Interaction Between the Guanine Amino Group and the Adenine Six Membered Ring Stabilizes the Unusual Conformation of the CpA Step in B-DNA

Abstract

The CpA step is dramatically overwound in several B-DNA oligonucleotide crystal structures and its AT pair is substantially shifted towards the cytosine of the preceding base pair and towards the minor groove. We show using a geometrical analysis of the crystal data and empirical potential calculations that a strong interaction between the guanine amino group and the adenine six membered ring is responsible for the unique conformational properties of the CpA step.     

Oligonucleotides with 2,6-Diaminopurine Base Replacing for Adenine: Synthesis and Properties

Abstract

Synthesis of three nucleoside building blocks with a benzoyl protected diaminopurine (DAP) base and their incorporation at different positions of DNA, RNA and hexitol oligomers (HNA) have been accomplished. DNA hairpins with a DAP substituted for one (or more) adenine in the loop structure were not found to be more stable. But the stability of RNA-hexitol as well as hexitol-hexitol duplexes improved when the adenine base was replaced with DAP.     

The Structure of the Carbohydrate Moiety of a Glycopeptide GP-I-b from Rhizopus Saccharogenic Amylase

The structure of the carbohydrate moiety of GP–I–b which is one out of three glycopeptides isolated from a Pronase digest of the saccharogenic amylase of Rhizopus javanicus sp. 3–46, was investigated by enzymatic and chemical techniques.

Nine moles of mannose followed by one mole of N-acetylglucosamine were released per mole of GP–I–b when it was treated sequentially with purified jack bean α-mannosidase and β-N-acetylglucosaminidase.

Methylation of GP–I–b gave 3, 6-di-O-methyl derivative from the N-acetylglucosamine residues, and 2, 3, 4, 6-tetra-O-methyl, 3, 4, 6-tri-O-methyl and 2, 4-di-O-methyl derivatives from the mannose residues in an approximate ratio of 3: 4: 2.

A smaller glycopeptide (F–l) containing two moles each of mannose and N-acetylglucosamine per mole of asparagine was obtained when GP–I–b was subjected to one step of the Smith degradation. Exhaustive methylation of F–l gave 3, 6-di-O-methyl derivative of Nacetylglucosamine, and 2, 3, 4, 6-tetra-O-methyl and 2, 3, 4-tri-O-methyl derivatives of mannose in a ratio of 1.00: 0.85.

Controlled acetolysis of GP–I–b yielded mannose, O-α-mannosyl-(l→2)-O-α-mannosyl-(l→3)-mannose and a smaller glycopeptide which was resistant to the acetolysis.

From these and previous evidences, the following structure was determined for GP–I–b.     

Influence on Insecticidal Activity of the 3-(3,4-Methylenedioxyphenyl) Group in the 1,4-Benzodioxanyl Moiety of Haedoxan

The influence on the insecticidal activity of haedoxan A of its 3-(3,4-methylenedioxyphenyl) group in the 1,4-benzodioxanyl moiety was examined with two (±)-(1S*,2R*,5R*,6S*)-6-[(2R*,3R*)-3-alkyl-6- methoxy-2-methoxymethyl-1,4-benzodioxan-7-yl]-2-(2,6-dimethoxyphenoxy)-1-hydroxy-3,7-dioxabicyclo-[3.3.0]octanes. Replacement of the methylenedioxyphenyl group of haedoxan by methyl and n-butyl group resulted in a large decrease in the activity, indicating the importance of the 3-aryl group for the potent insecticidal activity of haedoxan.     

2‐Azapurine Nucleosides: Synthesis,Properties, and Base Pairing of Oligonucleotides

This review deals with 2‐azapurine (imidazo[4,5‐d] [1,2,3]triazine) nucleosides and closely related analogs. Different routes are described to yield the desired target compounds, including a sequence of ring‐opening and ring‐closure reactions performed on purine nucleosides or direct glycosylation of a 2‐azapurine nucleobase with a sugar halide. Further, physical and spectroscopic properties of 2‐azapurine nucleosides are discussed, including fluorescence, ¹³C‐NMR data, single‐crystal X‐ray analyses, and conformation studies on selected compounds; new biological data are presented. The second part of this review is dedicated to oligonucleotides containing 2‐azapurines, including building‐block (phosphoramidite) preparation and their use in solid‐phase oligonucleotide synthesis. Base‐pairing properties of 2‐azapurine nucleosides as surrogates of canonical constituents of DNA were evaluated.     

