Rigid, Conjugated, Fluoresceinated Thymidine Triphosphates: Syntheses and Polymerase Mediated Incorporation into DNA Analogues.

Thoresen, Lars; Jiao, Guan-Sheng; Haaland, Wade C.; Metzker, Michael L.; Burgess, Kevin

doi:10.1002/chin.200402251

Cited by 7 publications

(9 citation statements)

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“…A condensation reaction of the resulting acid with porphyrin 5 under standard conditions produced bisporphyrin 8, which was converted to iodobisporphyrin. The 4-trimethylethynylphenyl group was introduced onto the iododerivative of 8 via palladium-mediated coupling with 4-trimethylsilylethynylphenyl boronic acid (36). The subsequent deprotection of the trimethylsilyl group yielded bisporphyrin 9.…”

Section: Resultsmentioning

confidence: 99%

Supramolecular polymer formed by reversible self-assembly of tetrakisporphyrin

Haino

Fujii

Watanabe

et al. 2009

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

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S-shaped tetrakisporphyrin 2 forms supramolecular polymeric assemblies via a complementary affinity of its bisporphyrin units in solution. The self-association constant determined by applying the isodesmic model is >10 6 L mol ؊1 , which suggests that a sizable polymer forms at millimolar concentrations at room temperature. The electron deficient aromatic guest (TNF) binds within the molecular clefts provided by the bisporphyrin units via a chargetransfer interaction. This guest complexation completely disrupts supramolecular polymeric assembly. The long, fibrous fragments of the polymeric assemblies were characterized by atomic-force microscopy imaging of a film cast on a mica surface. The polymeric assemblies have lengths of >1m and show a coiled structure with a higher level of organization. The approach discussed in this report concerning the quick preparation of supramolecular polymeric assemblies driven by noncovalent forces sets the stage for the preparation of a previously undescribed class of macromolecular porphyrin architectures.porphyrin ͉ supramolecular chemistry S ignificant effort has been directed toward elucidating the energy transport phenomena occurring in natural lightharvesting complexes. A variety of porphyrin-based model compounds have been created to mimic natural light-harvesting complexes with the goal of applying them to artificial lightharvesting systems and molecular photonic devices (1-4). Among them, nanometric multiporphyrin arrays are the most challenging target, wherein, their covalent synthesis offers a high stability and a precisely controlled arrangement of multiporphyrin arrays (5, 6). Unfortunately, the growth of size and complexity of these systems makes their synthesis tedious and inefficient.In contrast, supramolecular self-assembly is a versatile alternative and offers the quick construction of 1-, 2-, or 3-dimensional nanometric architectures that have discrete structures, properties, and functions in which the molecular components are held together by reversible interactions (7-11). Self-assembled nanometric multiporphyrin arrays having well-defined shapes and dimensions provide unique optical and electrochemical properties for photochemical energy conversion and storage. As a consequence, their practical applications can be foreseen in the field of molecular electronics: conductive molecular wires, switches, and photovoltaic cells. These creative developments should pave the way for research directions in creating key materials for emerging field of nanotechnology and science.Coordination-driven self-assembly of porphyrin is one of the most useful approaches for developing large and elaborate molecular architectures (12, 13). Hunter and coworkers developed unique self-assembled porphyrin arrays (14-18). Giant porphyrin arrays and large porphyrin wheels via metal coordination for modeling light-harvesting antenna have been reported by . Aida and coworkers have investigated self-assembled nanometric porphyrin arrays (27-29). There are limited examples of porphyrin self...

