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  • 1
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    Terminal lipophilization of a unique DNA dodecamer by various nucleolipid headgroups: Their incorporation into artificial lipid bilayers and hydrodynamic properties (2015)
    Beilstein-Institut
    Details
    Publication Date: 2015-06-01
    Description: A series of six cyanine-5-labeled oligonucleotides (LONs 10–15), each terminally lipophilized with different nucleolipid head groups, were synthesized using the recently prepared phosphoramidites 4b–9b. The insertion of the LONs within an artificial lipid bilayer, composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), was studied by single molecule fluorescence spectroscopy and microscopy with the help of an optically transparent microfluidic sample carrier with perfusion capabilities. The incorporation of the lipo-oligonucleotides into the bilayer was studied with respect to efficiency (maximal bilayer brightness) as well as stability against perfusion (final stable bilayer brightness). Attempts to correlate these parameters with the log P values of the corresponding nucleolipid head groups failed, a result which clearly demonstrates that not only the lipophilicity but mainly the chemical structure and topology of the head group is of decisive importance for the optimal interaction of a lipo-oligonucleotide with an artificial lipid bilayer. Moreover, fluorescence half-live and diffusion time values were measured to determine the diffusion coefficients of the lipo-oligonucleotides.
    Print ISSN: 2195-951X
    Electronic ISSN: 1860-5397
    Topics: Chemistry and Pharmacology
    Published by Beilstein-Institut
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  • 2
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    Specific DNA duplex formation at an artificial lipid bilayer: fluorescence microscopy after Sybr Green I staining (2014)
    Beilstein-Institut
    Details
    Publication Date: 2014-10-02
    Description: The article describes the immobilization of different probe oligonucleotides (4, 7, 10) carrying each a racemic mixture of 2,3-bis(hexadecyloxy)propan-1-ol (1a) at the 5’-terminus on a stable artificial lipid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). The bilayer separates two compartments (cis/trans channel) of an optical transparent microfluidic sample carrier with perfusion capabilities. Injection of unlabeled target DNA sequences (6, 8, or 9), differing in sequence and length, leads in the case of complementarity to the formation of stable DNA duplexes at the bilayer surface. This could be verified by Sybr Green I double strand staining, followed by incubation periods and thorough perfusions, and was visualized by single molecule fluorescence spectroscopy and microscopy. The different bilayer-immobilized complexes consisting of various DNA duplexes and the fluorescent dye were studied with respect to the kinetics of their formation as well as to their stability against perfusion.
    Print ISSN: 2195-951X
    Electronic ISSN: 1860-5397
    Topics: Chemistry and Pharmacology
    Published by Beilstein-Institut
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  • 3
    Electronic Resource
    Electronic Resource
    Spontane Öffnung des Pyrimidinringes in Pyrrolo[2,3-d]pyrimidinen nach intramolekularer Acylierung (1985)
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 68 (1985), S. 534-544 
    Details
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Spontaneous Opening of the Pyrimidine Ring of Pyrrolo[2,3-d]pyrimidines after Intramolecular AcylationPhase-transfer alkylation of 4-methoxy-2-methylthio-7H-pyrrolo[2,3-d]pyrimidine (2) with ethyl 3-bromopropionate leads regioselectively to the ester 3a. After displacement of its methylthio group and saponification of the ester function, the acid 3e is obtained which can be transferred to the functionalized deazahypoxanthine 3f by either treatment with dry HBr/glacial AcOH or by nucleophilic displacement of the 4-methoxide. Reaction of 3f with a H2O-soluble carbodiimide results in an intramolecular acylation at N(1) by the activated ester; the intermediate 4 undergoes spontaneous hydroxylation and subsequent opening of the pyrimidine ring under formation of the pyrrolo[1,2-a]pyrimidine derivative 6. Its structure was proved by X-ray analysis. Subsequent deformylation of 6 in alkaline medium leads to the compound 7 in almost quantitative yield.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/hlca.19850680226
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  • 4
    Electronic Resource
    Electronic Resource
    Stereoselective synthesis of pyrrolo[2,3-d]pyrimidine α- and β-D-ribonucleosides from anomerically pure D-ribofuranosyl chlorides: Solid-Liquid Phase-Transfer Glycosylation and 15N-NMR Spectra (1988)
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 71 (1988), S. 1573-1585 
    Details
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solid-liquid phase-transfer glycosylation (KOH, tris[2-(2-methoxyethoxy)ethye]amine ( = TDA-1), MeCN) of pyrrolo[2,3-d]pyrimidines such as 3a and 3b with an equimolar amount of 5-O-[(1,1 -dimethylethyl)dimethylsilyl]-2,3-O-(1-methylethylidene)-α-D-ribofuranosyl chloride (1) [6] gave the protected β-D-nucleosides 4a and 4b, respectively, stereoselectively (Scheme). The β-D-anomer 2 [6] yielded the corresponding α-D-nucleosides 5a and 5b with traces of the β-D-compounds. The 6-substituted 7-deazapurine nucleosides 6a, 7a, and 8 were converted into tubercidin (10) or its α-D-anomer (11). Spin-lattice relaxation measurements of anomeric ribonucleosides revealed that T1 values of H—C(8) in the α-D-series are significantly increased compared to H—C(8) in the β-D-series while the opposite is true for T1 of H—C(1′). 15N-NMR data of 6-substituted 7-deazapurine D-ribofuranosides were assigned and compared with those of 2′-deoxy compounds. Furthermore, it was shown that 7-deaza-2′deoxyadenosine ( = 2′-deoxytubercidin; 12) is protonated at N(1), whereas the protonation site of 7-deaza-2′-deoxyguanosine (20) is N(3).
