Synthesis Of Deoxyoligonucleotides Research Articles

The Degradation of dG Phosphoramidites in Solution

The reaction of 2′-deoxynucleoside phosphoramidites with water is an important degradation reaction that limits the lifetimes of reagents used for chemical deoxyoligonucleotide synthesis. The hydrolysis of nucleoside phosphoramidites in solution has therefore been investigated. The degree of degradation depends not only on the presence of water but also on the specific nucleoside, 2′-deoxyguanosine (dG) being especially susceptible. Additionally, the nature of the group protecting the exocyclic amine on the nucleoside base strongly influences the rate of hydrolysis. For dG, the degradation is second order in phosphoramidite concentration, indicating autocatalysis of the hydrolysis reaction. Comparison of the degradation rates of dG phosphoramidites with different protecting groups as well as with phosphoramidites containing bases that are structurally similar to dG affords clues to the nature of how dG catalyzes its own destruction and indicates a direct correlation between ease of protecting group removal and propensity to undergo autocatalytic degradation.

Silver Nanoassemblies Constructed from Boranephosphonate DNA

Spatially selective deposition of metal onto complex DNA assemblies is a promising approach for the preparation of metallic nanostructures with features that are smaller than what can be produced by top-down lithographic techniques. We have recently reported the ability of 2'-deoxyoligonucleotides containing boranephosphonate linkages (bpDNA) to reduce AuCl4(-), Ag(+), and PtCl4(2-) ions to the corresponding nanoparticles. Here we demonstrate incorporation of bpDNA oligomers into a two-dimensional DNA array comprised of tiles containing double crossover junctions. We further demonstrate the site-specific deposition of metallic silver onto this DNA structure which generates well-defined and preprogrammed arrays of silver nanoparticles. With this approach the size of the metallic features that can be produced is limited only by the underlying DNA template. These advances were enabled due to a new method for synthesizing bpDNA that uses a silyl protecting group on the DNA nucleobases during the solid-phase 2'-deoxyoligonucleotide synthesis.

ChemInform Abstract: Chemical Synthesis of Deoxyoligonucleotides and Deoxyoligonucleotide Analogs

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

1] Chemical synthesis of deoxyoligonucleotides and deoxyoligonucleotide analogs

Publisher Summary This chapter discusses advances in chemical methodologies, which include the development of new protecting group strategies and procedures for the attachment of reporter groups to DNA. Because of these achievements, the time required to synthesize DNA has been reduced, and an even larger repertoire of applications for synthetic deoxyoligonucleotides has been achieved. An attempt is made to review some of these many excellent contributions, but only one detailed protocol for labeling DNA is included. This is a relatively recent, unpublished procedure for attaching reporter groups to a new DNA analog called “dithioate DNA.” Deoxyoligonucleotides having a deoxynucleoside–OPS 2 O–deoxynucleoside linkage, dithioate DNA, are excellent mimics of natural DNA. At least partially, this is because they are isosteric and isoelectronic with normal DNA. They are, however, completely resistant to snake venom, calf spleen, P 1 exonucleases, all the nucleases found in HeLa nuclear and cytoplasmic extracts, and even the very potent exonucleolytic activity of T 4 DNA polymerase. These attractive features combined with the ability of dithioate DNA to form stable DNA duplexes have led to several potential applications.

Synthesis and structure assignments of amide protected nucleosides and their use as phosphoramidites in deoxyoligonucleotide synthesis.

The syntheses of several amide protected deoxyguanosine- as well as thymidine nucleosides are described. These compounds were synthesized according to the Mitsunobu reaction and Michael addition. In contradiction to previous studies we have discovered that the Michael addition gives only products derived from N-alkylation. The occurrence of N- or O-alkylation was assigned by means of two dimensional 1H, 1 3 C-COLOC-NMR spectroscopy. Further, we have found that the Mitsunobu reaction used for the protection of the amide function of dG is limited to alcohols without acidic hydrogen atoms. Amide protected phosphormidites (15, 16) were used for the preparation of deoxyoligonucleotides with a large number of guanine and thymine bases using two different coupling times. We have shown that there is no experimentally detectable difference in the quality of the products if the starting monomer is amide protected or not.

Polymer Supported Synthesis of Deoxyoligonucleotides using In Situ Prepared Deoxynucleoside 2-Cyanoethyl Phosphoramidites

Abstract 2-Cyanoethyl bis(diisopropylamino) phosphorodiamidite (1) is a stable and easily obtainable compound1 which, when activated with 0.5 eq. tetrazole, gives solutions of deoxyribonucleoside 2-cyano-ethyl phosphoramidites (2) useful for the synthesis of deoxyoligo-nucleotides. 2 Our results applying these in-situ prepared phosphoramidites for polymer-supported syntheses of a variety of deoxyoligonucleotides (DNA fragments) will be presented.

The Use of Nucleoside H-Phosphonates in the Synthesis of Deoxyoligonucleotides

Abstract Nucleoside H-phosphonates are valuable intermediates in the synthesis of deoxyoligonucleotides. The DBU salt form is more stable in solution and is consequently an improvement in routine synthesis of DNA.

