Covalent cross-linking of duplex DNA using 4-thio-2'-deoxyuridine as a readily modifiable platform for introduction of reactive functionality into oligonucleotides

Coleman, Robert S.; Pires, Richard M.

doi:10.1093/nar/25.23.4771

Cited by 34 publications

(25 citation statements)

References 34 publications

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“…30−39 Stringent hybridization conditions are unavailable in vivo, but selective reactivity of the cross-linker (e.g., reactivity only with pyrimidines) can be used to augment the poor hybridization selectivity of unstructured probes. 31,34,36,40 This approach applies only to mismatches located at the cross-linker’s target base and is susceptible to inadvertent covalent cross-linking of off-targets that hybridize transiently to a portion of the probe. Given the potential harm resulting from covalent capture of off-targets, the poor selectivity of unstructured probes is a major drawback for these efforts.…”

Section: Introductionmentioning

confidence: 99%

Selective Nucleic Acid Capture with Shielded Covalent Probes

et al. 2013

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Nucleic acid probes are used for diverse applications in vitro, in situ, and in vivo. In any setting, their power is limited by imperfect selectivity (binding of undesired targets) and incomplete affinity (binding is reversible, and not all desired targets bound). These difficulties are fundamental, stemming from reliance on base pairing to provide both selectivity and affinity. Shielded covalent (SC) probes eliminate the longstanding trade-off between selectivity and durable target capture, achieving selectivity via programmable base pairing and molecular conformation change, and durable target capture via activatable covalent cross-linking. In pure and mixed samples, SC probes covalently capture complementary DNA or RNA oligo targets and reject two-nucleotide mismatched targets with near-quantitative yields at room temperature, achieving discrimination ratios of 2–3 orders of magnitude. Semiquantitative studies with full-length mRNA targets demonstrate selective covalent capture comparable to that for RNA oligo targets. Single-nucleotide DNA or RNA mismatches, including nearly isoenergetic RNA wobble pairs, can be efficiently rejected with discrimination ratios of 1–2 orders of magnitude. Covalent capture yields appear consistent with the thermodynamics of probe/target hybridization, facilitating rational probe design. If desired, cross-links can be reversed to release the target after capture. In contrast to existing probe chemistries, SC probes achieve the high sequence selectivity of a structured probe, yet durably retain their targets even under denaturing conditions. This previously incompatible combination of properties suggests diverse applications based on selective and stable binding of nucleic acid targets under conditions where base-pairing is disrupted (e.g., by stringent washes in vitro or in situ, or by enzymes in vivo).

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Section: Introductionmentioning

confidence: 99%

Selective Nucleic Acid Capture with Shielded Covalent Probes

et al. 2013

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“…38 Coleman and Pires reported an effective molarity 3.1 M for alkylation of a guanine residue by a bromoacetamide unit connected by a five-atom linker to a 4-thiouridine residue on the opposing strand of a DNA duplex. 39 Beyond these two studies, there is little information addressing the important question: how large should we expect the kinetic and thermodynamic “payoffs” to be, when two reactive species are positioned within the structure of duplex DNA? Given that an assumption of increased effective molarity underlies the design of all nucleic acid-templated reactions it may be useful to gain additional quantitative information that speaks to this question.…”

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confidence: 99%

Effective molarity in a nucleic acid-controlled reaction

Catalano

Price

Gates

2016

Bioorganic & Medicinal Chemistry Letters

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Positioning of reactive functional groups within a DNA duplex can enable chemical reactions that otherwise would not occur to an appreciable extent. However, few studies have quantitatively defined the extent to which the enforced proximity of reaction partners in duplex DNA can favor chemical processes. Here, we measured substantial effective molarities (as high as 25 M) afforded by duplex DNA to a reaction involving interstrand cross-link formation between 2′-deoxyadenosine and a 2-deoxyribose abasic (Ap) site.

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“…[1][2][3][4][5][6][7] Their photo-induced crosslinking ability has been used to study the three-dimensional interaction of RNA-RNA or RNA-proteins at the atomic level. [1][2][3][4] The high nucleophilicity of the sulfur atom of 6-thioguanosine was used as a modification site of oligode-oxynucleotides (ODN).…”

Section: Introductionmentioning

confidence: 99%

“…[1][2][3][4] The high nucleophilicity of the sulfur atom of 6-thioguanosine was used as a modification site of oligode-oxynucleotides (ODN). [5][6][7] Recently, we developed the functionality-transfer reaction for the site-specific modification of DNA and RNA by utilizing the ODN containing 2 -deoxy-6-thioguanosine. The site-specific NO modification of the target cytosine was demonstrated by the NO transfer reaction from S-nitroso-6-thioguanosine in the ODN.…”

Section: Introductionmentioning

confidence: 99%

A New Odorless Procedure for the Synthesis of 2′-Deoxy-6-Thioguanosine and Its Incorporation into Oligodeoxynucleotides

Onizuka

Taniguchi

Sasaki

2009

Nucleosides, Nucleotides and Nucleic Acids

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6-S-[2-[(2-ethylhexyl)oxycarbonyl]ethyl)}-3',5'-O-bis(tert-butyldimethylsilyl)-2'-deoxy-6-thiogua nosine (2) was synthesized in high yield from the corresponding 6-O-mesitylenesulfonyl derivative by the reaction with 2-ethylhexyl 3-mercapto-propionate. The phosphoramidite precursor derived from 2 was successfully applied to an automated DNA synthesizer to produce 2'-deoxy-6-thioguanosine containing ODN. The results showed that 2-ethylhexyl 3-mercaptopropionate is useful as an odor less reagent and also as an S-protecting group of 2'-deoxy-6-thioguanosine.

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Covalent cross-linking of duplex DNA using 4-thio-2'-deoxyuridine as a readily modifiable platform for introduction of reactive functionality into oligonucleotides

Cited by 34 publications

References 34 publications

Selective Nucleic Acid Capture with Shielded Covalent Probes

Selective Nucleic Acid Capture with Shielded Covalent Probes

Effective molarity in a nucleic acid-controlled reaction

A New Odorless Procedure for the Synthesis of 2′-Deoxy-6-Thioguanosine and Its Incorporation into Oligodeoxynucleotides

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