N2‐Substituted 2′‐Deoxyguanosine Triphosphate Derivatives as Selective Substrates for Human DNA Polymerase κ

N²‐Alkyl‐2′‐deoxyguanosine triphosphate (N²‐alkyl‐dGTP) derivatives with methyl, butyl, benzyl, or 4‐ethynylbenzyl substituents were prepared and tested as substrates for human DNA polymerases. N²‐Benzyl‐dGTP was equal to dGTP as a substrate for DNA polymerase κ (pol κ), but was a poor substrate for pols β, δ, η, ι, or ν. In vivo reactivity was evaluated through incubation of N²‐4‐ethynylbenzyl‐dG with wild‐type and pol κ deficient mouse embryonic fibroblasts. CuAAC reaction with 5(6)‐FAM‐azide demonstrated that only cells containing pol κ were able to incorporate N²‐4‐ethynylbenzyl‐dG into the nucleus. This is the first instance of a Y‐family‐polymerase‐specific dNTP, and this method could be used to probe the activity of pol κ in vivo.     

R‐RAFT approach for the polymerization of N‐isopropylacrylamide with a star poly(ε‐caprolactone) core

Reversible addition‐fragmentation chain transfer (RAFT) polymerization is a more robust and versatile approach than other living free radical polymerization methods, providing a reactive thiocarbonylthio end group. A series of well‐defined star diblock [poly(ε‐caprolactone)‐b‐poly(N‐isopropylacrylamide)]₄ (SPCLNIP) copolymers were synthesized by R‐RAFT polymerization of N‐isopropylacrylamide (NIPAAm) using [PCL‐DDAT]₄ (SPCL‐DDAT) as a star macro‐RAFT agent (DDAT: S‐1‐dodecyl‐S′‐(α, α′‐dimethyl‐α″‐acetic acid) trithiocarbonate). The R‐RAFT polymerization showed a controlled/“living” character, proceeding with pseudo‐first‐order kinetics. All these star polymers with different molecular weights exhibited narrow molecular weight distributions of less than 1.2. The effect of polymerization temperature and molecular weight of the star macro‐RAFT agent on the polymerization kinetics of NIPAAm monomers was also addressed. Hardly any radical–radical coupling by‐products were detected, while linear side products were kept to a minimum by careful control over polymerization conditions. The trithiocarbonate groups were transferred to polymer chain ends by R‐RAFT polymerization, providing potential possibility of further modification by thiocarbonylthio chemistry. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

Functionalized polymers with metal complexing segments: a simple and high‐yield entry towards 2,2′:6′,2″‐terpyridine‐based oligomers

Williamson type ether reactions were utilized for a high yield reaction of 4′‐chloro‐2,2′:6′,2″‐terpyridine with α,ω‐dihydroxy‐functionalized poly(ethylene oxide) and poly(oxytetramethylene)s to obtain bis(terpyridine)‐terminated telechelics. The completeness of the functionalization was proven by NMR spectroscopy, GPC and MALDI‐TOF‐MS investigations. The addition of transition metal ions resulted in a polyaddition polymerization leading to the formation of extended metallo‐supramolecular polymers, as proven by UV/VIS spectroscopy titration experiments.     

Stabilization of a Bimolecular Triplex by 3′‐S‐Phosphorothiolate Modifications: An NMR and UV Thermal Melting Investigation

Triplexes formed from oligonucleic acids are key to a number of biological processes. They have attracted attention as molecular biology tools and as a result of their relevance in novel therapeutic strategies. The recognition properties of single‐stranded nucleic acids are also relevant in third‐strand binding. Thus, there has been considerable activity in generating such moieties, referred to as triplex forming oligonucleotides (TFOs). Triplexes, composed of Watson–Crick (W–C) base‐paired DNA duplexes and a Hoogsteen base‐paired RNA strand, are reported to be more thermodynamically stable than those in which the third strand is DNA. Consequently, synthetic efforts have been focused on developing TFOs with RNA‐like structural properties. Here, the structural and stability studies of such a TFO, composed of deoxynucleic acids, but with 3′‐S‐phosphorothiolate (3′‐SP) linkages at two sites is described. The modification results in an increase in triplex melting temperature as determined by UV absorption measurements. ¹H NMR analysis and structure generation for the (hairpin) duplex component and the native and modified triplexes revealed that the double helix is not significantly altered by the major groove binding of either TFO. However, the triplex involving the 3′‐SP modifications is more compact. The 3′‐SP modification was previously shown to stabilise G‐quadruplex and i‐motif structures and therefore is now proposed as a generic solution to stabilising multi‐stranded DNA structures.     

