Three-State Fluorescence of a 2-Functionalized Pyrene-Based RNA Label.

The pyrene-based RNA-fluorescence label 2-(2-pyrenylethynyl) adenosine (2PyA) shows triexponential fluorescence, which depends strongly on the excitation wavelength. Most strikingly, a structured, long-lived fluorescence is observed in solution at room temperature after excitation into the S state, which is shifted hypsochromically by 30 nm compared to excitation into the S state. This very unusual behavior is investigated in detail with steady-state and time-resolved emission spectroscopy, ultrafast transient absorption spectroscopy, and quantum chemical calculations with both wave functions (CC2-level) and density-functional theory (DFT).

The Three Possible 2-(Pyrenylethynyl) Adenosines: Rotameric Energy Barriers Govern the Photodynamics of These Structural Isomers.

This article presents a comprehensive study of the photophysics of 2-(2-pyrenylethynyl) adenosine and 2-(4-pyrenylethynyl) adenosine, which are structural isomers of the well-established fluorescent RNA label 2-(1-pyrenylethynyl) adenosine. We performed steady-state and ultrafast transient absorption spectroscopy studies along with time-resolved fluorescence emission experiments in different solvents to work out the interplay of locally excited and charge-transfer states. We found the ultrafast photodynamics to be crucial for the fluorescence decay behavior, which extends up to tens of nanoseconds and is partially multi-exponential.

Design, Synthesis, and Antiviral Activity of Novel Ribonucleosides of 1,2,3-Triazolylbenzyl-aminophosphonates.

A novel series of ribonucleosides of 1,2,3-triazolylbenzyl-aminophosphonates was synthesized through the Kabachnik-Fields reaction using I2 as catalyst followed by copper-catalyzed cycloaddition of the azide-alkyne reaction (CuAAC). All structures of the newly prepared compounds were characterized by (1) H NMR, (13) C NMR, and HRMS spectra. The structures of 2e, 2f, 3d, and 3g were further confirmed by X-ray diffraction analysis.

Inhibition of replication of hepatitis B virus in transgenic mice following administration of hepatotropic lipoplexes containing guanidinopropyl-modified siRNAs.

Chronic infection with hepatitis B virus (HBV) occurs commonly and complications that arise from persistence of the virus are associated with high mortality. Available licensed drugs have modest curative efficacy and advancing new therapeutic strategies to eliminate the virus is therefore a priority. HBV is susceptible to inactivation by exogenous gene silencers that harness RNA interference (RNAi) and the approach has therapeutic potential.

Crystal structure of 2-benzamido-N-(2,2-di-eth-oxy-eth-yl)benzamide.

In the title compound, C20H24N2O4, both peptide bonds adopt a trans configuration with respect to the -N-H and -C=O groups. The dihedral angle between the aromatic rings is 53.58 (4)°.

Use of guanidinopropyl-modified siRNAs to silence gene expression.

Silencing gene expression by harnessing the RNA interference (RNAi) pathway with short interfering RNAs (siRNAs) has useful analytical and potentially therapeutic application. To augment silencing efficacy of siRNAs, chemical modification has been employed to improve stability, target specificity, and delivery to target tissues. siRNAs incorporating guanidinopropyl (GP) moieties have demonstrated enhanced target gene silencing in cell culture and in vivo models of hepatitis B virus replication.

Selective uncaging of DNA through reaction rate selectivity.

The synthesis and use of the new nucleobase-caged nucleotides dT(pHP) and dT(NDEACM) is reported. Through a combination of time and wavelength selectivity four levels of selective uncaging with only two cages, and only two wavelengths, were obtained. The new residue dT(pHP) can be uncaged at 313 nm without the formation of unwanted cyclic pyridine dimers.

Benzimidazole-1,2,3-triazole hybrid molecules: synthesis and evaluation for antibacterial/antifungal activity.

A novel series of hybrid molecules 4a-i and 5a-i were prepared by condensation of 4-(trimethylsilylethynyl)benzaldehyde 1 with substituted o-phenylenediamines. These in turn were reacted with 2-(azidomethoxy)ethyl acetate in a Cu alkyne-azide cycloaddition (CuAAC) to generate the 1,2,3-triazole pharmacophore under microwave assistance. The newly synthesized compounds were examined for their in vitro antimicrobial activities against Gram-positive and Gram-negative bacteria and the phytopathogenic fungi Verticillium dahliae and Fusarium oxysporum f.

Three different fluoro- or chloro-substituted 1'-deoxy-1'-phenyl-β-D-ribofuranoses.

