Nucleotides: Part LXXVIII : Double Labeling of Nucleosides and Nucleotides

Maier, Thomas; Pfleiderer, Wolfgang

Nucleotides: Part LXXVIII : Double Labeling of Nucleosides and Nucleotides

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Datum

2010

Autor:innen

Maier, Thomas

Pfleiderer, Wolfgang

DOI (zitierfähiger Link)

https://doi.org/10.1002/hlca.201000253

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Chemie

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Helvetica Chimica Acta. Verlag Helvetica Chimica Acta, Wiley. 2010, 93(12), pp. 2365-2392. ISSN 0018-019X. eISSN 1522-2675. Available under: doi: 10.1002/hlca.201000253

Zusammenfassung

Several N(‐hydroxyalkyl)‐2,4‐dinitroanilines were transformed into their phosphoramidites (see 5 and 6 in Scheme 1) in view of their use as fluorescence quenchers, and modified 2‐aminobenzamides (see 9, 10, 18, and 19 in Scheme 1) were applied in model reactions as fluorophors to determine the relative fluorescence quantum yields of the 3′‐Aba and 5′‐Dnp‐3′‐Aba conjugates (Aba=aminobenzamide, Dnp=dinitroaniline). Thymidine was alkylated with N‐(2‐chloroethyl)‐2,4‐dinitroaniline (24) to give 25 which was further modified to the building blocks 27 and 28 (Scheme 3). The 2‐amino group in 29 was transformed by diazotation into the 2‐fluoroinosine derivative 30 used as starting material for several reactions at the pyrimidine nucleus (→31, 33, and 35; Scheme 4). The 3′,5′‐di‐O‐acetyl‐2′‐deoxy‐N²‐[(dimethylamino)methylene]guanosine (37) was alkylated with methyl and ethyl iodide preferentially at N(1) to 43 and 44, and similarly reacted N‐(2‐chloroethyl)‐2,4‐dinitroaniline (24) to 38 and the N‐(2‐iodoethyl)‐N‐methyl analog 50 to 53 (Scheme 5). The 2′‐deoxyguanosine derivative 53 was transformed into 3′,5′‐di‐O‐acetyl‐2‐fluoro‐1‐{2‐[(2,4‐dinitrophenyl)methylamino]ethyl}inosine (54; Scheme 5) which reacted with 2,2′‐[ethane‐1,2‐diylbis(oxy)]bis[ethanamine] to modify the 2‐position with an amino spacer resulting in 56 (Scheme 6). Attachment of the fluorescein moiety 55 at 56 via a urea linkage led to the doubly labeled 2′‐deoxyguanosine derivative 57 (Scheme 6). Dimethoxytritylation to 58 and further reaction to the 3′‐succinate 59 and 3′‐phosphoramidite 60 afforded the common building blocks for the oligonucleotide synthesis (Scheme 6). Similarly, 30 reacted with N‐(2‐aminoethyl)‐2,4‐dinitroaniline (61) thus attaching the quencher at the 2‐position to yield 62 (Scheme 7). The amino spacer was again attached at the same site via a urea bridge to form 64. The labeling of 64 with the fluorescein derivative 55 was straigthforward giving 65. and dimethoxytritylation to 66 and further phosphitylation to 67 followed known procedures (Scheme 7). Several oligo‐2′‐deoxynucleotides containing the doubly labeled 2′‐deoxyguanosines at various positions of the chain were formed in a DNA synthesizer, and their fluorescence properties and the T_ms in comparison to their parent duplexes were measured (Tables 1–5).

Fachgebiet (DDC)

540 Chemie

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ISO 690

MAIER, Thomas, Wolfgang PFLEIDERER, 2010. Nucleotides: Part LXXVIII : Double Labeling of Nucleosides and Nucleotides. In: Helvetica Chimica Acta. Verlag Helvetica Chimica Acta, Wiley. 2010, 93(12), pp. 2365-2392. ISSN 0018-019X. eISSN 1522-2675. Available under: doi: 10.1002/hlca.201000253

BibTex

@article{Maier2010-12-15Nucle-51883,
  year={2010},
  doi={10.1002/hlca.201000253},
  title={Nucleotides: Part LXXVIII : Double Labeling of Nucleosides and Nucleotides},
  number={12},
  volume={93},
  issn={0018-019X},
  journal={Helvetica Chimica Acta},
  pages={2365--2392},
  author={Maier, Thomas and Pfleiderer, Wolfgang}
}

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    <dcterms:abstract xml:lang="eng">Several N(‐hydroxyalkyl)‐2,4‐dinitroanilines were transformed into their phosphoramidites (see 5 and 6 in Scheme 1) in view of their use as fluorescence quenchers, and modified 2‐aminobenzamides (see 9, 10, 18, and 19 in Scheme 1) were applied in model reactions as fluorophors to determine the relative fluorescence quantum yields of the 3′‐Aba and 5′‐Dnp‐3′‐Aba conjugates (Aba=aminobenzamide, Dnp=dinitroaniline). Thymidine was alkylated with N‐(2‐chloroethyl)‐2,4‐dinitroaniline (24) to give 25 which was further modified to the building blocks 27 and 28 (Scheme 3). The 2‐amino group in 29 was transformed by diazotation into the 2‐fluoroinosine derivative 30 used as starting material for several reactions at the pyrimidine nucleus (→31, 33, and 35; Scheme 4). The 3′,5′‐di‐O‐acetyl‐2′‐deoxy‐N&lt;sup&gt;2&lt;/sup&gt;‐[(dimethylamino)methylene]guanosine (37) was alkylated with methyl and ethyl iodide preferentially at N(1) to 43 and 44, and similarly reacted N‐(2‐chloroethyl)‐2,4‐dinitroaniline (24) to 38 and the N‐(2‐iodoethyl)‐N‐methyl analog 50 to 53 (Scheme 5). The 2′‐deoxyguanosine derivative 53 was transformed into 3′,5′‐di‐O‐acetyl‐2‐fluoro‐1‐{2‐[(2,4‐dinitrophenyl)methylamino]ethyl}inosine (54; Scheme 5) which reacted with 2,2′‐[ethane‐1,2‐diylbis(oxy)]bis[ethanamine] to modify the 2‐position with an amino spacer resulting in 56 (Scheme 6). Attachment of the fluorescein moiety 55 at 56 via a urea linkage led to the doubly labeled 2′‐deoxyguanosine derivative 57 (Scheme 6). Dimethoxytritylation to 58 and further reaction to the 3′‐succinate 59 and 3′‐phosphoramidite 60 afforded the common building blocks for the oligonucleotide synthesis (Scheme 6). Similarly, 30 reacted with N‐(2‐aminoethyl)‐2,4‐dinitroaniline (61) thus attaching the quencher at the 2‐position to yield 62 (Scheme 7). The amino spacer was again attached at the same site via a urea bridge to form 64. The labeling of 64 with the fluorescein derivative 55 was straigthforward giving 65. and dimethoxytritylation to 66 and further phosphitylation to 67 followed known procedures (Scheme 7). Several oligo‐2′‐deoxynucleotides containing the doubly labeled 2′‐deoxyguanosines at various positions of the chain were formed in a DNA synthesizer, and their fluorescence properties and the T&lt;sub&gt;m&lt;/sub&gt;s in comparison to their parent duplexes were measured (Tables 1–5).</dcterms:abstract>
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