A firmly hybridizable, DNA-like architecture with DAD/ADA- and ADD/DAA-type nonnatural base pairs as an extracellular genetic candidate

Shirato, Wataru; Chiba, Junya; Inoûye, Masahiko

doi:10.1039/c4cc09486g

Cited by 9 publications

(15 citation statements)

References 43 publications

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“…11 Thus, it has been used for chemical fine-tuning of artificial DNA and RNA in synthetic biology. [12][13][14][15] TPI heterosynthon (R 2 2 (12) graph-set motif) 16,17 is very robust and reliable, and has been used in the construction of supramolecular assemblies since many years. 18 Rods, tapes and cyclic hexamers (rosettes) have been prepared using this synthon in the ADA/DAD complexes of cyanuric acid and melamine with a (1:1) stoichiometry.…”

Section: Introductionmentioning

confidence: 99%

Multifacial Recognition in Binary and Ternary Cocrystals from 5-Halouracil and Aminoazine Derivatives

Portalone

2018

Crystal Growth & Design

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A systematic analysis using single crystal X-ray diffraction was performed to explore the role exerted by potential intercomponent proton-transfer reactions in the supramolecular structures of A-B cocrystals formed by 5-haloderivatives of uracil (A) coupled with 2-aminoadenine simulants (aminoazines, B). Twelve new heterodimers were synthesized in different stoichiometry and cocrystallized by solvent co-grinding followed by solution crystallization. In the binary cocrystals, uracil or 1-methyluracil with halide modification at the 5 position (F, Cl, Br, I) were coupled with aminoaromatic N-heterocycles (melamine, 2,4,6-triaminopyrimidine, 2,6-diaminopyridine) as multivalent site for pyrimidine nucleobase recognition. The crystallographic analysis showed that, next to the expected neutral three-point hydrogen bonds (TPI), ionized TPI, favored by A → B proton transfer, can be used for WC multifacial recognition. Noteworthy, the formation of the charged TPI, which depends on the acid/base properties of the components, takes always place between the more acidic site of the 5halonucleobases (N3 atom) and the more basic site (imino N atom) of 2,4,6-triaminopyrimidine or 2,6diaminopyridine, and melamine recognition unit results to be insufficiently basic to accept a proton. The general ability of pyrimidine nucleobases to provide electron donating groups to halogen bonding has been confirmed in seven cocrystals containing the 5-chloro, 5-bromo or 5-iododerivatives coupled with melamine or 2,4,6-triaminopyrimidine. Considerations of the relative acidities of coformers A and of the relative basicities of coformers B allowed us to design and characterize by single-crystal X-ray diffraction the first ternary pyrimidine nucleobase-containing cocrystal based on the JANUS-WEDGE concept: the nucleobase-Janus-nucleobase (1:1:1) triad showing a 2,4,6-triamino pyrimidine molecule wedged via neutral and ionized TPI between the 5-fluorouracil/1-methyluracil pair in reverse WC fashion. ABSTRACTA systematic analysis using single crystal X-ray diffraction was performed to explore the role exerted by potential intercomponent proton-transfer reactions in the supramolecular structures of A-B cocrystals formed by 5-haloderivatives of uracil (A), coupled with 2-aminoadenine simulants (aminoazines, B). Twelve new heterodimers were synthesized in different stoichiometry and cocrystallized by solvent co-grinding followed by solution crystallization. In the binary cocrystals, uracil or 1-methyluracil with halide modification at the 5 position (F, Cl, Br, I) were coupled with amino-aromatic N-heterocycles (melamine, 2,4,6-triaminopyrimidine, 2,6-diaminopyridine) as multivalent site for pyrimidine nucleobase recognition. The crystallographic analysis showed that, next to the expected neutral three-point hydrogen bonds (TPI), ionized TPI, favored by A → B proton transfer, can be used for WC multifacial recognition. Noteworthy, the formation of the charged TPI, which depends on the acid/base properties of the components, takes always place between ...

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Section: Introductionmentioning

confidence: 99%

Multifacial Recognition in Binary and Ternary Cocrystals from 5-Halouracil and Aminoazine Derivatives

Portalone

2018

Crystal Growth & Design

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“…9 (see Basic Protocol 1) Tris(dibenzylideneacetone)dipalladium(0)-chloroform [Pd 2 (dba) 3 •CHCl 3 ; Aldrich] Copper(I) iodide (CuI; Sigma Aldrich) Triphenyl phosphine (PPh 3 ; Wako Pure Chemical) Argon Diisopropylamine (deoxygenated iPr 2 NH, bubbled with argon for 10 min prior to use) N,N-Dimethylformamide (deoxygenated DMF; bubbled with argon for 10 min prior to use) 5-Iodo-1-methyluracil [T*-I; prepared according to the procedure described in Robins et al (1982)] Ethyl acetate (EtOAc) Saturated NaCl aqueous solution (brine) Magnesium sulfate (MgSO 4 ) Silica gel (230-400 mesh, Merck) Methanol (MeOH) Chloroform (CHCl 3 ) 2-Amino-5-bromopyrimidine [A*-Br; prepared according to the procedure described in Paudler and Jovanovic (1983)] Bis(triphenylphosphine)palladium(II) dichloride [PdCl 2 (PPh 3 ) 2 ; Tokyo Chemical Institute] Triethylamine (deoxygenated Et 3 N; bubbled with argon for 10 min prior to use) 10% NaCl aqueous solution (10% NaCl) Potassium carbonate (K 2 CO 3 ) Acetone Dichloromethane (CH 2 Cl 2 ) 2,6-Diamino-5-iodopyrimidine [D*-I; prepared according to the procedure described in Shirato et al, 2015)] 1,1,1,3,3,3-Hexamethyldisilazane [deoxygenated (Me 3 Si) 2 NH, bubbled with argon for 10 min prior to use] Tetrahydrofuran (THF) 1% Citric acid aqueous solution (1% citric acid) 5% Na 2 CO 3 aqueous solution (5% Na 2 CO 3 ) 5-Iodo-1-methylisocytosine [C*-I; prepared according to the procedure described in Wellington et al (2009)] Sodium sulfate (Na 2 SO 4 ) Distilled water 28% Ammonia aqueous solution (conc. NH 4 OH) 5-Iodocytosine [iC*-I; prepared according to the procedure described in Doi et al, 2008 Perform Sonogashira coupling for preparing T*(DMTr)-nucleoside (see Fig.…”