Crystal structures are reported for three fluoro- or chloro-substituted 1'-deoxy-1'-phenyl-β-D-ribofuranoses, namely 1'-deoxy-1'-(2,4,5-trifluorophenyl)-β-D-ribofuranose, C11H11F3O4, (I), 1'-deoxy-1'-(2,4,6-trifluorophenyl)-β-D-ribofuranose, C11H11F3O4, (II), and 1'-(4-chlorophenyl)-1'-deoxy-β-D-ribofuranose, C11H13ClO4, (III). The five-membered furanose ring of the three compounds has a conformation between a C2'-endo,C3'-exo twist and a C2'-endo envelope. The ribofuranose groups of (I) and (III) are connected by intermolecular O-H···O hydrogen bonds to six symmetry-related molecules to form double layers, while the ribofuranose group of (II) is connected by O-H···O hydrogen bonds to four symmetry-related molecules to form single layers.

Synthesis of new 1,2,3-triazol-4-yl-quinazoline nucleoside and acyclonucleoside analogues.

In this study, we describe the synthesis of 1,4-disustituted-1,2,3-triazolo-quinazoline ribonucleosides or acyclonucleosides by means of 1,3-dipolar cycloaddition between various O or N-alkylated propargyl-quinazoline and 1'-azido-2',3',5'-tri-O-benzoylribose or activated alkylating agents under microwave conditions. None of the compounds selected showed significant anti-HCV activity in vitro.

Synthesis and antiproliferative activity of quinolone nucleosides against the human myelogenous leukemia k-562 cell line.

A set of 6-substituted quinolone nucleosides linked to aniline or phenol via N or O heteroatom-bridges presenting new compounds were synthesized by palladium-catalyzed Buchwald-Hartwig cross-coupling reactions. 6-Bromoquinolone nucleoside precursors, being protected by either benzoyl or TBDMS protecting groups on the ribose moiety, were subjected to different Buchwald-Hartwig conditions as the key step. Defined deprotection steps led, in good yields, to the final target compounds that carry, in position 3, either ester, acid, or amide functions.

Four related diethyl [(arylamino)(4-ethynylphenyl)methyl]phosphonates.

Crystal structures are reported for four related diethyl [(arylamino)(4-ethynylphenyl)lmethyl]phosphonate derivatives, namely diethyl [(4-bromoanilino)(4-ethynylphenyl)methyl]phosphonate, C19H21BrNO3P, (I), diethyl ((4-chloro-2-methylanilino){4-[2-(trimethylsilyl)ethynyl]phenyl}methyl)phosphonate, C23H31ClNO3PSi, (II), diethyl ((4-fluoroanilino){4-[2-(trimethylsilyl)ethynyl]phenyl}methyl)phosphonate, C22H29FNO3PSi, (III), and diethyl [(4-ethynylphenyl)(naphthalen-2-ylamino)methyl]phosphonate, C23H24NO3P, (IV). The conformation of the anilinobenzyl group is very similar in all four compounds. The P-C bond has an approximately staggered conformation, with the aniline and ethynylphenyl groups in gauche positions with respect to the P=O double bond.

5-[(1R,2R,4R)-2-Meth-oxy-1,7,7-tri-methylbi-cyclo-[2.2.1]hept-2-yl]-1H-tetra-zole.

The title compound, C12H20N4O, undergoes a phase transition on cooling. The room-temperature structure is tetra-gonal (P43212, Z' = 1), with the meth-oxy-bornyl group being extremely disordered. Below 213 K the structure is ortho-rhom-bic (P212121, Z' = 2), with ordered mol-ecules.

Inhibition of hepatitis B virus replication in cultured cells and in vivo using 2'-O-guanidinopropyl modified siRNAs.

Silencing hepatitis B virus (HBV) gene expression with exogenous activators of the RNA interference (RNAi) pathway has shown promise as a new mode of treating infection with the virus. However, optimizing efficacy, specificity, pharmacokinetics and stability of RNAi activators remains a priority before clinical application of this promising therapeutic approach is realised. Chemical modification of synthetic short interfering RNAs (siRNAs) provides the means to address these goals.

Biphenyl- and phenylnaphthalenyl-substituted 1H-imidazole-4,5-dicarbonitrile catalysts for the coupling reaction of nucleoside methyl phosphonamidites.

Crystal structures are reported for three substituted 1H-imidazole-4,5-dicarbonitrile compounds used as catalysts for the coupling reaction of nucleoside methyl phosphonamidites, namely 2-(3',5'-dimethylbiphenyl-2-yl)-1H-imidazole-4,5-dicarbonitrile, C19H14N4, (I), 2-(2',4',6'-trimethylbiphenyl-2-yl)-1H-imidazole-4,5-dicarbonitrile, C20H16N4, (II), and 2-[8-(3,5-dimethylphenyl)naphthalen-1-yl]-1H-imidazole-4,5-dicarbonitrile, C23H16N4, (III). The asymmetric unit of (I) contains two independent molecules with similar conformations. There is steric repulsion between the imidazole group and the terminal phenyl group in all three compounds, resulting in the nonplanarity of the molecules.

Conformational states of 2'-C-methylpyrimidine nucleosides in single and double nucleic acid stranded structures.