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/hlca.19880710623
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  • 5
    Electronic Resource
    Electronic Resource
    1-(2′-Deoxy-β-D-xylofuranosyl)thymine Building Blocks for Solid-Phase Synthesis and Properties of Oligo(2′-Deoxyxylonucleotides) (1991)
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 74 (1991), S. 748-760 
    Details
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 1-(2′-Deoxy-β-D-threo-pentofuranosyl)thymine (= 1-(2′-deoxy-β-D-xylofuranosyl)thymine; xTd; 2) was converted into its phosphonate 3b as well as its 2-cyanoethyl phosphoramidite 3c. Both compounds were used for solid-phase synthesis of d[(xT)12-T] (5), representing the first DNA fragment build up from 3′-5′-linked 2′-deoxy--β-D-xylonucleosides. Moreover, xTd was introduced into the innermost part of the self-complementary dodecamer d(G-T-A-G-A-A-xT-xT-C-T-A-C)2 (9). The CD spectrum of d[(xT)12-T] (5) exhibits reversed Cotton effects compared to d(T12) (6; see Fig. 1), implying a left-handed single strand. With d(A12) (7) it could be hybridized to form a propably Left-handed double strand d(A12) · d[(xT)12-T] (7·5) which was confirmed by melting experiments in combination with temperature-dependent CD spectroscopy. While 5 was hydrolyzed by snake-venom phosphodiesterase, it was resistant towards calf-spleen phosphodiesterase. The modified, self-complementary duplex 9 was hydrolyzed completely by snake-venom phosphodiesterase, at a twelvefold slower rate compared to unmodified 8; calf-spleen phosphodiesterase hydrolyzed 9 only partially.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/hlca.19910740408
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  • 6
    Electronic Resource
    Electronic Resource
    Xylose-DNA Containing the Four Natural Bases (1996)
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 79 (1996), S. 1451-1461 
    Details
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Oligonucleotides containing (2′-deoxy-β-D-xylofuranosyl)guanine have been prepared. For this purpose 2-aminoadenosine (5) was synthesized and converted to 2′-deoxy-β-D-xyloguanosine (1). The related 2′-deoxy-β-D-xyloisoguanosine (3) and 2′-deoxy-β-D-xyloxanthosine (4) were also synthesized. Compound 1 was converted to the phosphonate and phosphoramidite building blocks 10 and 11, respectively. The oligodeoxynucleotide (5′-3′)d(xG-xT-xA-xG-xA-xA-xT-xT-xC-xT-xA-xC-T) (18) formed a duplex with the same Tm as the parent (5′-3′)-(G-T-A-G-A-A-T-T-C-T-A-C) (19), but with an inverted CD spectrum.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/hlca.19960790518
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  • 7
    Electronic Resource
    Electronic Resource
    1-(2′-Deoxy-β-D-xylofuranosyl)cytosine: Base pairing of oligonucleotides with a configurationally altered sugar-phosphate backbone (1994)
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 77 (1994), S. 883-896 
    Details
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solid-phase synthesis of the oligo(2′-deoxynucleotides) 19 and 20 containing 2′-deoxy-β-D-xylocytidine (4) is described. For this purpose, 1-(2-deoxy-β-D-threo-pentofuranosyl)cytosine ( = 1-(2-deoxy-β-D-xylofuranosyl)-cytosine; 4) was protected at its 4-NH2 group with a benzoyl (→ 5) or an isobutyryl (→8) residue, and a dimethoxytrityl group was introduced at 5′-OH (→ 7, 10; Scheme 2). Compounds 7 and 10 were converted into the 3′-phosphonates 11a,b. While 19 could be hybridized with 21 and 22 under formation of duplexes with a two-nucleotide overhang on both termini (19 · 21: Tm 29°; 19 · 22: Tm 22°), the decamer 20 bearing four xCd residues could no longer be hybridized with one of the opposite strands. Moreover, the oligonucleotides d[(xC)8—C] (13), d[(xC)4—C] (14), d[C—(xC)4—C] (15), and d[C—(xC)3—C] (16) were synthesized. While 13 exhibits an almost inverted CD spectrum compared to d(C9) (17), the other oligonucleotides show CD spectra typical for regular right-handed single helices. At pH 5, d[(xC)8—C] forms a stable hemi-protonated duplex which exhibits a Tm of 60° (d[(CH+)9] · d(C9): Tm 36°). The thermodynamic parameters of duplex formation of (13H+ · 13) and (17H+ · 17) were calculated from their melting profiles and were found to be identical in ΔH but differ in ΔS (13H+ · 13: ΔS = -287 cal/K mol; 17H+ · 17: ΔS = -172 cal/K mol).