Section: Methodsmentioning

confidence: 99%

“…8. Collect the purified oligomers in several 1.5-mL microcentrifuge tubes, freeze the tubes in liquid nitrogen, then freeze dry by using a freeze dryer, characterize with MALDI-TOF mass spectrometry (the positive or negative ion mode, (Doi et al, 2008;Shirato et al, 2015).…”

Section: Methodsmentioning

confidence: 99%

Synthesis of Nonnatural Oligonucleotides Made Exclusively of Alkynyl C‐Nucleosides with Nonnatural Bases

Chiba

Inoûye

2015

CP Nucleic Acid Chemistry

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This unit describes detailed procedures for the preparation of nonnatural C-nucleosides comprising seven types of nonnatural nucleobases attached to 1'-position of 2'-deoxyribose through an acetylene bond with the β-configuration. In addition, derivatization of these alkynyl C-nucleosides into the corresponding phosphoramidites and the subsequent oligonucleotide synthesis are also presented. The processes are depicted in three parts. The first basic protocol deals with the synthesis of a key intermediate, 5-O-DMTr-protected 1-ethynyl-2-deoxy-β-D-ribofuranoside. The second basic protocol mentions the procedures of the preparation of nonnatural C-nucleosides by a palladium-catalyzed coupling reaction of the ethynyl intermediate and halogen-attached nonnatural nucleobases. The synthetic procedures of the corresponding nonnatural phosporamidites are also described. The third basic protocol presents the solid-phase, automated synthesis of nonnatural oligonucleotides composed exclusively of the nonnatural C-nucleotides.

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“…An analog with pseudouracil connected to the 2′‐position through a propynyl linker ( U W ) is also presented (Figure 1). Artificial genetic systems have previously been introduced where modified nucleobases were attached to the 1′‐position of a 2′‐deoxyribose through an ethynyl linker [33–34] . Altogether, U Z and U W represent two double‐headed nucleoside monomers each exposing a thymine Watson‐Crick face differently within the duplex core compared to that of the original U T monomer.…”

Section: Introductionmentioning

confidence: 99%

“…Artificial genetic systems have previously been introduced where modified nucleobases were attached to the 1'-position of a 2'-deoxyribose through an ethynyl linker. [33][34] Altogether, U Z and U W represent two double-headed nucleoside monomers each exposing a thymine Watson-Crick face differently within the duplex core compared to that of the original U T monomer. Based on the apparently larger space in the 2' • 1' setting allowing for instance purine-purine pairs, we hereby hope to find an alternative to U T that allows stronger binding and/or more specific base pairing.…”

Section: Introductionmentioning

confidence: 99%

Double‐Headed Nucleotides with Non‐Native Nucleobases: Synthesis and Duplex Studies

et al. 2021

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Double-headed nucleotides are DNA building blocks that store, in principle, twice as much information as native nucleotides due to the incorporation of an additional functional nucleobase. Herein, we present the development of two new doubleheaded nucleotides, U W and U Z, featuring a methylene-linked 5aza-7-deazaxanthine (Z) and a propynyl-linked pseudouracil (W), respectively, attached to the 2'-position of arabinouridine. These analogs are evaluated in DNA duplexes for their ability to act as dinucleotides, and the base-pairing specificities of the 2'nucleobases are compared to previous analogues. Although an improved discrimination was observed in the context of a cytosine mismatch using U Z , neither of the two new analogs gave rise to increased overall base-pairing fidelity possibly due to the formation of stable wobble pairs. Furthermore, we present an improved synthetic strategy for the preparation of the corresponding diaminopurine analog (U D), in which the key fluoro-to-amino substitution is achieved post-synthetically to avoid the use of doubly protected diaminopurines and complicated deprotections.

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A firmly hybridizable, DNA-like architecture with DAD/ADA- and ADD/DAA-type nonnatural base pairs as an extracellular genetic candidate

Cited by 9 publications

References 43 publications

Multifacial Recognition in Binary and Ternary Cocrystals from 5-Halouracil and Aminoazine Derivatives

Multifacial Recognition in Binary and Ternary Cocrystals from 5-Halouracil and Aminoazine Derivatives

Synthesis of Nonnatural Oligonucleotides Made Exclusively of Alkynyl C‐Nucleosides with Nonnatural Bases

Double‐Headed Nucleotides with Non‐Native Nucleobases: Synthesis and Duplex Studies

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