生物素标记寡核苷酸探针检测B群轮状病毒

用５′端接氨基标记法,用生物素对Ｂ群轮状病毒（ＧＢＲＶ）ＩＤＩＲ株具有群特异性的３片段基因上２３ｂｐ寡核苷酸序列进行标记,经高效薄层层析板（ＨＰＴＬＣ）纯化,制备了Ｂ群轮状病毒生物素寡核苷酸探针,探针显色灵敏度达１０Ｐｇ,与ＧＢＲＶ、ＫＢ６３株基因杂交可检测到１００ｐｇ靶序列,而与Ａ群和Ｃ群轮状病毒及无关基因均不产生杂交信号,该探针可用于Ｂ群轮状病毒的检测、鉴定,以及同群不同毒株间基因相关性研究。     

Synthesis and Hybridization Properties of Modified Oligonucleotides with PNA-DNA Dimer Blocks

Abstract

Different modified PNA-DNA dimer-analogous synthons (I and II) were synthesized as phosphoramidites. These dimer units were assembled by a 5′-modified deoxythymidine and a modified PNA monomer. These synthons were used in the routine coupling procedure for oligonucleotides. Therefore no PNA coupling chemistry is necessary to synthesize PNA-DNA chimeric oligonucleotides. Various deoxyoligonucleotides were synthesized introducing the dimer blocks I and II at different positions in the sequences. Melting temperatures of the modified oligonucleotides with their complementary DNA analogues were determined.

Backbone modifications of oligonucleotides are required in the antisense strategy for protection against endonucleolytic cleavage in biological environment. Peptide nucleic acids (PNA fragments) are known to be nuclease resistant analogues, which show stable and discriminating hybridization. For this reason we prepared chimeric PNA-DNA oligomers by incorporation of two different modified PNA-DNA dimer blocks (Scheme A) into oligonucleotides. Melting temperatures of the modified oligonucleotides with their complementary DNA were determined.     

Synthesis and Triplex Binding Properties of Oligonucleotides Containing a Novel Nucleobase

Abstract

The thiazolo-indole compound 1 bearing the complementary donor-acceptor-donor sites (dad) was designed for specific recognition of an AT inverted base pair in pyrimidine triple helix motif. It was successfully incorporated into 14-mer oligonucleotide using a serinol unit as sugar derivative. The triple helix hybridization studies were examined by means of thermal denaturation experiments with a 26-mer DNA duplex containing the AT inverted base pair.     

Properties of Oligonucleotides Containing the Transition Bases P and K

Abstract

The properties of the degenerate nucleosides dP and dK, in templates and primers were determined. dP was copied as either pyrimidine, dK as either purine. In primers, an equimolar mixture of the two nucleosides functioned as a universal base equivalent in both sequencing and the polymerase chain reactions. Cloning of DNA containing dP or dK produced transition mutations in vivo.     

Bridged Oligonucleotides with Smoothed Hybridization Properties as a Tool for Analysis of Nucleotide Sequences

Russian Journal of Bioorganic Chemistry - Bridged oligonucleotides that contain nonnucleotide inserts, i.e., diethylene glycol phosphate residues (DEG insert) have been studied. These...     

Physico-chemical and Biological Properties of Antisense Phosphodiester Oligonucleotides with Various Secondary Structures

Abstract

The influence of the secondary structure of oligonucleotides having a natural phosphodiester backbone on their ability to interact with DNA and RNA targets and on their resistance to the nucleolytic digestion is investigated. Oligonucleotides having hairpin, looped and snail-like structure are found to be much more stable to nuclease degradation in different biological media and inside cells than the linear ones. The structured oligonucleotides can also hybridise with their DNA and RNA targets.     

Isolation and Characterization of the Serotype g Carbohydrate Moiety from an Enzyme Lysate of Streptococcus mutans 6715 Cell Walls

The serotype-specific carbohydrate moiety of Streptococcus mutans was isolated by mild degradation of purified cell walls with a cell-wall lytic enzyme. Cell walls of serotype g S. mutans strain 6715 were digested with M1 enzyme, an endo-N-acetylmuramidase purified from culture supernatants of Streptomyces globisporus strain 1829. The enzyme lysate of the cell walls was applied to a CM Sephadex C-25 column to remove the M1 enzyme from the cell wall lysate and then subjected to Sephadex G-100 column chromatography. Carbohydrate antigens with serotype g specificity, designated M1g, and a peptidoglycan—polysaccharide complex lacking serotype specificity (M1PG) were separated. Purified serotype g antigen was also obtained by autoclaving the S. mutans 6715 whole cells in saline at 120 C for 30 min. The extract was applied to a DEAE Sephadex A-25 column to remove nucleic acids and teichoic acids. The unbound peak fraction was concentrated and re-chromatographed on a Bio-Gel P-100 column. The void volume fraction contained serotype g carbohydrate and was designated RRg antigen. M1g and RRg antigens formed a band of identity with anti-serotype g serum by immunodiffusion. These antigens were composed mainly of galactose, glucose, and rhamnose at an approximate weight ratio of 8 : 4 : 1, while constituent sugars of M1PG consisted of rhamnose and glucose, with no detectable galactose. M1g also contained peptidoglycan residues other than threonine, an interpeptide bridge component of the native cell wall peptidoglycan. Marked inhibition of the quantitative precipitin reaction between M1g and anti-serotype g serum was obtained with melibiose and galactose, which suggests that the immunodeterminant of the serotype g carbohydrate is an α-linked galactose-glucose terminal linkage.     

Synthesis of a Novel,Optically Active Uridine Analog Containing a 1,4-Dioxane Sugar Moiety. Synthesis of the Corresponding Dinucleotide

A new optically active uridine nucleoside analogue in which a substituted 1,4-dioxane ring functioned as the sugar analogue was prepared from L-tartaric acid. The nucleoside analogue was further converted into the corresponding protected dinucleotide.     

