Assembly of the Complete Eight‐Base Artificial Genetic Helix, xDNA, and Its Interaction with the Natural Genetic System

Gao, Jianmin; Liu, Haibo; Kool, Eric T.

doi:10.1002/anie.200500069

Cited by 91 publications

(109 citation statements)

References 50 publications

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“…Among these systems, particularly interesting is the expanded DNA (XDNA), obtained by Kool's group [48], where each DNA base is expanded with a benzene ring that is covalently bonded to the base and co-planar with it. Such expanded bases are able to pair with natural DNA bases by H-bonding, forming base pairs of expanded size, that stacks with each other and with natural bases, assembling helical motifs.…”

Section: Optical Response Of Dna Bases and Base Pairsmentioning

confidence: 99%

The challenge of predicting optical properties of biomolecules: What can we learn from time-dependent density-functional theory?

Castro

Marques

Varsano

et al. 2008

Comptes Rendus. Physique

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The suitability of the time-dependent density-functional theory (TDDFT) approach for the theoretical study of the optical properties of biomolecules is demonstrated by several examples. We critically discuss the limitations of available TDDFT implementations to address some of the present open questions in the description of the excited-state dynamics of biological complexes. The key objective of the present work is to address the performance of TDDFT in the linear response regime of the bio-molecular systems to the visible or near UV radiation - measured by, e.g. optical absorption or optical dichroism spectra. Although these spectra are essentially determined by the electronic degrees of freedom of small, optically active regions within the usually large biological systems, they can also be strongly influenced by environment effects (solvent, hosting protein, temperature, etc.). Moreover, many key biological processes consist of photo-induced dynamics (photoisomerisation, etc.), and their description requires a coupled treatment of electronic and nuclear degrees of freedom. We illustrate these aspects with a selection of paradigmatic biomolecular systems: chromophores in fluorescent proteins, porphyrins, DNA basis, the azobenzene dye, etc. To cite this article: A. Castro et al., C. R. Physique 10 (2009). © 2008

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Section: Optical Response Of Dna Bases and Base Pairsmentioning

confidence: 99%

The challenge of predicting optical properties of biomolecules: What can we learn from time-dependent density-functional theory?

Castro

Marques

Varsano

et al. 2008

Comptes Rendus. Physique

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show abstract

“…13-5) or yDNA (y for wide), retain the features of regular DNA, such as Watson-Crick base pairing and right-handed helicity, but possess an expanded diameter when in a double helix [64]. When xDNA nucleosides are incorporated into regular duplex DNA there is distortion of the backbone due to the increased size of the base pair (2.4 A ) [65], but a duplex comprised solely of xDNA shows enhanced stability compared to DNA due to enhanced stacking interactions [66,67]. xDNA and yDNA represent two novel genetic systems, possessing many of the features found in regular DNA, but their expanded sizes should make them distinct from DNA.…”

Section: Altered Basesmentioning

confidence: 99%

“…Because the base-pairing is not altered, x, y DNA are still capable of base-pairing with DNA and RNA but forming double helices with an expanded diameter and higher stability due to the increased stacking of the expanded bases [62,66]. Finally, orthogonality might simply be semantic in that genetic information encoded in such a way that it is ''meaningless'' to the cellular host, unless specific transliterases are provided.…”

Section: In Vivo Replicationmentioning

confidence: 99%

Self‐Replication in Chemistry and Biology

Holliger

Loakes

2009

Systems Biology and Synthetic Biology

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“…Recent work by Kool and coworkers [16][17][18][19][20][21][22] showed that duplex DNA containing a thymine analog with increased base-pair size can lead to more stable duplexes. When compared with the previous synthesis of the thymidine analogs, the chemistry reported here offered a more convenient preparation of another class of duplex DNA with an enlarged π system.…”

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confidence: 99%

Facile Photocyclization Chemistry of 5-Phenylthio-2‘-deoxyuridine in Duplex DNA

2006

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We report here the synthesis of 5-phenylthio-2'-deoxyuridine (d PhS U), its incorporation into oligodeoxynucleotides (ODNs), and its photocyclization chemistry. Irradiation of dinucleoside monophosphate d( PhS UG) and d PhS U-bearing duplex ODNs with 254 nm light results in the facile formation of a cyclic product where the C6 of uracil is covalently bonded to the C2 of the phenyl Yinsheng.Wang@ucr.edu. Supporting Information Available. NMR spectra of synthetic compounds, LC traces, MS data, and LC-MS/MS results. This material is available free of charge via Internet at http://pubs.acs.org. ring. The chemistry reported here may serve as the basis for the efficient preparation of a new class of duplex DNA with an extended π system. NIH Public AccessPhenylthio-substituted nucleosides have been successfully employed as photolabile precursors for the generation of carbon-centered radicals to mimic the deleterious effects of ionizing radiation 1-6 . In addition, it has been shown that the photoirradiation of pyrimidine nucleosides with a halogen atom being substituted at the C5 position may result in the formation of C5-centered radicals 7-10 . It remains unclear what the photochemistry is for pyrimidine nucleosides bearing a 5-thiophenyl moiety.In this study, we set out to explore this chemistry by first synthesizing 5-phenylthio-2'-deoxyuridine (d PhS U). The incorporation of a phenylthio group to the C5 of uracil was inspired from the previous procedures for the preparation of 8-benzyloxy-2'-deoxyguanosine 11 . In this regard, treatment of the commercially available 5-bromo-2'-deoxyuridine with thiophenol and sodium in DMSO renders the desired 5-phenylthio-2'-deoxyuridine in ∼47% yield (Scheme 1). We then synthesized the phosphoramidite building block of d PhS U following standard procedures 12 and inserted it into dinucleoside monophosphate and ODNs by automated solidphase synthesis (Scheme 1).We next examined the photochemistry of d( PhS UG) and d PhS U-bearing ODNs. Here we began our discussion with the major product isolated from the irradiation mixture of d( PhS UG) (The HPLC trace for the separation of the 254 nm irradiation mixture is shown in Figure 1a). Negative-ion ESI-MS of the major fraction eluting at 51.3-min gave an ion of m/z 661.8 ( Figure 1a, inset), and we designate the product as d ( To further elucidate the structure of the major product, we recorded its 1 H-NMR spectrum, which showed the presence of four aromatic protons ( Figure S5). These protons can be assigned to the protons of the phenyl group, which is supported by 2-D NOESY measurement ( Figure S6). The losses of the H6 proton of uracil and an aromatic proton from the phenyl ring support the proposed structure of the major photoproduct (Scheme 2). It is worth noting that the NMR spectra are also consistent with an alternative cyclic structure where the sulfur is bonded to the C6 of the uracil component. This possibility, however, can be excluded for two reasons. First, the formation of the latter product would necessitate th...

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Assembly of the Complete Eight‐Base Artificial Genetic Helix, xDNA, and Its Interaction with the Natural Genetic System

Cited by 91 publications

References 50 publications

The challenge of predicting optical properties of biomolecules: What can we learn from time-dependent density-functional theory?

The challenge of predicting optical properties of biomolecules: What can we learn from time-dependent density-functional theory?

Self‐Replication in Chemistry and Biology

Facile Photocyclization Chemistry of 5-Phenylthio-2‘-deoxyuridine in Duplex DNA

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