The hybridization performance of a set of 12-mer RNA:RNA duplexes containing 2'-C-methyluridine, 5-bromo-2'-C-methyluridine, or (2'S)-2'-deoxy-2'-C-methyluridine was analyzed. Melting point temperatures of the modified duplexes showed an important ΔT(m) decrease (-8.9 to -12.

Inhibition of hepatitis C virus RNA translation by antisense bile acid conjugated phosphorothioate modified oligodeoxynucleotides (ODN).

Background: The 5'-noncoding region (5'NCR) of the HCV-genome comprises an internal ribosome entry site essential for HCV-translation/replication. Phosphorothioate oligodeoxynucleotides (tS-ODN) complementary to this region can inhibit HCV-translation in vitro. In this study, bile acid conjugated tS-ODN were generated to increase cell-selective inhibition of 5'NCR-dependent HCV-translation.

Gene silencing by chemically modified siRNAs.

RNA interference (RNAi) has not only already risen as a gold standard for validating gene function in basic science studies, but also holds great promise as a new therapeutic paradigm. Advantages of RNAi-based therapeutics include relatively fast initial screening and the ability to target proteins not yet addressable by traditional drug design strategies. In this review we describe the development of chemically modified small inhibiting siRNAs and their application as potential therapeutics during the past decade.

2-({4-[4-(1H-Benzimidazol-2-yl)phen-yl]-1H-1,2,3-triazol-1-yl}meth-oxy)ethanol.

In the title molecule, C(18)H(17)N(5)O(2), the dihedral angle between the benzene plane and the benzimidazole plane is 19.8 (1)° and the angle between the benzene plane and the triazole plane is 16.7 (1)°.

Attachment of nitroxide spin labels to nucleic acids for EPR.

In addition to X-ray, NMR, and FRET, electron paramagnetic resonance (EPR) can be applied to elucidate the structure of different macromolecular systems and determine local surroundings of paramagnetic centers in DNA and RNA. This technique permits structural characterization as well as dynamic structural changes of macromolecular systems. To do so, free radicals with good stability must be introduced.

Postsynthetic on column RNA labeling via Stille coupling.

Stille Coupling is a versatile C-C bond forming reaction with high functional group tolerance under mild conditions. Our on column synthesis concept for RNA modification is based on the incorporation of iodo substituted nucleotide precursors to RNA during automated standard solid phase synthesis via TBDMS-, TC-, and ACE- protecting group strategies. Subsequently, the RNA, still bound on solid support, is ready for orthogonal postsynthetic functionalization via Stille cross-couplings utilizing the advantages of solid phase synthesis.

Synthesis of 2'-O-guanidinopropyl-modified nucleoside phosphoramidites and their incorporation into siRNAs targeting hepatitis B virus.

Synthetic RNAi activators have shown considerable potential for therapeutic application to silencing of pathology-causing genes. Typically these exogenous RNAi activators comprise duplex RNA of approximately 21 bp with 2 nt overhangs at the 3' ends. To improve efficacy of siRNAs, chemical modification at the 2'-OH group of ribose has been employed.

Synthesis of 1,4-disubstituted mono and bis-triazolocarbo-acyclonucleoside analogues of 9-(4-hydroxybutyl)guanine by Cu(I)-catalyzed click azide-alkyne cycloaddition.

A series of novel mono-1,2,3-triazole and bis-1,2,3-triazole acyclonucleoside analogues of 9-(4-hydroxybutyl)guanine was prepared via copper(I)-catalyzed 1,3-dipolar cycloaddition of N-9 propargylpurine, N-1-propargylpyrimidines/as-triazine with the azido-pseudo-sugar 4-azidobutylacetate under solvent-free microwave conditions, followed by treatment with K(2)CO(3)/MeOH, or NH(3)/MeOH. All compounds studied in this work were screened for their antiviral activities [against human rhinovirus (HRV) and hepatitis C virus (HCV)] and antibacterial activities against a series of Gram positive and negative bacteria.

Efficient microwave-assisted synthesis, antibacterial activity and high fluorescence of 5 benzimidazolyl-2'-deoxyuridines.

A series of novel C-5 benzimidazolyl-2'-deoxyuridines was synthesized in good yields under solvent-free conditions and microwave irradiation from 5-formyl-2'-deoxyuridine and arylenediamine derivatives in the presence of NaHSO(3) as catalyst. Their absorption and fluorescence spectra were measured. They showed intense fluorescence around 400-500nm with quantum yields between 0.

Biophysical characterization of α-amylase inhibitor Parvulustat (Z-2685) and comparison with Tendamistat (HOE-467).

Parvulustat is a small, highly active proteinaceous α-amylase inhibitor whose high-resolution NMR structure was recently solved in Frankfurt. Here, we present its biochemical and biophysical characterization. Several spectroscopic methods such as UV, fluorescence and CD were utilized to extract conformational changes upon modification of pH, temperature and chemical denaturant.