Determination of the Tautomeric Equlibrium of Ψ-Uridine in the Basic Solution

ICLAMP: a novel technique to explore adenosine deamination via inosine chemical labeling and affinity molecular purification

Recent developments in sequencing and bioinformatics have advanced our understanding of adenosine-to-inosine (A-to-I) RNA editing. Surprisingly, recent analyses have revealed the capability of adenosine deaminase acting on RNA (ADAR) to edit DNA:RNA hybrid strands. However, edited inosines in DNA remain largely unexplored. A precise biochemical method could help uncover these potentially rare DNA editing sites. We explore maleimide as a scaffold for inosine labeling. With fluorophore-conjugated maleimide, we were able to label inosine in RNA or DNA. Moreover, with biotin-conjugated maleimide, we purified RNA and DNA containing inosine. Our novel technique of inosine chemical labeling and affinity molecular purification offers substantial advantages and provides a versatile platform for further discovery of A-to-I editing sites in RNA and DNA.

Calculations of pKa Values for a Series of Naturally Occurring Modified Nucleobases

Modified nucleobases are found in functionally important regions of RNA and are often responsible for essential structural roles. Many of these nucleobase modifications are dynamically regulated in nature, with each modification having a different biological role in RNA. Despite the high abundance of modifications, many of their characteristics are still poorly understood. One important property of a nucleobase is its pK_a value, which has been widely studied for unmodified nucleobases, but not for the modified versions. In this study, the pK_a values of modified nucleobases were determined by performing ab initio quantum mechanical calculations using a B3LYP density functional with the 6-31+G(d,p) basis set and a combination of implicit-explicit solvation systems. This method, which was previously employed to determine the pK_a values of unmodified nucleobases, is applicable to a variety of modified nucleobases. Comparisons of the pK_a values of modified nucleobases give insight into their structural and energetic impacts within nucleic acids.

Total synthesis of pseudouridineviaHeck-typeC-glycosylation

Pseudouridine (1) was synthesized by functional group interconversions of the Heck adduct11from 2,4-dimethoxy-5-iodopyrimidine (8) and ribofuranoid glycal4.

Kinetico-mechanistic Studies on the Substitution Reactivity on the {Ru(II)(bpy)2} Core with Nucleosides and Nucleotides at Physiological pH

The kinetico-mechanistic study of the substitution reactions of the aquo ligands in cis-[Ru(bpy)2(H2O)2](2+) by different nucleotides and nucleosides has been conducted at pH close to the physiological value. The concentration dependence and thermal and pressure activation parameters have been measured to ascertain the activation via which reactions take place. Substitution processes are found associatively activated for nitrogen-bonded nucleosides or nucleotides, with outer-sphere hydrogen-bonded aggregates being determinant. For reactions leading to oxygen-bonded nucleotides, the process is clearly dissociatively activated. A selectively induced lability of the inert {Ru(II)(bpy)2} core is observed on the formation of nitrogen(amide)-bonded complexes at relatively low pH values, which might be relevant for the effective intercalation of designed, ruthenium(II)-bonded, aromatic rings.

Chemical Mutagenesis of an Emissive RNA Alphabet

An evolved fluorescent ribonucleoside alphabet comprising isomorphic purine ((tz)A, (tz)G) and pyrimidine ((tz)U, (tz)C) analogues, all derived from isothiazolo[4,3-d]pyrimidine as a common heterocyclic core, is described. Structural and biochemical analyses illustrate that the nucleosides, particularly the C-nucleosidic purine analogues, are faithful isomorphic and isofunctional surrogates of their natural counterparts and show improved features when compared to an RNA alphabet derived from thieno[3,4-d]-pyrimidine. The restoration of the nitrogen in a position equivalent to the purines' N7 leads to "isofunctional" behavior, as illustrated by the ability of adenosine deaminase to deaminate (tz)A as effectively as adenosine, the native substrate.

Kinetico-mechanistic studies of substitution reactions on cross-bridged cyclen Co(III) complexes with nucleosides and nucleotides

Kinetico-mechanistic studies on the substitution reactivity of the [Co{(μ-ET)cyclen}(H2O)2](3+) complex cation at pH values within the 6.0-7.0 range with biologically significant ligands have been carried out. The substitution processes have been found to occur exclusively on the mono-hydroxobridged [(Co{(μ-ET)cyclen}(H2O))2(μ-OH)](5+) species formed after equilibration of the cobalt complex in the relevant medium. The studies conducted on the substitution of the aqua/hydroxo ligands of this dinuclear species are indicative of a dominant role of outer-sphere complexation, involving hydrogen-bonding interactions. The values of the outer-sphere complex formation equilibrium constant are in line with the intervention of both the exiting aqua ligands and the NH groups at the encapsulating {(μ-ET)cyclen} ligand. These complexes result in the preferential formation of O- or N-bonded nucleotides depending on the structure of the base moiety of the ligand. Even the entry of the different donor bonded nucleotides is hampered by the hydrogen-bonding interaction with the dangling moiety of an already coordinated ligand. In general the overall substitution processes occur at a faster rate than those published for the fully alkylated encapsulating {(Me)2(μ-ET)cyclen} ligand derivative, as expected for the still available base-catalysing NH groups in the {(μ-ET)cyclen} ligand.

