DNA‐Templated Organic Synthesis: Nature's Strategy for Controlling Chemical Reactivity Applied to Synthetic Molecules

Li, Xiaoyü; Liu, David R.

doi:10.1002/anie.200400656

Cited by 513 publications

(360 citation statements)

References 190 publications

(406 reference statements)

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“…7,8 . The properties of DNA allow for its use to control both covalent chemistry 9 and the self-assembly of nanoscale objects, devices and lattices 10 Here, we show that these same features make it amenable to establishing structure-activity relationships relevant to the crystallization of CC.…”

Section: Introductionmentioning

confidence: 82%

Morphology Change of Calcium Carbonate in the Presence of Polynucleotides

Lukeman

Stevenson

Seeman

2008

Crystal Growth & Design

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Two-dimensional DNA lattices are grown under conditions that also are suitable for the magnesium-free growth of three-dimensional calcium carbonate crystals. These lattices are used to template morphology changes in calcium carbonate. The effects of DNA lattices, sub-assemblies, duplexes, single strands, dinucleotides, and mononucleotides on calcium carbonate morphology are studied. A "rotated" morphology of calcite is found to predominate when a critical concentration of any polynucleotide is reached in the templating solution.

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Section: Introductionmentioning

confidence: 82%

Morphology Change of Calcium Carbonate in the Presence of Polynucleotides

Lukeman

Stevenson

Seeman

2008

Crystal Growth & Design

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“…This disparity between functional and chemical diversity, coupled with the powerful functional properties of synthetic small molecule-nucleic acid conjugates (21)(22)(23)(24) led us to speculate that small molecule-RNA conjugates beyond those previously described may exist in modern cells as evolutionary fossils or even as novel RNAs with functions enabled by their modifications.…”

mentioning

confidence: 99%

A chemical screen for biological small molecule–RNA conjugates reveals CoA-linked RNA

Kowtoniuk

Shen

Heemstra

et al. 2009

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

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108

102

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Compared with the rapidly expanding set of known biological roles for RNA, the known chemical diversity of cellular RNA has remained limited primarily to canonical RNA, 3 -aminoacylated tRNAs, nucleobase-modified RNAs, and 5 -capped mRNAs in eukaryotes. We developed two methods to detect in a broad manner chemically labile cellular small molecule-RNA conjugates. The methods were validated by the detection of known tRNA and rRNA modifications. The first method analyzes small molecules cleaved from RNA by base or nucleophile treatment. Application to Escherichia coli and Streptomyces venezuelae RNA revealed an RNAlinked hydroxyfuranone or succinyl ester group, in addition to a number of other putative small molecule-RNA conjugates not previously reported. The second method analyzes nuclease-generated mononucleotides before and after treatment with base or nucleophile and also revealed a number of new putative small molecule-RNA conjugates, including 3 -dephospho-CoA and its succinyl-, acetyl-, and methylmalonyl-thioester derivatives. Subsequent experiments established that these CoA species are attached to E. coli and S. venezuelae RNA at the 5 terminus. CoA-linked RNA cannot be generated through aberrant transcriptional initiation by E. coli RNA polymerase in vitro, and CoA-linked RNA in E. coli is only found among smaller (Շ200 nucleotide) RNAs that have yet to be identified. These results provide examples of small molecule-RNA conjugates and suggest that the chemical diversity of cellular RNA may be greater than previously understood. mass spectrometry ͉ RNA modifications ͉ coenzyme A O ver the past few decades, RNA has emerged as much more than an intermediary in biology's central dogma. Ribozymes (1), riboswitches (2), microRNAs (miRNAs) (3), small interfering RNAs (siRNAs) (4), Piwi-interacting RNAs (piRNAs) (5), small nuclear RNAs (snRNAs) (6), CRISPR sRNAs (7), RNA transcriptional regulators (8), and long noncoding RNAs (9, 10) are all examples of RNAs that are thought to play a wide range of catalytic, regulatory, or defensive roles in the cell. Models of early biotic systems have proposed even broader roles for RNA, including the possibility that RNA-tethered molecules participated in RNA-templated chemical reactions as an early form of metabolism (11)(12)(13)(14)(15)(16).In contrast with these newer insights into its functional diversity, the known chemical diversity of natural RNA has remained limited primarily to canonical polyribonucleotides, 3Ј-aminoacylated tRNAs (17), modified nucleobases in a variety of RNAs (18), and 5Ј-capped mRNAs in eukaryotes (19)(20). This disparity between functional and chemical diversity, coupled with the powerful functional properties of synthetic small molecule-nucleic acid conjugates (21-24) led us to speculate that small molecule-RNA conjugates beyond those previously described may exist in modern cells as evolutionary fossils or even as novel RNAs with functions enabled by their modifications.To begin to explore this possibility, we have developed and implemented a ...