A Facile and Cost‐effective Electroanalytical Strategy for the Quantification of Deoxyguanosine and Deoxyadenosine in Oligonucleotides Using Screen‐printed Graphite Electrodes

The development of electroanalytical methods for the detection and quantification of nucleotides in DNA offers vital implications in assessing the degree of oxidation or epigenetic modification in DNA. Unfortunately, the electrochemical response of oligonucleotides is strongly influenced by the size, composition and nucleic base sequence. In this article, an optimized analytical procedure for the enzymatically breakdown of the oligonucleotides to their corresponding nucleotides for the evaluation of the electrochemical response through the use of square wave voltammetry (SWV) is presented. Enzymatic digestion of oligonucleotides has been optimized in terms of buffer composition, digestion time, strategy for stopping the enzymatic reaction and filtration requirement for enzyme removal, and then compared to an established protocol. Under the optimized protocol SWV response of a number of untreated and enzymatically digested six‐mer oligonucleotides, namely 5′‐GGGGGG‐3′, 5′‐AAAAAA‐3′, 5′‐CGCGCG‐3′ and 5′‐AAACGC‐3′ have been analysed, providing a higher sensitivity for the determination of guanosine and adenosine monophosphate species under digestion conditions with a more facile and cost effective procedure. The novel strategy for the enzymatically treated oligonucleotides in combination with the SWV response provides a proof of principle for feasible applications in the diagnosis of methylated guanosine in DNA as a potential biomarker due to its relation with cancer.     

A simple methodology for the synthesis of heterotelechelic protein–polymer–biomolecule conjugates

A synthetic protocol for the preparation of hetero‐biofunctional protein–polymer conjugates is described. A chain transfer agent, S,S‐bis (α,α′‐dimethyl‐α″‐acetic acid) trithiocarbonate was functionalized with α,ω‐pyridyl disulfide (PDS) groups, Subsequently, one of the PDS groups was covalently attached to bovine serum albumin (BSA) at the specific free thiol group on the cysteine residue through a disulfide linkage. The second PDS group remained intact, as it was found to be inaccessible to further BSA functionalization. The BSA‐macro‐reversible addition‐fragmentation chain transfer (RAFT) agent was then used to prepare BSA‐polymer conjugates via in situ polymerization of oligo (ethyleneglycol) acrylate and N‐(2‐hydroxypropyl) methacrylamide using an ambient temperature initiator, 4,4′‐azobis [2,9‐imidazolin‐2‐ethyl)propane] dihydrochloride in an aqueous medium. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS‐PAGE) confirmed that the in situ polymerization occurred at the protein surface where the RAFT agent was attached and the molecular weights of the BSA–polymer conjugates were found to increase concomitantly with monomer conversion and polymerization time. After polymerization the remaining terminal PDS groups were then utilized to attach thiocholesterol and a flurophore, rhodamine B to the protein–polymer conjugates via disulfide coupling. UV–Vis and fluorescence analyses revealed that ～80% of the protein conjugates were found to retain integral PDS end groups for further attachment to free thiol‐tethered precursors. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 1399–1405, 2010     

Selenium‐Doped Carbon Quantum Dots for Free‐Radical Scavenging

Heteroatom doping is an effective way to adjust the fluorescent properties of carbon quantum dots. However, selenium‐doped carbon dots have rarely been reported, even though selenium has unique chemical properties such as redox‐responsive properties owing to its special electronegativity. Herein, a facile and high‐output strategy to fabricate selenium‐doped carbon quantum dots (Se‐CQDs) with green fluorescence (quantum yield 7.6 %) is developed through the hydrothermal treatment of selenocystine under mild conditions. Selenium heteroatoms endow the Se‐CQDs with redox‐dependent reversible fluorescence. Furthermore, free radicals such as ^.OH can be effectively scavenged by the Se‐CQDs. Once Se‐CQDs are internalized into cells, harmful high levels of reactive oxygen species (ROS) in the cells are decreased. This property makes the Se‐CQDs capable of protecting biosystems from oxidative stress.     