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/hlca.19940770402
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  • 8
    Electronic Resource
    Electronic Resource
    Synthesis of 3-Deaza-2′-deoxyadenosine and 3-Deaza-2′,3′-dideoxyadenosine: Glycosylation of the 4-Chloroimidazo[4,5-c]pyridinyl Anion (1990)
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 73 (1990), S. 1602-1611 
    Details
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The convergent syntheses of 3-deazapurine 2′-deoxy-β-D-ribonucleosides and 2′,3′-dideoxy-D-ribonucleosides, including 3-deaza-2′-deoxyadenosine (1a) and 3-deaza-2′,3′-dideoxyadenosine (1b) is described. The 4-chloro-lH-imidazo[4,5-c]pyridinyl anion derived from 5 was reacted with either 2′-deoxyhalogenose 6 or 2′,3′-dideoxyhalogenose 10 yielding two regioisomeric (N1 and N3) glycosylation products. They were deprotected and converted into 4-substituted imidazo[4,5-c]pyridine 2′-deoxy-β-D-ribonucleosides and 2′,3′-dideoxy-D-ribonucleosides. Compounds 1a and 1b proved to be more stable against proton-catalyzed N-glycosylic bond hydrolysis than the parent purine nucleosides and were not deaminated by adenosine deaminase.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/hlca.19900730605
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  • 9
    Electronic Resource
    Electronic Resource
    Nucleosides. Part L.Part IL: [1].. Structure of lumazine N1-(2′-deoxy-D-ribonucleosides) ( = 1-(2′-deoxy-D-ribofuranosyl)pteridine-2,4(1H,3H)-diones): A revision of the anomeric configuration (1992)
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 75 (1992), S. 1267-1273 
    Details
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The anomeric configuration of the glycosidic bond in lumazine N1-(2′-deoxy-D-ribonucleosides) 1-6 was investigated by NOE difference spectroscopy. The former configurational assignment of the α - and β -D-anomers 1 and 2, 3 and 4, and 5 and 6, respectively, has to be reversed to be in agreement with the physical data. Additional proof is presented by X-ray analysis of 3 and 6. Chemical interconversions of 1-(2′-deoxy-β-D-ribofuranosyl)-6,7-diphenyllumazine (6) into 2,3′ -anhydrolumazine 2′-deoxyribonucleosides 16 and 17 are also in agreement with the revised anomeric configuration.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/hlca.19920750427
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  • 10
    Electronic Resource
    Electronic Resource
    Synthesis of 4-Substituted 1H-Benzimidazole 2′-Deoxyribonucleosides and Utility of the 4-Nitro Compound as Universal Base (1996)
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 79 (1996), S. 488-498 
    Details
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The stereoselective synthesis of 4-substituted 1H-benzimidazole 2′-deoxyribonucleosides is described. Regioisomeric (N1 and N3) β-D-deoxyribonucleosides 2a-c and 3a-c were formed. 13C-NMR Chemical shifts of the 1H-benzimidazole 2′-deoxy-β-D-ribofuranosides were correlated with point charges of C-atoms as well as with Hammett constants of the exocyclic substituents. Phosphonate and phosphoramidite building blocks of 4-nitro-1H-benzimidazole 2′-deoxyribofuranoside (2a) were prepared (see 4a, b). Oligonucleotides of the d(A20) type were synthesized in which the two central dA bases were replaced by 4-nitro-1H-benzimidazole residues. They were hybridized with oligomeric dT and related oligomers having the other conventional bases opposite to the 4-nitro-1H-benzimidazole moieties. Within these duplexes (12·13, 12·14, 12·15, and 12·16), the destabilization was almost independent of the mismatch which is required for a universal base. The thermodynamic data indicate that the 4-nitro-1H-benzimidazole residues do not form H-bonds with opposite bases but are stabilizing the duplex by stacking interactions and favorable entropic changes.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/hlca.19960790216
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