Sequence-specific transitions of the torsion angle gamma change the polar-hydrophobic profile of the DNA grooves: implication for indirect protein–DNA recognition

Variations of the shape and polarity of the DNA grooves caused by changes of the DNA conformation play an important role in the DNA readout. Despite the fact that non-canonical trans and gauche- conformations of the DNA backbone angle γ (O5′–C5′–C4′–C3′) are frequently found in the DNA crystal structures, their possible role in the DNA recognition has not been studied systematically. In order to fill in this gap, we analyze the available high-resolution crystal structures of the naked and complexed DNA. The analysis shows that the non-canonical γ angle conformations are present both in the naked and bound DNA, more often in the bound vs. naked DNA, and in the nucleotides with the A-like vs. the B-like sugar pucker. The alternative angle γ torsions are more frequently observed in the purines with the A-like sugar pucker and in the pyrimidines with the B-like sugar conformation. The minor groove of the nucleotides with non-canonical γ angle conformation is more polar, while the major groove is more hydrophobic than in the nucleotides with the classical γ torsions due to variations in exposure of the polar and hydrophobic groups of the DNA backbone. The propensity of the nucleotides with different γ angle conformations to participate in the protein–nucleic acid contacts in the minor and major grooves is connected with their sugar pucker and sequence-specific. Our findings imply that the angle γ transitions contribute to the process of the protein–DNA recognition due to modification of the polar/hydrophobic profile of the DNA grooves.     

Fotolisi Dell'Acqua e Riduzione Fotosintetica dei Coenzimi Piridinici in Cuscuta Epithymum

Abstract

Photolysis of water and photosynthetic reduction of pyridine nucleotides in CUSCUTA EPITHYMUM. — The reactions for the photolysis of water appear to be present in extracts prepared from seedlings of C. epithymum but not in the extracts prepared from filaments detached from the host (Trifolium repens). Extracts from both seedlings and filaments fail to catalyze the photosynthetic reduction of pyridine nucleotides. Together with the results previously obtained on the mechanism for the fixation of carbon dioxide, the present data suggest that a complete photosynthetic cycle is absent in this species of dodder.     

The Synthesis of Novel Transition State Analogues Related to Imidazole and Purine Nucleotides Involved in the De novo Biosynthesis of Purines

Abstract

5-Amino-4-sulphonamidoimidazole ribofuranosyl nucleosides and a related imidazothiadiazine dioxide nucleoside have been synthesized as potential inhibitors of enzymes involved in the de novo biosynthesis of purine nucleotides.     

FR3D: finding local and composite recurrent structural motifs in RNA 3D structures

New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, “Find RNA 3D” (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs whose geometric discrepancy with respect to the query motif falls below a user-specified cutoff discrepancy. This technique can be applied to RMSD searches. Candidate motifs identified geometrically may be further screened symbolically to identify those that contain particular basepair types or base-stacking arrangements or that conform to sequence continuity or nucleotide identity constraints. Purely symbolic searches for motifs containing user-defined sequence, continuity and interaction constraints have also been implemented. We demonstrate that FR3D finds all occurrences, both local and composite and with nucleotide substitutions, of sarcin/ricin and kink-turn motifs in the 23S and 5S ribosomal RNA 3D structures of the H. marismortui 50S ribosomal subunit and assigns the lowest discrepancy scores to bona fide examples of these motifs. The search algorithms have been optimized for speed to allow users to search the non-redundant RNA 3D structure database on a personal computer in a matter of minutes.     

Synthesis of New Acyclic Nucleoside Vinyl Phosphonates

Abstract

Chiral vinyl phosphonates, homomorphous with natural nucleotides, have been prepared starting from (S)-malic acid as potential monomers for the synthesis of acyclic polynucleotides.     

Parziale purificazione della DPN-chinasi da foglie di pisello

Abstract

PARTIAL PURIFICATION OF DPN-KINASE FROM PEA LEAVES. — The presence of DPN-kinase has been demonstrated in pea leaves. The enzyme has been purified about 100 fold from this material. The possible significance of DPN-kinase and TPN-phosphatase (FORTI et Al., 1962) in the interconversion of pyridine nucleotides is discussed.     

Non-inhibition of Acetylcholinesterase by cyclosal Nucleotides

Abstract

An acetylcholinesterase (AChE) assay based on the Rappaport method was established to investigate the behaviour of several cycloSal nucleotides against AChE from electrophorus electricus and human sources (purified enzymes). AChE is a physiologically essential enzyme as it catalyzes the hydrolysis of the neurotransmitter acetylcholine. No inhibition was observed in any of the cases.     

