Large-scale pyrosequencing of synthetic DNA: a comparison with results from Sanger dideoxy sequencing

Pyrosequencing is a relatively recent method for sequencing short stretches of DNA. Because both Pyrosequencing and Sanger dideoxy sequencing were recently used to characterize and validate DNA molecular barcodes in a large yeast gene-deletion project, a meta-analysis of those data allow an excellent and timely opportunity for evaluating Pyrosequencing against the current gold standard, Sanger dideoxy sequencing. Starting with yeast genomic DNA, parallel PCR amplification methods were used to prepared 4747 short barcode-containing constructs from 6000 Saccharomyces cerevisiae gene-deletion strains. Pyrosequencing was optimized for average read lengths of 25-30 bases, which included in each case a 20-mer barcode sequence. Results were compared with sequence data obtained by the standard Sanger dideoxy chain termination method. In most cases, sequences obtained by Pyrosequencing and Sanger dideoxy sequencing were of comparable accuracy, and the overall rate of failure was similar. The DNA in the barcodes is derived from synthetic oligonucleotide sequences that were inserted into yeast-deletion-strain genomic DNA by homologous recombination and represents the most significant amount of DNA from a synthetic source that has been sequenced to date. Although more automation and quality control measures are needed, Pyrosequencing was shown to be a fast and convenient method for determining short stretches of DNA sequence.     

Stereocontrolled assembly of the C3/C3' dideoxy core of lomaiviticin A/B and congeners

The dideoxy core (23) of lomaiviticinone and congener 15 were derived starting from (-)-quinic acid in a stereocontrolled fashion.     

Synthesis and Conformational Analysis of 1′‐ and 3′‐Substituted 2‐Deoxy‐2‐fluoro‐D‐ribofuranosyl Nucleosides

Convergent syntheses of the 9‐(3‐X‐2,3‐dideoxy‐2‐fluoro‐β‐D ‐ribofuranosyl)adenines 5 (X=N₃) and 7 (X=NH₂), as well as of their respective α‐anomers 6 and 8 , are described, using methyl 2‐azido‐5‐O‐benzoyl‐2,3‐dideoxy‐2‐fluoro‐β‐D ‐ribofuranoside ( 4 ) as glycosylating agent. Methyl 5‐O‐benzoyl‐2,3‐dideoxy‐2,3‐difluoro‐β‐D ‐ribofuranoside ( 12 ) was prepared starting from two precursors, and coupled with silylated N⁶‐benzoyladenine to afford, after deprotection, 2′,3′‐dideoxy‐2′,3′‐difluoroadenosine ( 13 ). Condensation of 1‐O‐acetyl‐3,5‐di‐O‐benzoyl‐2‐deoxy‐2‐fluoro‐β‐D ‐ribofuranose ( 14 ) with silylated N²‐palmitoylguanine gave, after chromatographic separation and deacylation, the N⁷‐β‐anomer 17 as the main product, along with 2′‐deoxy‐2′‐fluoroguanosine ( 15 ) and its N⁹‐α‐anomer 16 in a ratio of ca. 42 : 24 : 10. An in‐depth conformational analysis of a number of 2,3‐dideoxy‐2‐fluoro‐3‐X‐D ‐ribofuranosides (X=F, N₃, NH₂, H) as well as of purine and pyrimidine 2‐deoxy‐2‐fluoro‐D ‐ribofuranosyl nucleosides was performed using the PSEUROT (version 6.3) software in combination with NMR studies.     

Conformational restriction of nucleosides by spirocyclic annulation at C4' including synthesis of the complementary dideoxy and didehydrodideoxy analogues

The concept of spirocyclic restriction, when generically applied to nucleoside mimics, allows for the preparation of diastereomeric pairs carrying either a syn- or anti-oriented hydroxyl at C-5'. Reported herein are convenient synthetic routes to enantiomerically pure 1-oxaspiro[4.4]nonanes featuring fully dihydroxylated end products as well as congeners having dideoxy and didehydrodideoxy substitution patterns. Notable use is made of the capacity for introducing unsaturation in the furanose sector via phenylsulfenylation and the incorporation of uracil and thymine by way of their silylated derivatives under catalysis with stannic chloride.     

