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Gunji, Hiroki; Vasella, Andrea

doi:10.1002/1522-2675(20001108)83:11<2975::aid-hlca2975>3.3.co;2-u

HCA

2000

DOI: 10.1002/1522-2675(20001108)83:11<2975::aid-hlca2975>3.3.co;2-u

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Hiroki Gunji

Andrea Vasella

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Cited by 18 publications

(53 citation statements)

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“…68 ppm[7]) agree with this assignment. The presence of the 8-Br substituent leads to a stronger downfield shift similarly as observed for the iodide 3.…”

supporting

confidence: 83%

Oligonucleosides with a Nucleobase-Including Backbone, Part 3, Synthesis of Acetyleno-Linked Adenosine Dimers

Gunji

Vasella

2000

HCA

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The adenosine‐derived dimers 14a – d and 15b – d have been prepared by coupling the protected 8‐iodoadenosines 3 and 13 with the C(5′)‐ethynylated adenosine derivatives 5, 6, 11, and 12 (Scheme 4). Similarly, the 5′‐epimeric dimer 16 was prepared by coupling 3 with the alkyne 8 (Scheme 5). The propargylic alcohol 4 was transformed into the N‐benzoylated alkyne 5 and into the amine 6, while the epimeric alcohol 7 was converted to the epimeric amine 8 and the 5′‐deoxy analogues 11 and 12 (Scheme 3). Cross‐coupling of the iodoadenosine 13 with the alkyne 5 to 14a was optimised; it is influenced by the N‐benzoyl and the Et3SiO group of the alkyne, but hardly by the N‐benzoyl group of the 8‐iodoadenosine. The alkyne is most reactive when it is O‐silylated, but not N‐benzoylated. Cross‐coupling of the 5′‐deoxyalkynes proceeded more slowly. The dimers 14a – d, 15b – d, and 16 were obtained in good yields (Table 2). Deprotection of 14d and 16 led to 18 and 20, respectively (Scheme 5). The diols 17 and 19 and the hexols 18 and 20 prefer the syn‐conformation in (D6)DMSO, completely for unit II and ≥80% for unit I; they exhibit partially persistent intramolecular O(5′)−H⋅⋅⋅N(3) H‐bonds. The persistence increases from 18% (unit I of 19), 32% (unit II of 17 and 19), 45% (unit I of 17), 52% (unit II of 18 and 20), and 55% (unit I of 20) to 82% (unit I of 18).

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“…68 ppm[7]) agree with this assignment. The presence of the 8-Br substituent leads to a stronger downfield shift similarly as observed for the iodide 3.…”

supporting

confidence: 83%

Oligonucleosides with a Nucleobase-Including Backbone, Part 3, Synthesis of Acetyleno-Linked Adenosine Dimers

Gunji

Vasella

2000

HCA

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“…1 are investigated by molecular-dynamics (MD) simulations. MD Simulations of the 5'-d(CGTAAGCTCGATAG)-3'´5'-d(CTATC-GAGCTTACG)-3' duplex (1) and the 5'-d(CGTAAGCTCGATAG)-3'´5'-d(CTATC-GA*GCTTACG)-3' duplex (2) have been performed in aqueous solution at a doublestrand concentration of 8 mm, a NaCl concentration of 0.2m, an apparent pH value of 7, a temperature of 300 K, and a pressure of 1 atm. The trajectories of DNA configurations and energies are analyzed in terms of interaction energies, overall structure, population of Watson-Crick H-bonds, and atom-positional fluctuations.…”

mentioning

confidence: 99%

Oligonucleotide Analogues with a Nucleobase-Including Backbone, Part 7, Molecular Dynamics Simulation of a DNA Duplex Containing a 2′-Deoxyadenosine 8-(Hydroxymethyl)-Derived Nucleotide