Synthesis of 3′-C-Phosphono Nucleosides from α,β-Unsaturated Lactone

Abstract

The reaction of 5-protected α,β-unsaturated γ-lactone 4 with trialkylphosphite gave 3′-C-dialkylphosphono-erythro lactone 5 in high yields. The lactone 5 was reduced with DIBAL to the corresponding lactol, which was converted to the acetate 6 by treatment with acetic anhydride in pyridine. The acetate 6 was coupled with silylated thymine in the presence of TMS-triflate and the resulting anomeric mixture of nucleotides could be separated chromatographically and after desilylation using TBAF in THF the 3′-C-dialkylphosphono nucleosides 7 and 8 were obtained.     

Synthesis and Antiviral Evaluation of Novel 5′-Norcarboacyclic Phosphonic Acid Nucleosides

This article describes a very simple route for synthesizing a novel 5′-norcarboacyclic nucleotides. The condensation of the mesylates 17 and 18 with the natural nucleosidic bases (A,U,T,C) under standard nucleophilic substitution (K₂CO₃, 18-Crown-6, DMF) and deprotection afforded the target nucleotide analogues 27–34. In addition, these compounds were evaluated for their antiviral properties against various viruses.     

INTRACELLULAR Ca2+-MOBILIZING ADENINE NUCLEOTIDES. SYNTHESIS AND BIOLOGICAL ACTIVITY OF CYCLIC ADP-CARBOCYCLIC-RIBOSE AND C-GLYCOSIDIC ANALOG OF ADENOPHOSTIN A

We designed novel Ca²⁺-mobilizing purine nucleotides, cyclic ADP-carbocycl-icribose 4, and its inosine congener 5, and C-glycosidic adenophostin A 6. In the synthesis of cADPR analogs, the intramolecular condensation to form the pyrophosphate linkage should be the key step. We developed an efficient method for forming such an intramolecular pyrophosphate linkage by the activation of the phenylthiophosphate group with I₂ or AgNO₃. Using this method, we achieved to synthesize the target compounds 4 and 5. The synthesis of C-glycosidic analog 6 of adenophostin A was achieved using a temporary silicon-tethered radical coupling reaction for constructing (3′α, 1″α)-C-glycosi-dic structure as the key step.     

The Synthesis of RNA Containing the Modified Nucleotides N 2-Methylguanosine and N 6, N 6-Dimethyladenosine

Abstract

The phosphoramidites of the naturally occurring modified nucleotides N ²-methylguanosine and N ⁶,N ⁶-dimethyladenosine were synthesized and incorporated into short oligoribonucleotides. Described are the syntheses of the phosphoramidites and the procedures used to deprotect oligoribonucleotides in which the O ⁶ of m²G is protected with a 2-(p-nitrophenyl)ethyl group.     

Assunzione di Fosforo32 da Parte di Cuscuta Epithymum Parassita di Trifolium Repens

Abstract

Uptake of Phosporus-P³² by CUSCUTA EPITHYMUM parasitic of TRIFOLIUM REPENS. — Filaments of C. epithymum, parasitic on T. repens, partially immersed in a solution containing KH₂P³²O₄, uptake from the host solely, or mainly, radioactive ortophosphate. Radioactive hexose phosphates and radioactive nucleotides present in the extracts prepared from C. epithymum, appear to be the result of the metabolization by the dodder of the orthophosphate uptaken from the host.     

Synthesis and Properties of an Initiation Codon Analog Consisting of 2′-O-Methyl Nucleotides

Abstract

An initiation codon analog consisting of 2′-O-methyl nucleotides (AmUmG) was synthesized and examined for its binding efficiency to E. coli ribosomes with fMetRNA^fMet and also its stability in binding assay systems for comparison with those of r(AUG) and d(ATG). AmUmG was found completely resistant to nucleases under the conditions used.     