Synthetic studies directed toward dideoxy lomaiviticinone lead to unexpected 1,2-oxazepine and isoxazole formation

In the course of studies directed toward the synthesis of dideoxy lomaiviticinone, 3-(nitromethyl)cyclohexenones 2a (X = H) and 2b (X = I) were prepared. The corresponding enolates were reacted with naphthazarin (1) and unexpectedly afforded 1,2-oxazepine 3 and isoxazole 4, respectively. Rationale for their formation is proposed.     

Scalable Syntheses of Both Enantiomers of DNJNAc and DGJNAc from Glucuronolactone: The Effect of N‐Alkylation on Hexosaminidase Inhibition

The efficient scalable syntheses of 2‐acetamido‐1,2‐dideoxy‐D ‐galacto‐nojirimycin (DGJNAc) and 2‐acetamido‐1,2‐dideoxy‐D ‐gluco‐nojirimycin (DNJNAc) from D ‐glucuronolactone, as well as of their enantiomers from L ‐glucuronolactone, are reported. The evaluation of both enantiomers of DNJNAc and DGJNAc, along with their N‐alkyl derivatives, as glycosidase inhibitors showed that DGJNAc and its N‐alkyl derivatives were all inhibitors of α‐GalNAcase but that none of the epimeric DNJNAc derivatives inhibited this enzyme. In contrast, both DGJNAc and DNJNAc, as well as their alkyl derivatives, were potent inhibitors of β‐GlcNAcases and β‐GalNAcases. Neither of the L ‐enantiomers showed any significant inhibition of any of the enzymes tested. Correlation of the in vitro inhibition with the cellular data, by using a free oligosaccharide analysis of the lysosomal enzyme inhibition, revealed the following structure–property relationship: hydrophobic side‐chains preferentially promoted the intracellular access of iminosugars to those inhibitors with more‐hydrophilic side‐chain characteristics.     

Reagent‐Controlled α‐Selective Dehydrative Glycosylation of 2,6‐Dideoxy‐ and 2,3,6‐Trideoxy Sugars

We have found that activating either 2,3‐bis(2,3,4‐trimethoxyphenyl)cyclopropenone or 2,3‐bis(2,3,4‐trimethoxyphenyl)cyclopropene‐1‐thione with oxalyl bromide results in the formation of a species that promotes the glycosylation between 2,6‐dideoxy‐sugar hemiacetals and glycosyl acceptors in good yield and high α‐selectivity. Both reactions are mild and tolerate a number of sensitive functional groups including highly acid‐labile 2,3,6‐trideoxy‐sugar linkages.     

Synthesis and Evaluation of Paromomycin Derivatives Modified at C(4′)

The 2‐amino‐2‐deoxy‐α‐D ‐glucopyranosyl moiety (ring I) of paromomycin was replaced by a 2,4‐diamino‐2,4‐dideoxy‐α‐D ‐glucopyranosyl, 2,4‐diamino‐2,4‐dideoxy‐α‐D ‐galactopyranosyl, 2‐amino‐2‐deoxy‐α‐D ‐galactopyranosyl, or 3,4,5‐trideoxy‐4‐aza‐α‐D ‐erythro‐heptoseptanosyl moiety to investigate the effect of the substituent at C(4′) on the interaction with ribosomal RNA. The triflate 6 was prepared from the key intermediate pentaazido 3′,6′‐dibenzyl ether 5 , and the hexosulose 10 was obtained by oxidation of 5 with Dess–Martin's periodinane. Stereoselective reduction of 10 with NaBH₄ gave the alcohol 11 that was transformed into the triflate 12 . The epimeric hexaazides 7 and 13 were obtained by treating the triflates 6 and 12 , respectively, with tetrabutylammonium azide. Periodate cleavage of glycol 2 yielded the dialdehyde 24 that was reductively aminated with aniline and benzylamine to give the 3,4,5‐trideoxy‐4‐aza‐α‐D ‐erythro‐heptoseptanosides 25 and 26 , respectively. Standard azide reduction and debenzylation yielded 9 (2,4‐diamino‐2,4‐dideoxy‐α‐D ‐galactopyranosyl ring I), 13 (2‐amino‐2‐deoxy‐α‐D ‐galactopyranosyl ring I), 17 (2,4‐diamino‐2,4‐dideoxy‐α‐D ‐glucopyranosyl ring I), and 27 and 28 (3,4,5‐trideoxy‐4‐aza‐α‐D ‐erythro‐heptoseptanosyl ring I). The derivatives 9 and 13 possessing a D ‐galacto‐configured ring I were less active than the corresponding D ‐gluco‐analogues 17 and paromomycin ( 1 ), respectively. The C(4′)‐aminodeoxy derivative 17 (D ‐gluco ring I) and the known 4′‐deoxyparomomycin ( 23 ), prepared by a new route, displayed slightly lower antibacterial activities than paromomycin ( 1 ). Cell‐wall permeability is not responsible for the unexpectedly low activity for 17 , as shown by cell‐free translation assays. The results evidence that the orientation of the substituent at C(4′) is more important than its nature for drug binding and activity.     