15] Chemical synthesis of deoxyoligonucleotides by the phosphoramidite method

Publisher Summary This chapter discusses the chemical synthesis of deoxy oligonucleotides by the phosphoramidite method. It discusses the synthesis methodology; detailed protocols for preparing the silica support, the phosphoramidite, and deoxy oligonucleotides; and the purification of synthetic deoxyribo nucleic acid (DNA). The phosphite triester approach to DNA synthesis using deoxynucleoside phosphoramidite as synthons has become the method of choice for the preparation of deoxy oligonucleotides. The general synthetic strategy involves adding mononucleotides sequentially to a deoxynucleoside, attached covalently to a silica-based insoluble polymeric support. Reagents, starting materials, and side products are then removed simply by filtration. At the conclusion of the synthesis, the deoxy oligonucleotide is chemically freed of blocking groups, hydrolyzed from the support, and purified to homogeneity by either polyacrylamide gel electrophoresis (PAGE) or high-performance liquid chromatography (HPLC). These preformed synthons are especially attractive for preparing DNA on automatic or semiautomatic DNA synthesizers, or for those who plan to manually synthesize a large number of deoxy oligonucleotides.

ChemInform Abstract: Phosphorothioite Method. Part 1. A New Type of Internucleotidic Bond Formations Involving Simultaneous Oxidation Process by Use of Deoxyoligonucleoside Phosphorothioites as New Key Intermediates for Deoxyoligonucleotide Synthesis.

AbstractThe phosphorothioites (III) are synthesized by reaction of the thymidine (I) and the reagent (II).

ChemInform Abstract: Nucleoside H‐Phosphonates: Valuable Intermediates in the Synthesis of Deoxyoligonucleotides.

AbstractDie Kondensation zwischen (I) und (II) liefert in Gegenwart von Pivaloylchlorid (III) das Nucleosid‐H‐phosphonat (IV), das mit Iod zum Phosphat (V) oxidiert wird.

Phosphorothioite method. 1. A new type of internucleotidic bond formation involving simultaneous oxidation process by use of deoxyoligonucleoside phosphorothioites as new key intermediates for deoxyoligonucleotide synthesis

Phosphorothioite method. 1. A new type of internucleotidic bond formation involving simultaneous oxidation process by use of deoxyoligonucleoside phosphorothioites as new key intermediates for deoxyoligonucleotide synthesis

ChemInform Abstract: Polymer‐supported Synthesis of Deoxyoligonucleotides Using in situ Prepared Deoxynucleoside 2‐Cyanoethyl Phosphoramidites.

AbstractBy 1H‐tetrazole catalysed in situ phosphitylation of the nucleoside (I) with the (easily obtained) reagent (II) the dnucleoside‐3′‐phosphoramidites (III) are obtained.

Nucleoside h-phosphonates: Valuable intermediates in the synthesis of deoxyoligonucleotides

Nucleoside H-Phosphonates are used directly in the synthesis of H-phosphonate linked deoxyoligonucleotides. A rapid and simplified procedure for the synthesis of deoxyoligonucleotides is described.

Synthesis of DNA via deoxynucleoside H-phosphonate intermediates.

Deoxynucleoside H-phosphonates are used in the chemical synthesis of deoxyoligonucleotides up to 107 bases in length. The biological activity of the synthetic DNA is assessed by cloning into M13 and sequencing. An improved synthesis of protected deoxynucleoside H-phosphonates is also described.

L-Methyl-Z-(2′-Hydroxyphenyl)Imidazole–A Catalytic Phosphate protecting group in deoxyoligonucleotide synthesis

Abstract The rate of condensation using the phosphate triester method of deoxyoligonucleotide synthesis is dramatically increased by the introduction of a phosphate protecting group bearing a nuclcophilic catalyst in the proper position. Following condensation (resulting in the formation of a phosphate triester) the catalytic protecting group can be removed leaving a dinucleotide, or the condensation reaction can be repeated to synthesize an oligonucleotide. This development is a significant advance in the chemical synthesis of deoxyoligonucleotides.

1-Methyl-2-(2-hydroxyphenyl)imidazole: a catalytic phosphate protecting group in deoxyoligonucleotide synthesis

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT1-Methyl-2-(2-hydroxyphenyl)imidazole: a catalytic phosphate protecting group in deoxyoligonucleotide synthesisBrian C. Froehler and Mark D. MatteucciCite this: J. Am. Chem. Soc. 1985, 107, 1, 278–279Publication Date (Print):January 1, 1985Publication History Published online1 May 2002Published inissue 1 January 1985https://doi.org/10.1021/ja00287a065RIGHTS & PERMISSIONSArticle Views144Altmetric-Citations17LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (284 KB) Get e-Alerts Get e-Alerts

In situ activation of bis-dialkylaminophosphines--a new method for synthesizing deoxyoligonucleotides on polymer supports.

Deoxynucleoside phosphoramidites can be prepared in good yield from deoxynucleosides, bis- dialkylaminophosphines , and the corresponding dialkylamine hydrotetrazolide or tetrazole as catalysts. These phosphoramidites generated in situ lead to the direct synthesis of deoxyoligonucleotides on polymer supports.

Color coded triarylmethyl protecting groups useful for deoxypolynucleotide synthesis.

Triarylmethyl groups having different colors but similar chemical reactivities in acid were examined as potential aids for monitoring the stepwise addition of mononucleotides to a deoxyoligonucleotide. The successful application of these protecting groups to deoxyoligonucleotide synthesis on polymer supports was demonstrated.

ChemInform Abstract: NEW METHODS FOR SYNTHESIZING DEOXYOLIGONUCLEOTIDES

Deoxynucleoside phosphoramidites are prepared in good yield from doexynucleosides, bis-dialkylamino-phosphines, with the corresponding dialkylamine hydrotetrazolide or tetrazole as catalyst for the reaction. These phosphoramidites generated in situ lead to the direct synthesis of deoxyoligonucleotides on polymer supports.

Dialkylformamidines: depurination resistant N6-protecting group for deoxyadenosine.

Sterically hindered N6-dialkylformamidine protected deoxyadenosine is more stable to acidic depurination than N6-benzoyldeoxyadenosine and is potentially a valuable protecting group in the synthesis of deoxyoligonucleotides.