Czechtizky¹,

Daura²,

Vasella³

et al. 2001

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The structure and stability of a 14-mer DNA duplex containing a nucleotide analog with a hydroxymethyl substituent at the C(8) of 2'-deoxyadenosine has been investigated by molecular-dynamics simulation. The DNA duplex studied has the sequence 5'-d(CGTAAGCTCGATAG)-3'´5'-d(CTATCGA*GCTTACG)-3', where the O(3') of the dG 6 nucleotide in the second strand is linked through a phosphinato group with the O(10) of the dA* 7 2'-deoxyadenosine-derived nucleotide. Previous experimental results showed that the stability of this duplex in aqueous solution of 0.1m NaCl at pH 7 and room temperature is significantly lower than that of the corresponding unmodified DNA duplex. Comparison of molecular-dynamics trajectories of the unmodified and modified B-DNA duplexes in aqueous solution, at similar conditions than the experiment, shows that the substitution of the dA nucleotide by the dA* nucleotide in the second strand induces stretching of the double helix, which results in opening of the grooves and consequent exposure of the double-helix core to the solvent.

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“…± We have conceived oligonucleotide analogues with a nucleobaseincluding backbone (Fig. 1, B); these compounds should allow us to answer the question of whether the structural differentiation between nucleobase and backbone in DNA, RNA, and their analogues 1 ) is a prerequisite for the formation of stable homoand/or heteroduplexes [6] [7].…”

mentioning

confidence: 99%

“…Similarly to DNA, they should be water-soluble. These analogues possess phosphinato groups between OÀC(3') and a oxymethyl substituent at C (8) or C(6) of neighbouring 2'-deoxyadenosyl or 2'-deoxyuridyl units, respectively. Fig.…”

mentioning

confidence: 99%

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Oligonucleotide Analogues with a Nucleobase-Including Backbone, Part 5, 2′-Deoxy-8-(hydroxymethyl)adenosine- and 2′-Deoxy-6-(hydroxymethyl)uridine-Derived Phosphoramidites: Synthesis and Incorporation into 14-Mer DNA Strands

Czechtizky

Vasella

2001

HCA

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The pairing propensity of new DNA analogues with a phosphinato group between OÀC(3') and a newly introduced OCH 2 group at C(8) and C(6) of 2'-deoxyadenosine and 2'-deoxyuridine, respectively, was evaluated by force-field calculations and Maruzen model studies. These studies suggest that these analogues may form autonomous pairing systems, and that the incorporation of single modified units into DNA 14mers is compatible with duplex formation. To evaluate the incorporation, we prepared the required phosphoramidites 3 and 4 from 2'-deoxyadenosine and 2'-deoxyuridine, respectively. The phosphoramidite 5 was similarly prepared to estimate the influence of a CH 2 OH group at C(8) on the duplex stability. The modified 14-mers 6 ± 9 were prepared by solid-phase synthesis. Pairing studies show a decrease of the melting temperature by 2.58 for the duplex 13´9, and of 6 ± 88 for the duplexes 10´6, 11´6, 13´7, and 14´8, as compared to the unmodified duplexes.

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Cited by 18 publications

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Oligonucleosides with a Nucleobase-Including Backbone, Part 3, Synthesis of Acetyleno-Linked Adenosine Dimers

Oligonucleosides with a Nucleobase-Including Backbone, Part 3, Synthesis of Acetyleno-Linked Adenosine Dimers

Oligonucleotide Analogues with a Nucleobase-Including Backbone, Part 7, Molecular Dynamics Simulation of a DNA Duplex Containing a 2′-Deoxyadenosine 8-(Hydroxymethyl)-Derived Nucleotide

Oligonucleotide Analogues with a Nucleobase-Including Backbone, Part 5, 2′-Deoxy-8-(hydroxymethyl)adenosine- and 2′-Deoxy-6-(hydroxymethyl)uridine-Derived Phosphoramidites: Synthesis and Incorporation into 14-Mer DNA Strands

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