The vaccinia virus HindIII K fragment encodes a novel protein belonging to the serpin superfamily

The 1983-base pair nucleotide sequence of the EcoRI-HindIII fragment of vaccinia virus Tiantan strain HindIII K clone is determined by the dideoxy chain termination method. A search in the NBRF protein sequence database using FASTA and other microcomputer programs reveals that several proteins belonging to the serpin (serine protease inhibitor) superfamily have striking similarities to the protein encoded by the HindIII K1 ORF. On the basis of the dot-matrix analysis and sequence alignment, the K1-encoded protein is shown as a novel member of the serpin superfamily. The putative reactive site and switch sequence of this novel serpin are then compared with those of other serpins. The probable evolutionary and possible functional relationships are discussed.     

Identification and Role of a 6‐Deoxy‐4‐Keto‐Hexosamine in the Lipopolysaccharide Outer Core of Yersinia enterocolitica Serotype O:3

The outer core (OC) region of Yersinia enterocolitica serotype O:3 lipopolysaccharide is a hexasaccharide essential for the integrity of the outer membrane. It is involved in resistance against cationic antimicrobial peptides and plays a role in virulence during early phases of infection. We show here that the proximal residue of the OC hexasaccharide is a rarely encountered 4‐keto‐hexosamine, 2‐acetamido‐2,6‐dideoxy‐D ‐xylo‐hex‐4‐ulopyranose (Sugp) and that WbcP is a UDP‐GlcNAc‐4,6‐dehydratase enzyme responsible for the biosynthesis of the nucleotide‐activated form of this rare sugar converting UDP‐2‐acetamido‐2‐deoxy‐D ‐glucopyranose (UDP‐D ‐GlcpNAc) to UDP‐2‐acetamido‐2,6‐dideoxy‐D ‐xylo‐hex‐4‐ulopyranose (UDP‐ Sugp). In an aqueous environment, the 4‐keto group of this sugar was present in the 4‐dihydroxy form, due to hydration. Furthermore, evidence is provided that the axial 4‐hydroxy group of this dihydroxy function was crucial for the biological role of the OC, that is, in the bacteriophage and enterocoliticin receptor structure and in the epitope of a monoclonal antibody.     

芳环缩合核苷衍生物的合成

A novel efficient synthetic route to 1,3-dihydrobenzo[c]furan glycone was developed and the corresponding 5-fluoro, 5-iodo uracil and guanosine derivatives, the aromatic analogues of the well known antiviral 2＇,3＇-dideoxy-2＇,3＇-dihydronucleosides （d4N）, were synthesized.     

Synthesis of Different 3,5‐Diazidofuranoses: A New and General Synthesis Pathway

Diamino‐ and diazidofuranoses represent useful precursors, for example, for the synthesis of substituted nucleosides and metal complexes, respectively. Known procedures for their synthesis lack the availability of cheap starting materials, adequate yields, and the access to all possible diastereomeres. Therefore, 3,5‐diazido‐3,5‐dideoxy‐ and ‐2,3,5‐trideoxyfuranoses both with ribo‐ and xylo‐configuration were prepared using different approaches.     

