Bioinspired organic chemistry

Webb, Simon J.

doi:10.1039/b515108m

Cited by 4 publications

(3 citation statements)

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“…7). They were able to show by 1 H NMR spectroscopy at 50 1C in buffered D 2 O that the substrate was first encapsulated within the self-assembled M 4 L 6 ''container'' host, underwent rearrangement within the cavity, then hydrolysed outside the cavity. Rate accelerations were observed for several allyl enammonium substrates, with a maximum acceleration of 850-fold.…”

Section: Mimics Of Protein Functionmentioning

confidence: 99%

“…Although this review does not address every report of important research in biomaterials or the interaction of bioinspired molecules with materials, the occasional highlight is described; in some cases initial work was highlighted in last year's review. 1 Much like last year, this report categorises research according to the biomolecule from which it draws inspiration, although the addition of a section on prebiotic chemistry and chirality transfer reflects the volume of important research produced in this area in 2006. Highlights in this review include: molecular machines were shown to operate at a macroscopic level for the first time; increased insight into the mechanism of asymmetric amplification in amino acid catalysis; and further advances in understanding and replicating biomembrane behaviour.…”

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Bioinspired organic chemistry

Webb

2007

Annu. Rep. Prog. Chem., Sect. B: Org. Chem.

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were right-handed and antiparallel, with base-pairing analogous to that in natural DNA. The key difference was grooves that were wider and shallower than those in Bform DNA, with less helical character (B12 base pairs per turn). It also shows, as expected from melting studies, that there is extensive base stacking both between and within strands. 2 The authors also unveiled a new type of ''doublewide'' naphthohomologated DNA, in which widened pyrimidine homologues were incorporated into oligopeptides. On account of the rigid aromatic core, these bases were found to be fluorescent, and exhibit extremely strong base-stacking, although strong basestacking was evident even in the single strands, which made measuring interstrand complexation difficult and left it unclear if these ''doublewide'' DNA strands formed sequence-selective antiparallel duplexes. 3 Kim and Kool have developed other types of fluorescent nucleotides based on 2-pyrido-or 2-quino-benzimidazoles that could be incorporated into DNA strands; the fluorescence of these metal-complexing bases underwent significant changes upon exposure to metal ions, particularly Ag(I), Cd(II), Pd(II), Pt(II) and Zn(II). 4 Several researchers have developed other fluorescent bases by appending fluorescent groups away from the site of base-pairing. Pyrene excimer formation has been used to probe DNA structure, 5 to detect deletion polymorphisms, 6 and to probe the B-to Z-DNA duplex transition. 7 A chemically cleavable nucleotide with an appended BODIPY group has also exhibited potential as a reversible terminator for DNA sequencing by synthesis. 8 Rather than develop new types of modified bases, Sintim and Kool have studied the previously reported modified bases 2-thio-and 4-thiothymidine (2-thioT and 4-thioT, respectively) in more detail. They found that 2-thioT increased duplex stability and paired with A with greater selectivity than did T with A, whilst 4-thioT decreased duplex stability but gave a stronger base pair with G than even the natural T-A base pair. Interestingly, both artificial bases could be enzymatically incorporated into DNA with faster rates than the natural bases. 9 The expansion of the genetic alphabet has usually revolved around the synthesis of artificial nucleotides that can mimic the hydrogen bonding functionality of the natural system. However, the well-known isosteric approach used in drug discovery can also be applied to the development of artificial nucleotides. In particular, it has been found DNA polymerases will pair purine-shaped bases with pyrimidine-shaped bases. Both 2,4-difluorotoluene and 2,4-dichlorotoluene deoxyribonucleosides are isosteres of thymidine; these are highly active substrates for DNA polymerases and will encode replication opposite A. Nonetheless, established studies have not established whether the size or the shape is more important for uptake by DNA polymerase. Kool and co-workers have synthesised compounds with conservative variations on the 2,4-dichlorotoluene deoxyribonucleoside structure. They discovered that ...

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Section: Mimics Of Protein Functionmentioning

confidence: 99%

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confidence: 99%

Bioinspired organic chemistry

Webb

2007

Annu. Rep. Prog. Chem., Sect. B: Org. Chem.

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“…At the cellular level, living organisms store and process genetic information encoded by a set of four DNA nucleobases (A, C, G, and T), which combine according to Watson-Crick hydrogen-bonding rules. There have been many attempts to expand the unique function and applications of DNA [1,2]. Approaches considered to date include editing the DNA backbone (e.g., polyamide nucleic acids (PNA), locked nucleic acids (LNA), and xeno-nucleic acids (XNA) [3,4,5]), modifying the nucleobase functional groups (e.g., difluorotoluene, isoguanine, and 2,6-diaminopurine [6,7,8,9]), or changing the underlying nucleobase composition (e.g., propynyl isocarbostyril and fleximers [10,11,12]).…”

Section: Introductionmentioning

confidence: 99%

Computational Evaluation of Nucleotide Insertion Opposite Expanded and Widened DNA by the Translesion Synthesis Polymerase Dpo4

2016

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Expanded (x) and widened (y) deoxyribose nucleic acids (DNA) have an extra benzene ring incorporated either horizontally (xDNA) or vertically (yDNA) between a natural pyrimidine base and the deoxyribose, or between the 5-and 6-membered rings of a natural purine. Far-reaching applications for (x,y)DNA include nucleic acid probes and extending the natural genetic code. Since modified nucleobases must encode information that can be passed to the next generation in order to be a useful extension of the genetic code, the ability of translesion (bypass) polymerases to replicate modified bases is an active area of research. The common model bypass polymerase DNA polymerase IV (Dpo4) has been previously shown to successfully replicate and extend past a single modified nucleobase on a template DNA strand. In the current study, molecular dynamics (MD) simulations are used to evaluate the accommodation of expanded/widened nucleobases in the Dpo4 active site, providing the first structural information on the replication of (x,y)DNA. Our results indicate that the Dpo4 catalytic (palm) domain is not significantly impacted by the (x,y)DNA bases. Instead, the template strand is displaced to accommodate the increased C1'-C1' base-pair distance. The structural insights unveiled in the present work not only increase our fundamental understanding of Dpo4 replication, but also reveal the process by which Dpo4 replicates (x,y)DNA, and thereby will contribute to the optimization of high fidelity and efficient polymerases for the replication of modified nucleobases.

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Bioinspired Organic Chemistry

Webb

2007

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Bioinspired organic chemistry

Cited by 4 publications

References 106 publications

Bioinspired organic chemistry

Bioinspired organic chemistry

Computational Evaluation of Nucleotide Insertion Opposite Expanded and Widened DNA by the Translesion Synthesis Polymerase Dpo4

Bioinspired Organic Chemistry

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