A convenient synthesis of 5′-amino-5′-deoxythymidine and preparation of peptide-DNA hybrids

Tetzlaff, Charles N.; Schwope, Ina; Bleczinski, Colleen F.; Steinberg, Joshua; Richert, Clemens

doi:10.1016/s0040-4039(98)00788-6

Cited by 59 publications

(92 citation statements)

References 17 publications

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“…similar for all three test compounds, demonstrating that at the intermediate salt concentration our MALDI-based assay provides results comparable to those of the traditional single compound assay. This was also true for an exploratory experiment involving a peptide-DNA hybrid 17 (data not shown). A control experiment with 1 mM cholic acid in the incubation medium gave much stronger signal for the cholic acid-DNA hybrid 3 at 70°C (Fig.…”

Section: Resultsmentioning

confidence: 53%

“…Terminally modified oligonucleotide 3 was prepared by coupling cholic acid to 5'-amino terminal DNA on controlled pore glass (cpg) and deprotecting with ammonium hydroxide containing cresol as described previously for amino acid-DNA hybrids. 17 Oligonucleotides were purified by RP-18 HPLC using a gradient of CH 3 18 of the original procedure. 19 According to trityl release from the last extension step of the synthesis, the loading of DNA strands was 45 nmoles per mg solid.…”

Section: Experimental Chemicalsmentioning

confidence: 99%

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Monitoring the hybridization of the components of oligonucleotide mixtures to immobilized DNA via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Bleczinski

Richert

1998

Rapid Commun. Mass Spectrom.

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Reported here is how the hybridization of individual components of oligonucleotide mixtures to solid-phase bound complementary strands can be monitored simultaneously by quantitative matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). Three oligonucleotides, a DNA heptamer, a DNA octamer and a DNA octamer with a terminal cholic acid appendage were used as the test mixture. Upon cooling in the presence of a complementary undecamer on controlled pore glass, depletion of the components from the solution was observed. The resulting hybridization curves show the same relative affinities as traditional UV melting curves with single components and their complement. Assays of the kind described here may be used to select high affinity binders from combinatorial libraries of modified antisense oligonucleotides.

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Section: Resultsmentioning

confidence: 53%

Section: Experimental Chemicalsmentioning

confidence: 99%

Monitoring the hybridization of the components of oligonucleotide mixtures to immobilized DNA via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Bleczinski

Richert

1998

Rapid Commun. Mass Spectrom.

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“…A sarcosine residue was introduced between the succinyl linker and the internal reference amino acid to make the nucleosideϪresin linkage sufficiently stable to the basic conditions required to remove the Fmoc group. [7,22] The synthesis proceeded smoothly up until the incorporation of the linker, but problems were encountered beyond removal of the monomethoxytrityl group. We had great difficulties in coupling Fmoc-methionine to the H 2 Nlinker-nucleotide-resin, and blocking of the N-terminus with Phac 2 O once the Fmoc group had been eliminated was not straightforward either (see below).…”

Section: Resultsmentioning

confidence: 99%

Alternative Procedures for the Synthesis of Methionine-Containing Peptide−Oligonucleotide Hybrids

et al. 2000

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The synthesis of methionine-containing peptide−oligonucleotide hybrids has been found to be best accomplished by a stepwise solid-phase approach in which peptide assembly using the sulfoxide derivative of methionine is followed by elongation of the oligonucleotide chain using the phosphite triester methodology, ammonia deprotection, and reduction of the sulfoxide to thioether by reaction with N-

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“…Phosphoramidites (dA Bz , dC Bz , T, dG dmf ) and reagents for DNA synthesis were from Proligo (Hamburg, Germany), except for dG dmfloaded controlled pore glass (cpg), which was from ABI (Warrington, UK). Phosphoramidites of modified nucleosides or caps used in this work, namely phosphoramidites of 5'-amino-2',5'-dideoxynucleosides (N*), [9,[37][38][39][40] stilbene phosphoramidites [20] and pyrenemetylpyrrolidonol phosphoramidite [9] were prepared as previously reported. The 5'-acylamidooligonucleotides (2 a, c, t; 3 a, c, t), phosphoramidates (11 a-t), primer (9) and 2-methylimidazolides (10 a-t) were prepared as described previously.…”

Section: Methodsmentioning

confidence: 99%

Tuning the Reaction Site for Enzyme‐Free Primer‐Extension Reactions through Small Molecule Substituents

Stütz

Richert

2006

Chemistry A European J

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The replication of genetic information relies on the template-directed extension of DNA primers catalyzed by polymerases. The active sites of polymerases accept four different substrates and ensure fidelity and processivity for each of them. Because of the pivotal role of catalyzed primer extension for life, it is important to better understand this reaction on a molecular level. Here we present results from primer-extension reactions performed with chemical systems that show high reactivity in the absence of polymerases. Small molecular caps linked to the 5'-terminus of templates are shown to enhance the rate and selectivity of primer extension driven by 2-methylimidazolides as activated monomers for any of the four different templating bases (A, C, G, and T). The most consistent effect is provided by a stilbene carboxamide residue, rather than larger aromatic or aliphatic substituents. Up to 20-fold rate enhancements were achieved for the reactions at the terminus of the template. The preference for a medium size cap can be explained by competing interactions with both the oligonucleotides and the incoming deoxynucleotide. The data also show that there is no particularly intractable problem in combining promiscuity with fidelity. Exploratory experiments involving a longer template and a downstream-binding strand with a 5'-cap show up to 38-fold rate acceleration over the same reaction templated by a single overhanging nucleotide.

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A convenient synthesis of 5′-amino-5′-deoxythymidine and preparation of peptide-DNA hybrids

Cited by 59 publications

References 17 publications

Monitoring the hybridization of the components of oligonucleotide mixtures to immobilized DNA via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Monitoring the hybridization of the components of oligonucleotide mixtures to immobilized DNA via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Alternative Procedures for the Synthesis of Methionine-Containing Peptide−Oligonucleotide Hybrids

Tuning the Reaction Site for Enzyme‐Free Primer‐Extension Reactions through Small Molecule Substituents

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