Synthesis of a New C(1→2)‐Linked Iminodisaccharide Starting from Levoglucosenone

Methyl 2‐deoxy‐2‐[(1S)‐2,5‐dideoxy‐2,5‐imino‐L ‐ribitol‐1‐C‐yl)‐α‐D ‐glucopyranoside ((+)‐ 6 ) was obtained from the product of Nozaki‐Kishi coupling of 2,5‐{[(tert‐butoxy)carbonyl]imino}‐2,5‐dideoxy‐3,4‐O‐isopropylidene‐L ‐ribose ((−)‐ 9 ) and 4‐O‐benzyl‐6‐O‐[(benzyloxy)methyl]‐3‐deoxy‐2‐O‐[(trifluoromethyl)sulfonyl]‐α‐D ‐erythro‐hex‐2‐enopyranoside ((+)‐ 12 ). The alkenyl triflate (+)‐ 12 was derived from levoglucosenone ( 1 ).     

Asymmetric Total Synthesis of the Complex Polycyclic Xanthone FD‐594

A highly convergent approach was developed to achieve the first asymmetric and scalable total synthesis of FD‐594, a complex polycyclic xanthone natural product from Streptomyces sp. TA‐0256, in a longest linear sequence (LLS) of 20 steps. The trans‐9,10‐dihydrophenanthrene‐9,10‐diol fragment (B‐C‐D ring) was generated through a new strategy involving asymmetric dihydroxylation followed by Cu‐mediated oxidative cyclization. Late‐stage stereoselective glycosylation assembled the angular hexacyclic framework with a β‐linked 2,6‐dideoxy trisaccharide fragment.     

Dideoxy fingerprinting of low-level nucleotide variation in mitochondrial DNA of the human blood fluke, Schistosoma japonicum.

Dideoxy fingerprinting (ddF) is an efficient method for the detection of sequence changes in polymerase chain reaction (PCR)-amplified DNA fragments. It is a hybrid between single-strand conformation polymorphism (SSCP) and dideoxy sequencing, employing only one dideoxynucleotide in the reaction. We report the application of ddF for the display of low-level nucleotide variation in the mitochondrial (mt) NADH dehydrogenase subunit 1 (ND1) (404 bp) in the human blood fluke, Schistosoma japonicum. Variant samples differing by 1-6 nucleotides could be readily differentiated from one another by their characteristic and reproducible ddF profiles. The findings indicate the potential of this method to screen for point mutation in any parasite genes.     

Bromodimethylsulfonium Bromide Catalyzed Synthesis of Methyl 2‐Dexoy‐4,6‐O‐benzylidene Galactopyranoside from Galactal and the Rapid Route to 2,3‐ and 2,6‐Dideoxygalactopyranoses

4,6‐O‐Benzylidenation of D‐galactal with PhCH(OCH₃)₂ catalyzed by bromodimethylsulfonium bromide leads to methyl 2‐dexoy‐4,6‐O‐benzylidene galactopyranoside efficiently, which serves as a key intermediate to the ready preparation of 2,3‐ and 2,6‐dideoxy galactopyranosides.     