SYNTHESIS OF A NEW 5′-O-TRIPHOSPHATE ANALOG OF 5-METHYL 2′-O-DEOXYCYTIDINE. PRELIMINARY IN VITRO LABELING FOR NON-RADIOACTIVE DETECTION OF DNA

We report the synthesis of the triphosphate of 5-methyl 4-N-[6-(p-bromobenzamido)hex-1-yl]-2′-O-deoxycytidine 3A . We also analyzed the formation of intramolecular H-bonds of 5-methyl 4-N-{n-[6-(p-bromobenzamido) caproyl amino]alk-1-yl}-2′-deoxycytidine compounds, and confirmed their presence by ¹H-NMR studies. In vitro DNA labeling with modified nucleotides is preliminarily evaluated.     

Dynamics of Ribosomal RNA Structure

Abstract

The structural dynamics of ribosomal 5S RNAs have been investigated by probing single strandedness through enzymatic cleavage and chemical modification. This comparative study includes 5S rRNAs from E. coli, B. stearothermophilus, T. thermophilics, H. cutirubrum, spinach chloroplast, spinach cytomplasm, and Artemia salina. The structural studies support a unique tertiary interaction in eubacterial 5S rRNAs, involving nucleotides around positions 43 and 75. In addition long range structural effects are demonstrated in E. coli 5S rRNA due to the conversion of C to U at position 92.     

Molecular phylogenetics and definition of the Acrapex minima Janse group (Lepidoptera,Noctuidae, Apameini,Sesamiina) with the description of four new species from the Afrotropics

Five morphologically similar species of Acrapex Hampson (Lepidoptera, Noctuidae, Noctuinae, Apameini), from sub-Saharan Africa are reviewed, including four new species that are described: Acrapex mondogeneta Le Ru n. sp., A. mubale Le Ru n. sp., A. robe Le Ru n. sp. and A. rubona Le Ru n. sp. These five species belong to a species complex that we hereby define as the Acrapex minima group. Host plants of three species are recorded; Acrapex minima is recorded for the first time on a host plant, Digitaria natalensis Stent; A. mondogeneta on Hyparrhenia hirta (L.) Stapf and A. rubona on Imperata cylindrica (L.) P. Beauv. We also conducted molecular phylogenetics (using both Bayesian inference and maximum likelihood) and molecular species delimitation analyses (Poisson tree processes) on a six gene multi-marker dataset (four mitochondrial and two nuclear gene fragments; 4582 nucleotides in length) of 42 specimens and 22 species, including 23 specimens from the Acrapex minima group. The results of the corresponding analyses support the monophyly of the group and the species status of the newly described taxa.     

The Synthesis of Deuterionucleosides

Abstract

The synthesis of deuterionucleosides for site-specific incorporation into oligo-DNA or -RNA is herein reviewed for NMR or biological studies. The review covers the following aspects: (i) deuteration of the aglycone; (ii) single-site chemical deuteration of the sugar residues; (iii) multiple-site chemical deuteration of the sugar residues; (iv) enzymatic synthesis of deuterated nucleosides or nucleotides; and (v) synthesis of labelled nucleosides with multiple isotopes.     

Transition Metal Complexes of 5-Amino-1-β-D-Ribofuranosylimidazole-4-Carboxylic Acid 5′-Phosphate,an Intermediate in the de novo Biosynthesis of Purine Nucleotides: Synthesis and Effects on Enzyme Activity

Abstract

Transition metal complexes [Cu(II), Co(I1) and Ni(II)] of 5-amino-l-β-D-ribofuranosylimidazole-4-carboxylic acid have been prepared and shown to form a series of stoichiometry ML₂, nM(OH₂) (n = 0,1,2) and structures have been assigned. Analogous complexes of 5-amino-l-β-D-ribofuranosylimidazole-4-carboxy1ic acid 5′-phosphate (CAIR), a central intermediate in the de novo pathway to purine nucleotides, produced in aqueous solution have been found to affect the activity of the enzyme AIR- carboxylase (E.C. 4.1.1.21).     

Highly regioselective methylation of inosine nucleotide: an efficient synthesis of 7-methylinosine nucleotide

Abstract

A facile, straightforward, reliable, and an efficient chemical synthesis of inosine nucleotides such as 7-methylinosine 5′-O-monophosphate, 7-methylinosine 5′-O-diphosphate, and 7-methylinosine 5′-O-triphosphate, starting from the corresponding inosine nucleotide is delineated. The present methylation reaction of inosine nucleotide utilizes dimethyl sulfate as a methylating agent and water as a solvent at room temperature. It is noteworthy that the present methylation reaction proceeds smoothly under aqueous conditions that is highly regioselective to afford exclusive 7-methylinosine nucleotide in good yields with high purity (>99.5%).