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“…DNA-templated chemistry takes advantage of the remarkable self-recognition properties of DNA. 40 It serves as scaffold that allows defined spatial arrangement of DNA-bound reaction partners. We successfully applied this concept to DBC-based micelles.…”

Section: Dbc Micelles As Templates For Chemical Reactions and Virus Cmentioning

confidence: 99%

DNA Block Copolymers: Functional Materials for Nanoscience and Biomedicine

2012

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W e live in a world full of synthetic materials, and the development of new technologies builds on the design and synthesis of new chemical structures, such as polymers. Synthetic macromolecules have changed the world and currently play a major role in all aspects of daily life. Due to their tailorable properties, these materials have fueled the invention of new techniques and goods, from the yogurt cup to the car seat belts. To fulfill the requirements of modern life, polymers and their composites have become increasingly complex. One strategy for altering polymer properties is to combine different polymer segments within one polymer, known as block copolymers. The microphase separation of the individual polymer components and the resulting formation of well defined nanosized domains provide a broad range of new materials with various properties. Block copolymers facilitated the development of innovative concepts in the fields of drug delivery, nanomedicine, organic electronics, and nanoscience.Block copolymers consist exclusively of organic polymers, but researchers are increasingly interested in materials that combine synthetic materials and biomacromolecules. Although many researchers have explored the combination of proteins with organic polymers, far fewer investigations have explored nucleic acid/polymer hybrids, known as DNA block copolymers (DBCs). DNA as a polymer block provides several advantages over other biopolymers. The availability of automated synthesis offers DNA segments with nucleotide precision, which facilitates the fabrication of hybrid materials with monodisperse biopolymer blocks. The directed functionalization of modified single-stranded DNA by WatsonÀCrick base-pairing is another key feature of DNA block copolymers. Furthermore, the appropriate selection of DNA sequence and organic polymer gives control over the material properties and their self-assembly into supramolecular structures. The introduction of a hydrophobic polymer into DBCs in aqueous solution leads to amphiphilic micellar structures with a hydrophobic polymer core and a DNA corona.In this Account, we discuss selected examples of recent developments in the synthesis, structure manipulation and applications of DBCs. We present achievements in synthesis of DBCs and their amplification based on molecular biology techniques. We also focus on concepts involving supramolecular assemblies and the change of morphological properties by mild stimuli. Finally, we discuss future applications of DBCs. DBC micelles have served as drug-delivery vehicles, as scaffolds for chemical reactions, and as templates for the self-assembly of virus capsids. In nanoelectronics, DNA polymer hybrids can facilitate size selection and directed deposition of single-walled carbon nanotubes in field effect transistor (FET) devices.

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DNA‐Templated Organic Synthesis: Nature's Strategy for Controlling Chemical Reactivity Applied to Synthetic Molecules

Cited by 513 publications

References 190 publications

Morphology Change of Calcium Carbonate in the Presence of Polynucleotides

Morphology Change of Calcium Carbonate in the Presence of Polynucleotides

A chemical screen for biological small molecule–RNA conjugates reveals CoA-linked RNA

DNA Block Copolymers: Functional Materials for Nanoscience and Biomedicine

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