“Post‐It” Type Connected DNA Created with a Reversible Covalent Cross‐Link

Tomás‐Gamasa, María; Serdjukow, Sascha; Su, Meng; Müller, Markus; Carell, Thomas

doi:10.1002/anie.201407854

Cited by 27 publications

(26 citation statements)

References 45 publications

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“…25–28 In addition, interstrand cross-links have been used for the stabilization of duplex DNA in structural biology and materials science applications. 29–36 There exist a wide structural variety of DNA-DNA cross-links that are important in toxicology, medicine, structural biology, and materials science. 25,26,32,35–37 The detection and characterization of interstrand cross-links in DNA is a challenging task.…”

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confidence: 99%

Characterization of Interstrand DNA–DNA Cross-Links Using the α-Hemolysin Protein Nanopore

et al. 2015

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Nanopore-based sensors have been studied extensively as potential tools for DNA sequencing, characterization of epigenetic modifications such as 5-methylcytosine, and detection of microRNA biomarkers. In the studies described here, the α-hemolysin protein nanopore embedded in a lipid bilayer was used for the detection and characterization of interstrand cross-links in duplex DNA. Interstrand cross-links are important lesions in medicinal chemistry and toxicology because they prevent the strand separation that is required for read-out of genetic information from DNA in cells. In addition, interstrand cross-links are used for the stabilization of duplex DNA in structural biology and materials science. Cross-linked DNA fragments produced unmistakable current signatures in the nanopore experiment. Some cross-linked substrates gave irreversible current blocks of >10 min, while others produced long current blocks (10–100 s) before the double-stranded DNA cross-link translocated through the α-hemolysin channel in a voltage-driven manner. The duration of the current block for the different cross-linked substrates examined here may be dictated by the stability of the duplex region left in the vestibule of the nanopore following partial unzipping of the cross-linked DNA. Construction of calibration curves measuring the frequency of cross-link blocking events (1/τon) as a function of cross-link concentration enabled quantitative determination of the amounts of cross-linked DNA present in samples. The unique current signatures generated by cross-linked DNA in the α-HL nanopore may enable the detection and characterization of DNA cross-links that are important in toxicology, medicine, and materials science.

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confidence: 99%

Characterization of Interstrand DNA–DNA Cross-Links Using the α-Hemolysin Protein Nanopore

et al. 2015

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“…This is usually unacceptable from a preparative perspective. Alternatively, elegant syntheses of structurally-defined cross-linked duplexes have been devised (Balkrishnen et al, 1996; Carrette et al, 2013; Gao and Orgel, 1999; Gruppi et al, 2014; Haque et al, 2014; Harwood et al, 2000; Hentshel et al, 2012; Hong et al, 2006; Manoharan et al, 1999; Mukherjee et al, 2014; Nakatani et al, 2002; Nishimoto et al, 2013; Noll et al, 2001; O'Flaherty et al, 2013; Pujari et al, 2014; Schärer, 2005; Tomás-Gamasa et al, 2014; Ye et al, 2013), but many of these multi-step organic reaction sequences may not be practical in many of the biochemical and materials science laboratories with interests in cross-linked DNA. In the work described here, we sought a simple, benchtop procedure for the synthesis of DNA duplexes containing a site-specific interstrand cross-link that employs inexpensive commercially available enzymes, chemicals, and oligodeoxynucleotides.…”

Section: Commentarymentioning

confidence: 99%

Simple, High‐Yield Syntheses of DNA Duplexes Containing Interstrand DNA‐DNA Cross‐Links Between an N⁴‐Aminocytidine Residue and an Abasic Site

Varela

Gates

2016

CP Nucleic Acid Chemistry

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The protocol describes the preparation and purification of interstrand DNA-DNA cross-links derived from the reaction of an N4-aminocytidine residue with an abasic site in duplex DNA. The procedures employ inexpensive, commercially-available chemicals and enzymes to carry out post-synthetic modification of commercially-available oligodeoxynucleotides. The yield of cross-linked duplex is typically better than 90%. If purification is required, the cross-linked duplex can be readily separated from single-stranded DNA starting materials by denaturing gel electrophoresis. The resulting covalent hydrazone-based cross-links are stable under physiologically-relevant conditions and may be useful for biophysical studies, structural analyses, DNA repair studies, and materials science applications.

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“…Previous attempts to overcome this involvedt he use of enzymes [27] or covalent crosslinking of strands. [28][29][30][31][32] Cassinelli et al recently reportedt he partial crosslinkingo fD NA origami staple strandsb yc opper-catalyzed azide-alkyne cycloaddition. [33] The disulfide bond is one of the main contributors to the stabilityo fp rotein tertiarys tructure.…”

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Dynamic Chemistry of Disulfide Terminated Oligonucleotides in Duplexes and Double‐Crossover Tiles

Stefano

Gothelf

2016

ChemBioChem

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Designed nanostructures formed by self-assembly of multiple DNA strands suffer from low stability at elevated temperature and under other denaturing conditions. Here, we propose a method for covalent coupling of DNA strands in such structures by the formation of disulfide bonds; this allows disassembly of the structure under reducing conditions. The dynamic chemistry of disulfides and thiols was applied to crosslink DNA strands with terminal disulfide modifications. The formation of disulfide-linked DNA duplexes consisting of three strands is demonstrated, as well as a more-complex DNA double-crossover tile. All the strands in the fully disulfide-linked structures are covalently and geometrically interlocked, and it is demonstrated that the structures are stable under heating and in the presence of denaturants. Such a reversible system can be exploited in applications where higher DNA stability is needed only temporarily, such as delivery of cargoes to cells by DNA nanostructures.

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“Post‐It” Type Connected DNA Created with a Reversible Covalent Cross‐Link

Cited by 27 publications

References 45 publications

Characterization of Interstrand DNA–DNA Cross-Links Using the α-Hemolysin Protein Nanopore

Characterization of Interstrand DNA–DNA Cross-Links Using the α-Hemolysin Protein Nanopore

Simple, High‐Yield Syntheses of DNA Duplexes Containing Interstrand DNA‐DNA Cross‐Links Between an N⁴‐Aminocytidine Residue and an Abasic Site

Dynamic Chemistry of Disulfide Terminated Oligonucleotides in Duplexes and Double‐Crossover Tiles

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“Post‐It” Type Connected DNA Created with a Reversible Covalent Cross‐Link

Cited by 27 publications

References 45 publications

Characterization of Interstrand DNA–DNA Cross-Links Using the α-Hemolysin Protein Nanopore

Characterization of Interstrand DNA–DNA Cross-Links Using the α-Hemolysin Protein Nanopore

Simple, High‐Yield Syntheses of DNA Duplexes Containing Interstrand DNA‐DNA Cross‐Links Between an N4‐Aminocytidine Residue and an Abasic Site

Dynamic Chemistry of Disulfide Terminated Oligonucleotides in Duplexes and Double‐Crossover Tiles

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Simple, High‐Yield Syntheses of DNA Duplexes Containing Interstrand DNA‐DNA Cross‐Links Between an N⁴‐Aminocytidine Residue and an Abasic Site