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Section: Resultsmentioning

confidence: 99%

Supramolecular polymer formed by reversible self-assembly of tetrakisporphyrin

Haino

Fujii

Watanabe

et al. 2009

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

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“…Since the Sonogashira reaction of halogenated dNTPs with terminal acetylenes is a reliable single-step method for introduction of functionalized alkyne-linked substituents, 31,39,40 we envisaged N-(propargyl)-chloroacetamide (1) 41 as a suitable building block and prepared it from propargylamine and chloroacetyl chloride. The aqueous Sonogashira reactions of 5iodo-2′-deoxycytidine mono-(dC I MP) or triphosphate (dC I TP), as well as of 7-iodo-7-deazaadenine dNMP (dA I MP) or dNTP (dA I TP) with propargyl-chloroacetamide 1, were performed under previously reported conditions in the presence of Pd(OAc) 2 and triphenylphosphine-3,3′,3″-trisulfonate (TPPTS) in a water/acetonitrile mixture (2:1).…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Chloroacetamide-Linked Nucleotides and DNA for Cross-Linking with Peptides and Proteins

et al. 2016

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Nucleotides, 2'-deoxyribonucleoside triphosphates (dNTPs), and DNA probes bearing reactive chloroacetamido group linked to nucleobase (cytosine or 7-deazadaenine) through a propargyl tether were prepared and tested in cross-linking with cysteine- or histidine-containing peptides and proteins. The chloroacetamide-modifed dNTPs proved to be good substrates for DNA polymerases in the enzymatic synthesis of modified DNA probes. Modified nucleotides and DNA reacted efficiently with cysteine and cysteine-containing peptides, whereas the reaction with histidine was sluggish and low yielding. The modified DNA efficiently cross-linked with p53 protein through alkylation of cysteine and showed potential for cross-linking with histidine (in C277H mutant of p53).

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“…Alkyne-modified nucleosides have also received significant interest as biochemical probes. The small, linear, and rigid alkyne connection can allow a wide range of fluorescent (Okamoto et al, 2003;Thoresen et al, 2003;Dioubankova et al, 2004;Hwang et al, 2004;Jiao et al, 2004;Wagner et al, 2005) and spin label probes (Strube et al, 2001;Gannett et al, 2002;Obeid et al, 2008), as well as other reactive or probe moieties (Beilstein and Grinstaff, 2001;Weizman and Tor, 2002;Brázdilová et al, 2007;Vrábel et al, 2007;Kalachova et al, 2012), to be attached to DNA in biochemical studies. The most common way to alkynylate nucleoside bases is through the palladium-catalyzed coupling of halonucleosides with terminal alkynes, which is known as the Sonogashira reaction.…”

Section: Commentary Background Informationmentioning

confidence: 99%

“…Water is less toxic than DMF and allows for easier product isolation. In addition, the methodology can be applied to nucleotides, which are difficult to solubilize in organic solvents (Thoresen et al, 2003;Collier and Wagner, 2006). The optimized catalyst system for this reaction is based on Pd(OAc) 2 , TXPTS, and CuI.…”

Section: Commentary Background Informationmentioning

confidence: 99%

Aqueous‐Phase Sonogashira Alkynylation to Synthesize 5‐Substituted Pyrimidine and 8‐Substituted Purine Nucleosides

Cho

Shaughnessy

2012

CP Nucleic Acid Chemistry

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In this unit, an efficient method for the synthesis of alkyne-modified nucleosides in an aqueous solvent system is described. The method allows direct palladium-catalyzed alkynylation of readily available unprotected 8-bromo-2'-deoxyguanosine (8-BrdG), 8-bromo-2'-deoxyadenosene (8-BrdA), 8-bromoadenosine (8-BrA), and 5-iodo-2'-deoxyuridine (5-IdU) precursors. The optimal catalyst is derived from palladium acetate, tri-(2,4-dimethyl-5-sulfonatophenyl)phosphane (TXPTS), and CuI.

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Rigid, Conjugated, Fluoresceinated Thymidine Triphosphates: Syntheses and Polymerase Mediated Incorporation into DNA Analogues.

Abstract: For Abstract see ChemInform Abstract in Full Text.

Cited by 7 publications

References 1 publication

Supramolecular polymer formed by reversible self-assembly of tetrakisporphyrin

Supramolecular polymer formed by reversible self-assembly of tetrakisporphyrin

Chloroacetamide-Linked Nucleotides and DNA for Cross-Linking with Peptides and Proteins

Aqueous‐Phase Sonogashira Alkynylation to Synthesize 5‐Substituted Pyrimidine and 8‐Substituted Purine Nucleosides

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