An approach to metal-assisted DNA base pairing: novel β-C-nucleosides with a 2-aminophenol or a catechol as the nucleobase

Tanaka, Kentaro; Tasaka, Motoyuki; Cao, Hui; Shionoya, Mitsuhiko

doi:10.1016/s0928-0987(00)00210-4

Cited by 32 publications

(10 citation statements)

References 26 publications

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“…used as a control to focus on the biases introduced during amplification and not during chemical synthesis [for example, because of incomplete nucleotide deprotection (37); thus, the 10 24 -fold amplified libraries are referred to as having been amplified 10 21 -fold]. Values of f rel N (n) − 1 reflect the amplification bias for or against nucleotide N at position n, with zero indicating no bias and positive and negative deviations indicating that, during amplification, the nucleotide is enriched or depleted, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…For the populations amplified with a 1-min extension time (Fig. 4B), after the full 10 21 -fold amplification, the only off-diagonal elements in the normalized C(n,n′) matrix with values in excess of 0.001 were C(1, 2) = 0.0014 for the population of sequences that retained the unnatural base pair and C(−1, −2) = 0.0011 and C(1, 2) = 0.0012 for the population of sequences that lost the unnatural base pair. For the population amplified with a 4-min extension time, all pairwise correlations were less than 0.0007 (SI Appendix, Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Although many candidate unnatural base pairs have been reported (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21), only a few are actually replicable by DNA polymerases (10,11,13,16). Moreover, it is clear that most applications will require that the unnatural base pair not only be replicated with high efficiency and fidelity but also, that replication be at least approximately independent of sequence context.…”

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confidence: 99%

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Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet

Malyshev

Dhami²,

Quach³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

162

130

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The natural four-letter genetic alphabet, comprised of just two base pairs (dA-dT and dG-dC), is conserved throughout all life, and its expansion by the development of a third, unnatural base pair has emerged as a central goal of chemical and synthetic biology. We recently developed a class of candidate unnatural base pairs, exemplified by the pair formed between d5SICS and dNaM. Here, we examine the PCR amplification of DNA containing one or more d5SICS-dNaM pairs in a wide variety of sequence contexts. Under standard conditions, we show that this DNA may be amplified with high efficiency and greater than 99.9% fidelity. To more rigorously explore potential sequence effects, we used deep sequencing to characterize a library of templates containing the unnatural base pair as a function of amplification. We found that the unnatural base pair is efficiently replicated with high fidelity in virtually all sequence contexts. The results show that, for PCR and PCR-based applications, d5SICS-dNaM is functionally equivalent to a natural base pair, and when combined with dA-dT and dG-dC, it provides a fully functional six-letter genetic alphabet.expanded genetic alphabet | hydrophobic | artificial DNA | unnatural nucleotides | bioinformatics E xpansion of the genetic alphabet to include an unnatural base pair has emerged as a central goal of chemical and synthetic biology. Success would represent a remarkable integration of orthogonal synthetic components into a fundamental biological system and build the foundation for a semisynthetic organism with increased potential for information storage and retrieval (1). Moreover, the constituent unnatural nucleotides could be used to site-specifically label DNA or RNA with different functionalities of interest (2-4) and potentially revolutionize the already ubiquitous in vitro applications of nucleic acids, such as aptamer and DNA/RNAzyme selections (5, 6), PCR-based diagnostics (7, 8), and DNA-based nanomaterials and devices (9).Although many candidate unnatural base pairs have been reported (10-21), only a few are actually replicable by DNA polymerases (10,11,13,16). Moreover, it is clear that most applications will require that the unnatural base pair not only be replicated with high efficiency and fidelity but also, that replication be at least approximately independent of sequence context. Sequence dependencies would cause biased amplification and effectively preclude many uses of the unnatural base pair. No candidate unnatural base pair has been shown to be replicated without sequence bias, and thus, none can yet claim functional equivalence to a natural base pair.In general, the most promising unnatural base pair candidates currently available have been developed by pursuing one of two different strategies. The first strategy, pioneered in the work by Benner and coworkers (22), relies on the use of nucleotide analogs bearing nucleobases that pair through complementary hydrogen bonding (H-bonding) patterns that are orthogonal to those patterns of the natural pairs. Early ef...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

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Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet

Malyshev

Dhami²,

Quach³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

162

130

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“…[59] They synthesized the o-phenylenediamine-palladium complex 2 and later the derivatives 3, [60] 4, [61] and 5 [62] in solution but did not initially report the incorporation of these nucleosides into oligonucleotides (Figure 4). …”

Section: First-generation Metal-base Pairsmentioning

confidence: 99%

DNA–Metal Base Pairs

2007

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Recent developments show encouraging results for the use of DNA as a construction material for nanometer-sized objects. Today, however, DNA-based molecular nanoarchitectures are constructed with mainly unmodified or at best end-modified oligonucleotides, thus shifting the development of functionalized DNA structures into the limelight. One of most recent developments in this direction is the substitution of the canonical Watson-Crick base pairs by metal complexes. In this way "metal-base pairs" are created, which could potentially impart magnetic or conductive properties to DNA-based nanostructures. This review summarizes research which started almost 45 years ago with the investigation of how metal ions interact with unmodified DNA and which recently culminated in the development of artificial ligand-like nucleobases so far able to coordinate up to ten metal ions inside a single DNA duplex in a programmable fashion.

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“…[59] Sie synthetisierten den o-Phenylendiamin-Palladiumkomplex 2 und später dessen Derivate 3, [60] 4 [61] und 5 [62] in Lösung, aber berichteten nicht über den Einbau dieser Nucleoside in Oligonucleotide (Abbildung 4).…”

Section: Metall-basenpaare Der Ersten Generationunclassified

DNA‐Metall‐Basenpaare

Clever¹,

Kaul²,

Carell³

2007

Angewandte Chemie

160

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Neuere Entwicklungen, die darauf abzielen, DNA als funktionelles Baumaterial für Nanoobjekte zu verwenden, zeigen vielversprechende Ergebnisse. In der Vergangenheit wurden molekulare DNA‐Nanoarchitekturen aus unmodifizierten oder bestenfalls endgruppenmodifizierten Oligonucleotiden aufgebaut, sodass derzeit die Entwicklung von funktionalisierten DNA‐Strukturen im Rampenlicht der Forschung steht. Eine der neuesten Entwicklungen in diese Richtung ist der Austausch der kanonischen Watson‐Crick‐Basenpaare durch Metallkomplexe zur Erzeugung von Metall‐Basenpaaren, die DNA‐Nanostrukturen magnetische oder elektrisch leitende Eigenschaften verleihen könnten. Dieser Kurzaufsatz fasst die Forschung auf diesem Gebiet zusammen, die vor fast 45 Jahren mit der Untersuchung der Interaktion von Metallen mit unmodifizierter DNA begann und nun ihren Höhepunkt in der Synthese künstlicher, ligandenähnlicher Nucleobasen findet, die bereits imstande sind, bis zu zehn Metallionen innerhalb eines einzelnen DNA‐Doppelstrangs programmierbar zu koordinieren.

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An approach to metal-assisted DNA base pairing: novel β-C-nucleosides with a 2-aminophenol or a catechol as the nucleobase

Cited by 32 publications

References 26 publications

Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet

Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet

DNA–Metal Base Pairs

DNA‐Metall‐Basenpaare

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