Synthesis and Properties of Bacteriorhodopsin Analogs Containing Electron-Density Labels in the Chromophore Moiety

A method for synthesis of retinal analogs labeled with electron-density groups is suggested. The interaction of these polyene compounds with bacterioopsin in apomembrane of Halobacterium salinarum was tested. A retinal analog containing a crown-ether receptor group is able to interact readily with bacterioopsin giving rise to rapid formation of a pigment with absorption maximum at 460 nm. This pigment is capable of undergoing cyclic photoconversion. The crown-bacteriorhodopsin photocycle is extremely slow and its quantum efficiency is very low (3% of that in native bacteriorhodopsin). This photocycle includes an M-like intermediate with a differential absorption maximum at 380 nm. A retinal analog in which the -ionone ring is replaced by ferrocene moiety forms a stable chromoprotein with the main absorption band at 483 nm and a shoulder near 590-610 nm.     

The 1,1-Dianisyl-2,2,2-trichloroethyl Moiety as a New Protective Group for the Synthesis of Dinucleostde Trifluoromethylphosphonates

Abstract

The new 1,1-Dianisyl-2,2,2-trichloroethyl moiety (DATE) is used as an acid and base stable protective group for nucleosides. 5′-O-DATE-thymidine and 3′-O-acetyl-thymidine are phosphorylated with CF₃P(NR₂)₂ to the corresponding thymidine trifluoromethylphosphonous amidites. These building blocks are coupled with appropriate protected thymidines to a dinucleotide trifluoromethylphosphonate.

     

Facile and Rapid Deprotection Conditions for the Cleavage of Synthetic Oligonucleotides from 1,4-Anhydroerythritol-Based Universal Polymer Support

In our previous report [Kumar, P.; Dhawan, G.; Chandra, R.; Gupta, K.C. Polyamine-assisted rapid and clean cleavage of oligonucleotides from cis-diol bearing universal support. Nucl. Acids Res. 2002, 30, e130 (1-8)], we demonstrated polyamine-mediated deprotection of oligonucleotides from cis-diol group bearing universal polymer support (I). However, vulnerability of the conventional dC^bz to modifications under these conditions compelled us to employ dC^ac during synthesis of oligonucleotide using conventional synthons. Here, a new set of simple and rapid deprotection conditions has been developed for the complete cleavage of oligonucleotides from the 1,4-anhydroerythritol-based universal polymer support employing conventional dC^bz synthon. Using manganese-imidazole complex in aqueous ammonium hydroxide (～30%), fully deprotected oligonucleotide sequences were obtained in 40 min, which were analyzed on reverse phase-HPLC and compared with the standard oligomers in terms of their retention time. Finally, their biological compatibility was established by analyzing PCR amplified products of npsA gene of N. meningitidis.     

Enhanced Fluorescence in the Binding of Oligonucleotides With a Pyrene Group in the Sugar Fragment to Complementary Polynucleotides

Abstract

The fluorescence intensity and lifetime of oligonucleotides with a pyrenylmethyl group at the specific sugar residue were increased upon binding to their complementary polynucleotide in aqueous solution. The present oligonucleotide-pyrene conjugates provide new fluorescent probes for detection of specific nucleic acids.     

Solid Phase Synthesis and Chromatographic Characteristics of Nucleophilic Agents Conjugated with Oligonucleotides Containing 5'-Terminal Carboxyl Group

Conjugates of amines or short peptides with oligonucleotides containing 5'-terminal carboxyl group were prepared by solid phase chemical synthesis. A correlation between the physicochemical parameters and retention times of the synthesized conjugates was established by ion-pair reversed-phase HPLC.     

Amino Acid Nucleic Acids: Synthesis and Hybridization Properties of a Novel Class of Antisense Oligonucleotides

Abstract

Oligonucleotides containing novel phoshoramidite 12 were synthesized and studied for their hybridization properties for the first time. Interestingly, these modified oligonucleotides showed a remarkable resistance to exonuclease.     

Chromium Picolinate Modulates Serotonergic Properties and Carbohydrate Metabolism in a Rat Model of Diabetes

Chromium picolinate (CrPic) has shown both antidepressant and antidiabetic properties. In this study, the effects of CrPic on serotonergic properties and carbohydrate metabolism in diabetic rats were evaluated. Sixty male Sprague-Dawley rats were divided into four groups. (1) The control group received only standard diet (8?% fat). (2) The CrPic group was fed standard diet and CrPic (80?μg CrPic per kilogram body mass (b.m.)/day), for 10?weeks (microgram/kilogram b.m./day). (3) The HFD/STZ group fed a high-fat diet (HFD, 40?% fat) for 2?weeks and then received streptozotocin (STZ, 40?mg/kg, i.p.) (i.v.) HFD-STZ-CrPic group treated as the previous group and then were administered CrPic. CrPic administration to HFD/STZ-treated rats increased brain chromium levels and improved all measurements of carbohydrate metabolism and serotonergic properties (P?相似文献