Highly efficient syntheses of [methyl-11C]thymidine and its analogue 4'-[methyl-11C]thiothymidine as nucleoside PET probes for cancer cell proliferation by Pd(0)-mediated rapid C-[11C]methylation

Pd(0)-mediated rapid couplings of CH(3)I (and then [(11)C]CH(3)I) with excess 5-tributylstannyl-2'-deoxyuridine and -4'-thio-2'-deoxyuridine were investigated for the syntheses of [methyl-(11)C]thymidine and its stable analogue, 4'-[methyl-(11)C]thiothymidine as PET probes for cancer diagnosis. The previously reported conditions were attempted using Pd(2)(dba)(3)/P(o-CH(3)C(6)H(4))(3) (1 : 4 in molar ratio) at 130 °C for 5 min in DMF, giving desired products only in 32 and 30% yields. Therefore, we adapted the current reaction conditions developed in our laboratory for heteroaromatic compounds. The reaction using CH(3)I/stannane/Pd(2)(dba)(3)/P(o-CH(3)C(6)H(4))(3)/CuCl/K(2)CO(3) (1 : 25 : 1 : 32 : 2 : 5) at 80 °C gave thymidine in 85% yield. Whereas, CH(3)I/stannane/Pd(2)(dba)(3)/P(o-CH(3)C(6)H(4))(3)/CuBr/CsF (1 : 25 : 1 : 32 : 2 : 5) including another CuBr/CsF system promoted the reaction at a milder temperature (60 °C), giving thymidine in 100% yield. Chemo-response of thiothymidine-precursor was different from thymidine system. Thus, the above optimized conditions including CuBr/CsF system gave 4'-thiothymidine only in 40% yield. The reaction using 5-fold amount of CuBr/CsF at 80 °C gave much higher yield (83%), but unexpectedly, the reaction was accompanied by a considerable amount of undesired destannylated product. Such destannylation was greatly suppressed by changing to a CuCl/K(2)CO(3) system using CH(3)I/stannane/Pd(2)(dba)(3)/P(o-CH(3)C(6)H(4))(3)/CuCl/K(2)CO(3) (1 : 25 : 1 : 32 : 2 : 5) at 80 °C, giving the 4'-thiothymidine in 98% yield. The each optimized conditions were successfully applied to the syntheses of the corresponding PET probes in 87 and 93% HPLC analytical yields. [(11)C]Compounds were isolated by preparative HPLC after the reaction conducted under slightly improved conditions, exhibiting sufficient radioactivity of 3.7-3.8 GBq and specific radioactivity of 89-200 GBq µmol(-1) with radiochemical purity of ≥99.5% for animal and human PET studies.

Molecular modeling of some 1H-benzimidazole derivatives with biological activity against Entamoeba histolytica: a comparative molecular field analysis study

Comparative molecular field analysis (CoMFA) was performed on a set of 1H-benzimidazole derivatives. Molecular modeling and 3D-QSAR were employed to determine the tautomeric form that would probably fit a target receptor in Entamoeba histolytica. CoMFA results suggest that the antiamoebic activity is favored with steric bulk at position 5 of the benzimidazole ring and low electron density on the group at position 2. To the best of our knowledge this is the first 3D-QSAR study performed for benzimidazoles as antiamoebic agents. The CoMFA models derived will be very valuable to design new and more potent compounds against E. histolytica.

Synthesis of helix 69 of Escherichia coli 23S rRNA containing its natural modified nucleosides, m(3)Psi and Psi

The synthesis of 3-methylpseudouridine (m(3)Psi) phosphoramidite, 5'-O-[benzhydryloxybis(trimethylsilyloxy)silyl]-2'-O-[bis(2-acetoxyethoxy)methyl]-3-methylpseudouridine-3'-(methyl-N,N-diisopropyl)phosphoramidite, is reported. Selective pivaloyloxymethyl protection of the Psi N1 followed by methylation at N3 was used to generate the naturally occurring pseudouridine analogue. The m(3)Psi phosphoramidite was used in combination with pseudouridine (Psi) and standard base phosphoramidites to synthesize a 19-nucleotide RNA representing helix 69 of Escherichia coli 23S ribosomal RNA (rRNA) (residues 1906-1924), containing a single m(3)Psi at position 1915 and two Psi's at positions 1911 and 1917. Our synthesis of the fully modified helix 69 RNA demonstrates the ability to make milligram quantities of RNA that can be used for further high-resolution structure studies. Site-selective introduction of the methyl group at the N3 position of pseudouridine at position 1915 causes a slight increase in the thermodynamic stability of the RNA hairpin relative to pseudouridine; RNAs containing either uridine or 3-methyluridine at position 1915 have similar stability. One-dimensional imino proton NMR and circular dichroism spectra of the modified RNAs reveal that the methyl group does not cause any substantial changes in the RNA hairpin structure.