Transient and Switchable (Triethylsilyl)ethynyl Protection of DNA against Cleavage by Restriction Endonucleases

Kielkowski, Pavel; Macíčková-Cahová, Hana; Pohl, Radek; Hocek, Michal

doi:10.1002/anie.201102898

Cited by 56 publications

(26 citation statements)

References 47 publications

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“…Although the phosphoramidites derived from nucleosides 1 , 2 , and 4 have been reported, the phosphoramidite of 7‐triisopropylsilylethynyl‐7‐deaza‐2′‐deoxyadenosine ( 9 a ) was still unknown; only its monophosphate has been described recently . To synthesize building block 9 a , Sonogashira cross‐coupling was performed on 7‐iodo‐7‐deaza‐dA ( 6 ) with (triisopropylsilyl)acetylene to afford nucleoside 3 (Scheme ).…”

Section: Resultsmentioning

confidence: 99%

Circular DNA by “Bis‐Click” Ligation: Template‐Independent Intramolecular Circularization of Oligonucleotides with Terminal Alkynyl Groups Utilizing Bifunctional Azides

Yang

Seela

2015

Chemistry A European J

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A highly effective and convenient "bis-click" strategy was developed for the template-independent circularization of single-stranded oligonucleotides by employing copper(I)-assisted azide-alkyne cycloaddition. Terminal triple bonds were incorporated at both ends of linear oligonucleotides. Alkynylated 7-deaza-2'-deoxyadenosine and 2'-deoxyuridine residues with different side chains were used in solid-phase synthesis with phosphoramidite chemistry. The bis-click ligation of linear 9- to 36-mer oligonucleotides with 1,4-bis(azidomethyl)benzene afforded circular DNA in a simple and selective way; azido modification of the oligonucleotide was not necessary. Short ethynyl side chains were compatible with the circularization of longer oligonucleotides, whereas octadiynyl residues were used for short 9-mers. Compared with linear duplexes, circular bis-click constructs exhibit a significantly increased duplex stability over their linear counterparts. The intramolecular bis-click ligation protocol is not limited to DNA, but may also be suitable for the construction of other macrocycles, such as circular RNAs, peptides, or polysaccharides.

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Section: Resultsmentioning

confidence: 99%

Circular DNA by “Bis‐Click” Ligation: Template‐Independent Intramolecular Circularization of Oligonucleotides with Terminal Alkynyl Groups Utilizing Bifunctional Azides

Yang

Seela

2015

Chemistry A European J

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“…They recognize four‐ to eight‐nucleotide (nt) palindromic sequences through specific interactions in the major groove and cleave them into fragments containing either cohesive or blunt ends. Little attention was paid to the influence of major‐groove modifications on this recognition and cleavage2 until we recently systematically studied 7‐modified 7‐deazaadenines3 and 5‐modified pyrimidines4 and found a surprising tolerance of many restriction endonucleases (REs) to modifications at A and U but not at C. The fact that bulky modifications prevent the cleavage whereas some smaller groups are tolerated was utilized for protection and for chemical5 and photochemical6 switching of the RE cleavage of DNA. The protection from cleavage was also used as a new strategy in gene cloning7 and for an efficiency study of competitive incorporation of modified versus unmodified nucleotides 8…”

Section: Introductionmentioning

confidence: 99%

Polymerase Synthesis of DNAs Bearing Vinyl Groups in the Major Groove and their Cleavage by Restriction Endonucleases

2014

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DNA molecules containing 5-vinyluracil, 5-vinylcytosine, or 7-deaza-7-vinyladenine were prepared by polymerase incorporation of the corresponding vinyl-modified 2'-deoxyribonucleoside triphosphates, and the influence of the vinyl group in the major groove of DNA on the cleavage by diverse type II restriction endonucleases (REs) was studied. The presence of 5-vinyluracil was tolerated by most of the REs, whereas only some REs were able to cleave sequences containing 7-deaza-7-vinyladenine. The enzyme ScaI was found to cleave DNA containing 5-vinylcytosine efficiently but not DNA containing the related 5-ethynylcytosine. All other REs failed to cleave sequences containing any cytosine modifications.

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“…Since previously we only reported [14,15] switcho no ft he cleavage through deprotection of DNA, this is the first example of the opposite process of switching off the cutting. Weo ptimized the CuAACr eaction conditions to minimize the DNA damage and non-specific complexation with copper.…”

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confidence: 62%

Turning Off Transcription with Bacterial RNA Polymerase through CuAAC Click Reactions of DNA Containing 5‐Ethynyluracil

Slavíčková

Janoušková

Šimonová

et al. 2018

Chemistry A European J

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Copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) click reaction in the major groove of DNA containing 5-ethynyluracil (U ) with azides was used for turning off sequence-specific protein-DNA interactions. The concept was first demonstrated on switching off cleavage of short modified DNA by restriction endonuclease BamHI-HF. Finally, DNA template containing U was used for in vitro transcription with E. coli RNA polymerase and the transcription was turned off by CuAAC with 3-azidopropane-1,2-diol or 3-azido-7-hydroxycoumarin.

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Transient and Switchable (Triethylsilyl)ethynyl Protection of DNA against Cleavage by Restriction Endonucleases

Cited by 56 publications

References 47 publications

Circular DNA by “Bis‐Click” Ligation: Template‐Independent Intramolecular Circularization of Oligonucleotides with Terminal Alkynyl Groups Utilizing Bifunctional Azides

Circular DNA by “Bis‐Click” Ligation: Template‐Independent Intramolecular Circularization of Oligonucleotides with Terminal Alkynyl Groups Utilizing Bifunctional Azides

Polymerase Synthesis of DNAs Bearing Vinyl Groups in the Major Groove and their Cleavage by Restriction Endonucleases

Turning Off Transcription with Bacterial RNA Polymerase through CuAAC Click Reactions of DNA Containing 5‐Ethynyluracil

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