Template-Directed Oligonucleotide Strand Ligation, Covalent Intramolecular DNA Circularization and Catenation Using Click Chemistry

Kumar, Ravindra; El‐Sagheer, Afaf H.; Tumpane, John; Lincoln, Per; Wilhelmsson, L. Marcus; Brown, Tom

doi:10.1021/ja070273v

Cited by 257 publications

(245 citation statements)

References 21 publications

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“…68 Oxime circularization was also used for circularization of RNA, although only small circles (tetramers) were prepared. 69 Other circularization procedures involve copper catalyzed azide alkyne cycloaddition (CuAAC) 70,71 (Fig. 1f), strategies for photoligation, 72 or conjugation of metal binding ligands such as terpyridine to the 5 0 -and 3 0 -end of the oligonucleotide to be circularized (Fig.…”

Section: Chemical Strategiesmentioning

confidence: 99%

In vitro circularization of RNA

Müller

Appel

2016

RNA Biology

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Over the past 2 decades, different types of circular RNAs have been discovered in all kingdoms of life, and apparently, those circular species are more abundant than previously thought. Apart from circRNAs in viroids and viruses, circular transcripts have been discovered in rodents more than 20 y ago and recently have been reported to be abundant in many organisms including humans. Their exact function remains still unknown, although one may expect extensive functional studies to follow the currently dominant research into identification and discovery of circRNA by sophisticated sequencing techniques and bioinformatics. Functional studies require models and as such methods for preparation of circRNA in vitro. Here, we will review current protocols for RNA circularization and discuss future prospects in the field.Abbreviations: AMP, adenosine monophosphate; AppRNA, 5 0 -adenylated RNA; ATP, adenosine triphosphate; bp, base pair; CEV-A, citrus exocortis viroid strain A; circRNA, circular RNA; ciRNA, circular intronic RNA; CuAAC, cupper catalyzed azide alkyne cycloaddition; EDC, ethyl-3-(3 0 -dimethylaminopropyl)-carbodiimide; HIV, human immunodeficiency virus; IEciRNA, intron-exon circular RNA; nt, nucleotide; PIE, permuted intron exon; T4 Dnl, T4 DNA Ligase; T4 Rnl, T4 RNA Ligase

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Section: Chemical Strategiesmentioning

confidence: 99%

In vitro circularization of RNA

Müller

Appel

2016

RNA Biology

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“…One important factor for consideration when making DNA nanodevice is the preparation yield 28,31 . Since D2Cs produced in our approach do not appear to be based on extensive base-pairing interactions, their preparation may suffer from lower reaction yield.…”

Section: Articlementioning

confidence: 99%

Engineering interlocking DNA rings with weak physical interactions

Shen

Tram

et al. 2014

Nat Commun

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Catenanes are intriguing molecular assemblies for engineering unique molecular devices. The resident rings of a catenane are expected to execute unhindered rotation around each other, and to do so, they must have weak physical interactions with each other. Due to sequence programmability, DNA has become a popular material for nanoscale object engineering. However, current DNA catenanes, particularly in the single-stranded (ss) form, are synthesized through the formation of a linking duplex, which makes them less ideal as mobile elements for molecular machines. Herein we adopt a random library approach to engineer ssDNA [2] catenanes (two interlocked DNA rings) without a linking duplex. Results from DNA hybridization, double-stranded catenane synthesis and rolling circle amplification experiments signify that representative catenanes have weak physical interactions and are capable of operating as independent units. Our findings lay the foundation for exploring free-functioning interlocked DNA rings for the design of elaborate nanoscale machines based on DNA.

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“…We chose this highly selective and efficient reaction for nucleic acid ligation for several reasons: (i) alkynes and azides can readily be attached to nucleic acids; (ii) the reaction proceeds efficiently in aqueous media; (iii) it can be triggered by addition of Cu I ; and (iv) the resultant triazole ring is chemically robust and generally considered to be non-toxic. When we started this project ourselves and others had already shown that this reaction to be compatible with DNA (Gartner et al 2003;Kanan et al 2004;Kumar et al 2007). The new challenge was to design a biocompatible triazole linkage that can be tolerated by DNA and RNA polymerase enzymes in vitro and in vivo.…”

Section: Introductionmentioning

confidence: 99%

A triazole linkage that mimics the DNA phosphodiester group in living systems

El‐Sagheer

Brown²

2015

Quart. Rev. Biophys.

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Abstract. We describe the development of a chemical process based on the CuAAC reaction (click chemistry) to ligate DNA strands and produce an unnatural triazole backbone linkage. The chemical reaction is templated by a complementary DNA splint which accelerates the reaction and provides the required specificity. The resultant 1,4-triazole linkage is read through by DNA and RNA polymerases and is biocompatible in bacterial and human cells. This work has implications for the synthesis of chemically modified genes and other large modified DNA and RNA constructs.

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Template-Directed Oligonucleotide Strand Ligation, Covalent Intramolecular DNA Circularization and Catenation Using Click Chemistry

Cited by 257 publications

References 21 publications

In vitro circularization of RNA

In vitro circularization of RNA

Engineering interlocking DNA rings with weak physical interactions

A triazole linkage that mimics the DNA phosphodiester group in living systems

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