Sugar‐based hydrophilic polyurethanes and polyureas

Novel linear homogeneous polyurethanes and polyureas with enhanced hydrophilic character have been successfully prepared from sugar‐based monomers having their hydroxyl groups free or partially protected. By the reaction of primary hydroxyl groups of xylitol with dimethyl hexamethylene dicarbamate (HMDC) or di‐tert‐butyl‐4,4′‐diphenyl methyl dicarbamate (MDC), two new linear semicrystalline polyurethanes [PU(X‐HMDC) and PU(X‐MDC)] have been prepared. Likewise, by the reaction of xylitol with the analogous diisocyanates hexamethylene diisocyanate (HMDI) or 4,4′‐methylenebis(phenyl isocyanate) (MDI), similar polyurethanes [PU(X‐HMDI) and PU(X‐MDI)] were obtained. However, these latter polyurethanes present some degree of crosslinking because of the higher reactivity of the diisocyanate comonomers. Linear hydrophilic polyureas having free hydroxyl groups joined to the main chain have also been prepared by the reaction of the same diisocyanates (HMDI and MDI) with 1,6‐diamino‐1,6‐dideoxy‐D ‐mannitol and 1,6‐diamino‐1,6‐dideoxy‐3:4‐O‐isopropylidene‐D ‐mannitol. As far as we are aware, this kind of polyhydroxylated polyurea has not been previously described in the literature. The new polymers were characterized by standard methods (elemental analyses, gel permeation chromatography, IR, and NMR). The polyurethanes were hydrolytically degradable under physiological conditions, in contrast with less‐hydrophilic linear polyurethanes previously described. The thermal properties of the novel polymers were investigated by thermogravimetric analysis and differential scanning calorimetry. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

Synthesis of a tetrasaccharide repeating unit of O-antigenic polysaccharide of Salmonella enteritidis by use of unique and odorless dodecyl thioglycosyl donors

The first total synthesis of a unique tetrasaccharide repeating unit of lipopolysaccharide from Salmonella enteritidis has been accomplished by assembly of dodecyl thioglycosides. The crucial key steps were preparation of a rare branched dideoxy sugar, d-tyvelose (3,6-dideoxy-d-arabino-d-hexose) and sequential regioselective glycosylation at 2,3-positions of a central d-mannose residue 5 with d-tyvelose 6 and d-galactose donors 7.     

Synthesis and Hybridization Properties of an Oligonucleotide Consisting of 1′,4′‐Anhydro‐2′,5′‐dideoxy‐2′‐(thymin‐1‐yl)‐D‐altritol

The novel oligonucleotide analogue 7 , consisting of 1′,4′‐anhydro‐2′,5′‐dideoxy‐2′‐(thymin‐1‐yl)‐D ‐altritol ( 4 ), residues was synthesized by the phosphoramidite approach on an automated DNA synthesizer. The phosphoramidite building block 6 was obtained by phosphitylation of the corresponding isonucleoside 5 . Oligoisonucleotide 7 contains an extended phosphodiester linkage with a higher flexibility. Oligoisonucleotide 7 was studied with respect to hybridization properties, enzymatic stability, and CD spectra. It exhibits a high stability towards snake‐venom phosphodiesterase and an acceptable hybridization to complementary single‐stranded DNA and RNA.     

Synthesis of a Phosphorylated Disaccharide Fragment of the O‐Specific Polysaccharide of Vibrio cholerae O139, Functionalized for Conjugation

The title disaccharide, 2‐{2‐{2‐[(2‐ethoxy‐3,4‐dioxocyclobut‐1‐en‐1‐yl)amino]ethoxy}ethoxy}ethyl 2‐O‐(3,6‐dideoxy‐α‐L ‐xylo‐hexopyranosyl)‐β‐d‐ galactopyranoside cyclic 4,6‐(potassium phosphate) ( 2 ), was synthesized from the two isomeric linker‐equipped galactose acceptors 9 and 10 , obtained by phosphorylation of 2‐[2‐(2‐azidoethoxy)ethoxy]ethyl 3‐O‐benzyl‐β‐d‐ galactopyranoside ( 8 ), which were glycosylated with ethyl 2,4‐di‐O‐benzyl‐3,6‐dideoxy‐1‐thio‐β‐l‐ xylo‐hexopyranoside ( 12 ; Scheme). Mainly the fully protected α‐(1 → 2)‐linked products 13 α and 14 α were formed. Catalytic hydrogenolysis/hydrogenation effected global deprotection, thereby removing the chirality at the P‐atom, and simultaneously converted the azido group in the linker to an amino group (→ 15 ). Final treatment with diethyl squarate (= 3,4‐diethoxycyclobut‐3‐ene‐1,2‐dione) gave target compound 2 , amenable for conjugation to proteins.