molybdenum(II) cyclopentadienyl amidinate (CPAM) bis(carbonyl) complex [Cp*Mo{N(iPr)C(Ph)N(iPr)}(CO)₂] (Cp*=η⁵‐C₅Me₅) serves as a precatalyst for the high‐yielding photocatalytic production of COS from CO and S₈ under near‐ambient conditions (e.g., 10 psi, 25 °C). Further documented is the isolation and structural characterization of several key transition‐metal intermediates which collectively support a novel molybdenum(IV)‐based catalytic cycle as being operative. Finally, in the presence of an excess amount of a primary amine, it is demonstrated that this catalytic system can be successfully used for the “on‐demand” generation and utilization of COS as a chemical reagent for the synthesis of ureas.     

A Nontrigonal Tricoordinate Phosphorus Ligand Exhibiting Reversible “Nonspectator” L/X‐Switching

We report here a “nonspectator” behavior for an unsupported L ‐function σ³‐P ligand (i.e. P{N[o‐NMe‐C₆H₄]₂}, 1a ) in complex with the cyclopentadienyliron dicarbonyl cation (Fp⁺). Treatment of 1a ?Fp⁺ with [(Me₂N)₃S][Me₃SiF₂] results in fluoride addition to the P‐center, giving the isolable crystalline fluorometallophosphorane 1a^F ?Fp that allows a crystallographic assessment of the variance in the Fe?P bond as a function of P‐coordination number. The nonspectator reactivity of 1a ?Fp⁺ is rationalized on the basis of electronic structure arguments and by comparison to trigonal analogue (Me₂N)₃P?Fp⁺ (i.e. 1b ?Fp⁺), which is inert to fluoride addition. These observations establish a nonspectator L/X‐switching in (σ³‐P)–M complexes by reversible access to higher‐coordinate phosphorus ligand fragments.     

15N Chemically Induced Dynamic Nuclear Polarization (15N‐CIDNP) Investigations of the Peroxynitrite Decay and Nitration of N‐Acetyl‐L‐tyrosine

During the decay of (¹⁵N)peroxynitrite (O?¹⁵NOO ^? ) in the presence of N‐acetyl‐L ‐tyrosine (Tyrac) in neutral solution and at 268 K, the ¹⁵N‐NMR signals of ¹⁵NO and ¹⁵NO show emission (E) and enhanced absorption (A) as it has already been observed by Butler and co‐workers in the presence of L ‐tyrosine (Tyr). The effects are built up in radical pairs [CO , ¹⁵NO ]^S formed by O? O bond scission of the (¹⁵N)peroxynitrite? CO₂ adduct (O?¹⁵NO? OCO ). In the absence of Tyrac and Tyr, the peroxynitrite decay rate is enhanced, and ¹⁵N‐CIDNP does not occur. This is explained by a chain reaction during the peroxynitrite decay involving N₂O₃ and radicals NO ^. and NO . The interpretation is supported by ¹⁵N‐CIDNP observed with (¹⁵N)peroxynitrite generated in situ during reaction of H₂O₂ with N‐acetyl‐N‐(¹⁵N)nitroso‐dl ‐tryptophan ((¹⁵N)NANT) at 298 K and pH 7.5. In the presence of Na¹⁵NO₂ at pH 7.5 and in acidic solution, ¹⁵N‐CIDNP appears in the nitration products of Tyrac, 1‐(¹⁵N)nitro‐N‐acetyl‐L ‐tyrosine (1‐¹⁵NO₂‐Tyrac) and 3‐(¹⁵N)nitro‐N‐acetyl‐L ‐tyrosine (3‐¹⁵NO₂‐Tyrac). The effects are built up in radical pairs [Tyrac ^. , ¹⁵NO ]^F formed by encounters of independently generated radicals Tyrac ^. and ¹⁵NO . Quantitative ¹⁵N‐CIDNP studies show that nitrogen dioxide dependent reactions are the main if not the only pathways for yielding both nitrate and nitrated products.     

Energetic Materials Based on the 5‐Azido‐3‐nitro‐1, 2,4‐tri­azolate Anion

This study presents the preparation of 5‐azido‐3‐nitro‐1H‐1, 2,4‐triazole ( 1 ) in both good yield and high purity, starting from commercially available chemicals in a three step synthesis. Furthermore, several metal and nitrogen‐rich salts with sodium ( 3 ), potassium ( 4 ), cesium ( 5 ), silver ( 6 ), lead ( 7 ), ammonium ( 8 ), guanidinium ( 9 ), and aminoguanidinium ( 10 ) were prepared by simple acid‐base reactions. All compounds were well characterized by various means, including vibrational (IR, Raman) and multinuclear (¹H, ¹³C, ¹⁴N, ¹⁵N) NMR spectroscopy, mass spectrometry, and DSC. Additionally the structure of 7 was determined by single‐crystal X‐ray diffraction. The sensitivities towards various outer stimuli (impact, friction, electrostatic discharge) were determined according to BAM standards. The metal salts were tested as potential primary explosives utilizing various preliminary tests.     

Synthesis and spectral characterization of N‐[2‐(4‐halophenoxy)‐3‐(3‐chlorophenyl)‐3, 4‐dihydro‐2H‐1,3,2‐λ5‐benzoxazaphosphinin‐2‐yliden]‐N‐substituted amines by the Staudinger reaction

The synthesis of the title compounds was accomplished in four steps. The synthetic route involves the preparation of Schiff's base by reacting salicylaldehyde with m‐chloroaniline in EtOH. The Schiff's base was then reduced with NaBH₄/MeOH. In the second step, PCl₃ was reacted with p‐chlorophenol/p‐bromophenol in THF in the presence of Et₃N to obtain P(III) dichloride derivatives. The reduced Schiff's base and dichloride derivatives were reacted in equimolar quantities in the presence of Et₃N in THF to get the cyclized product. Alkyl azides were prepared by reacting alkyl bromides with sodium azide, and then alkyl azides were treated with the cyclized product to obtain the title compounds. The structure of these novel compounds was elucidated by elemental analysis, IR, ¹H, ¹³C, ³¹P NMR, and mass spectroscopy. © 2010 Wiley Periodicals, Inc. Heteroatom Chem 21:499–504, 2010; View this article online at wileyonlinelibrary.com . DOI 10.1002/hc.20639