Synthetic Strategies and Parameters Involved in the Synthesis of Oligodeoxyribonucleotides According to the Phosphoramidite Method

Beaucage, Serge L.; Caruthers, Marvin H.

doi:10.1002/0471142700.nc0303s00

Cited by 42 publications

(40 citation statements)

References 119 publications

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“…Homothymidinylated decamer 3 bearing a reactive primary amine group on the 5Ј-end was synthesised by standard phosphoramidite chemistry by using commercial 5Ј-amino-modifier C6. [14] The preparation of tetrahydro-5-hexaheliceneamine 4 (Scheme 1) started from tetrahydrohexahelicene 5, which is easily accessible by utilising [2+2+2] cycloisomerisation of the aromatic triyne. [15] By treatment of 5 with nitronium tetrafluoroborate, nitro derivative 6 was isolated as the major product in good yield.…”

Section: Resultsmentioning

confidence: 99%

Reaction of Isocyanate‐Functionalised Silicon Wafers with Complex Amino Compounds

et al. 2007

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Section: Resultsmentioning

confidence: 99%

Reaction of Isocyanate‐Functionalised Silicon Wafers with Complex Amino Compounds

et al. 2007

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“…Oligonucleotide Synthesis and Purification-Oligonucleotides were synthesized using standard phosphoramidite chemistry (29). All phosphoramidites, including the 5Ј-fluorescein phosphoramidite (6-(3Ј,6Ј-dipivaloylfluoresceinyl-6-carboxamido)-hexyl-1-O-(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidite), and the 3Ј-dabcyl CPG supports (1-dimethoxytrityloxy-3-[O-(N-4Ј-carboxy-4-(dimethylamino)-azobenzene)-3-aminopropyl)]-propyl-2-O-succinoyl-alkylamino-controlled pore glass) were purchased from Glen Research.…”

Section: Methodsmentioning

confidence: 99%

Mechanistic Studies of Hairpin to Duplex Conversion for Trinucleotide Repeat Sequences

Figueroa

Delaney

2010

Journal of Biological Chemistry

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The expansion of a trinucleotide repeat sequence, such as CAG/CTG, has been pinpointed as the molecular basis for a number of neurodegenerative disorders. It has been proposed that as part of the expansion process, these repetitive sequences adopt non-B conformations such as hairpins. However, the prevalence of these hairpins and their contributions to the DNA expansion have not been well defined. In this work, we utilized a molecular beacon strategy to examine the stability of the (CAG) 10 hairpin and also its behavior in the presence of the complementary (CTG) 10 hairpin. We find that the two hairpins represent kinetically trapped species that can coexist but irreversibly convert to duplex upon thermal induction. Furthermore, as monitored by fluorescence and optical analysis, modifications to the base composition of either the loop or stem region have a profound effect on the ability of the trinucleotide repeat hairpins to convert to duplex. Additionally, the rate of duplex formation is also reduced with these loop and stem-modified hairpins. These results demonstrate that the trinucleotide repeat hairpins can convert to duplex via two independent mechanisms as follows: the loop-loop interactions found in kissing hairpins or the stem-stem interactions of a cruciform.

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“…Oligonucleotides were synthesized on an Applied Biosystems Model 381A (ABI, Foster City, CA) DNA synthesizer using protocols and reagents for standard phosphoramidite chemistry [25]. A solution of 3H -1,2-benzodithiol-3-one 0.05 M in acetonitrile was used as an oxidizer for the formation of thionophosphotriester internucleoside linkages [26].…”

Section: Methodsmentioning

confidence: 99%

Characterization of specific noncovalent complexes between guanidinium derivatives and single-stranded DNA by MALDI

Ohara

Smietana

Vasseur

2006

J. Am. Soc. Mass Spectrom.

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Noncovalently bound complexes between highly basic sites of 12 guanidinium compounds and single-stranded DNA were studied using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. 6-Aza-2-thiothymine (ATT) was used as the matrix in the presence of ammonium citrate, and spectra were recorded in the positive ion mode. Detailed control experiments confirmed unambiguously the high selectivity and specificity of the guanidinium moiety for phosphate groups of DNA. The results verify the binding stoichiometry and show preferential binding of hydrophobic binders (pyrene and anthracene guanidinium derivatives) to all sequences examined. In addition, we demonstrate that electrostatic noncovalent interactions are strengthened with phosphorothioate analogs of DNA. These results clearly highlight the structure-directing role of the self-assembling organic species and strongly emphasize the significance of concentration, hydrophobicity, hydrogen-bonding, and pi-pi interactions of the artificial receptor in the formation of these noncovalent complexes. Because of the ability of DNA-binding compounds to influence gene expression, and therefore cell proliferation and differentiation, the interactions described above could be important in providing a better understanding of the mechanism of action of these noncovalent genetic regulators.

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Synthetic Strategies and Parameters Involved in the Synthesis of Oligodeoxyribonucleotides According to the Phosphoramidite Method

Cited by 42 publications

References 119 publications

Reaction of Isocyanate‐Functionalised Silicon Wafers with Complex Amino Compounds

Reaction of Isocyanate‐Functionalised Silicon Wafers with Complex Amino Compounds

Mechanistic Studies of Hairpin to Duplex Conversion for Trinucleotide Repeat Sequences

Characterization of specific noncovalent complexes between guanidinium derivatives and single-stranded DNA by MALDI

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