Regioselective synthesis of symmetrical pyridyl selenium compounds by bromine–magnesium exchange of bromopyridines using isopropyl magnesium chloride: X‐ray crystal structure of 2,2′,5,5′‐tetrabromo‐3,3′‐dipyridyldiselenide

2,2′‐Dipyridyl‐3,3′‐dipyridyl,5,5′‐dipyridyl‐diselenides have been synthesized by a convenient method employing non‐cryogenic conditions. Various bromopyridines (2‐Bromopyridine, 2,5‐dibromopyridines and 2,3,5‐Tribromopyridines) undergo selective monobromine–magnesium exchange to yield the corresponding pyridyl magnesium chlorides at room temperature upon treatment with ⁱPrMgCl. The resulting pyridyl magnesium chloride is quenched with elemental selenium, which upon further oxidation affords the above diselenides in good yields. The compounds prepared using this methodology have been characterized by elemental analysis, IR, NMR (¹H, ¹³C, ⁷⁷Se) and mass spectral analysis. The molecular structure of 2,2′,5,5′‐Tetrabromo‐3,3′‐dipyridyldiselenide has been established by single‐crystal X‐ray diffraction analysis. It exists as a dimeric form due to the non‐bonding interactions between the selenium of one pyridine moiety and the hydrogen of the other. Copyright © 2004 John Wiley & Sons, Ltd.     

A microchip electrophoretic assay for DNA methyltransferase activity based on methylation‐sensitive endonuclease DpnⅡ

DNA methylation is a significant epigenetic modification and the methods for the detection of DNA methyltransferase (MTase) activity are important due to aberrant methylation closely related to the occurrence of cancer. In this study, a simple and rapid microchip electrophoresis (ME) coupled with LED‐induced fluorescence (LEDIF) method was presented for the detection of Dam MTase activity. This strategy was based on methylation‐sensitive endonuclease DpnⅡ which could recognize the same specific site 5′‐GATC‐3′ with Dam MTase in double‐stranded DNA (dsDNA). The adenines in the specific site could be methylated by Dam MTase, then the special site could not be digested by DpnⅡ. Both methylated dsDNA and unmethylated dsDNA could be analyzed by ME‐LEDIF after stained by SYBR gold. The results showed the fluorescence intensities of methylated dsDNA were directly proportional to Dam MTase activities in the range of 0.5–20 U/mL with a detection limit of 0.12 U/mL. Furthermore, the method could successfully be applied to evaluation experiments of Dam MTase inhibitors. The results confirmed the ME‐LEDIF method is a promising approach for inhibitors screening of DNA MTase and development of anticancer drugs     

An efficient synthetic route to well‐defined theta‐shaped copolymers

A series of well‐defined θ‐shaped copolymers composed of polystyrene (PS) and poly(ε‐caprolactone) (PCL) with controlled molecular weight and narrow molecular weight distribution have been successfully synthesized without any purification procedure by the combination of atom transfer radical polymerization (ATRP), ring‐opening polymerization (ROP), and the “click” chemistry. The synthetic process involves two steps: (1) synthesis of AB₂ miktoarm star copolymers, which contain one PCL chain terminated with two acetylene groups and two PS chains with two azido groups at their one end, (α,α′‐diacetylene‐PCL) (ω‐azido‐PS)₂, by ROP, ATRP, and the terminal group transformation; (2) intramolecular cyclization of AB₂ miktoarm star copolymers to produce well‐defined pure θ‐shaped copolymers using “click” chemistry under high dilution. The ¹H NMR, FTIR, and gel permeation chromatography techniques were applied to characterize the chemical structures of the resultant intermediates and the target polymers. Their thermal behavior was investigated by DSC. The mobility decrease of PCL chain across PS ring in the theta‐shaped copolymers restricts the crystallization ability of PCL segment. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 2620–2630, 2009     

Selectivity in anionic and cationic ring‐opening polymerizations of tetramethyl‐1‐(3′‐trifluoromethylphenyl)‐1‐phenylcyclotrisiloxane and tetramethyl‐1‐[3′,5′‐bis(trifluoromethyl)phenyl]‐1‐phenylcyclotrisiloxane

Anionic and cationic ring‐opening polymerizations of two novel cyclotrisiloxanes, tetramethyl‐1‐(3′‐trifluoromethylphenyl)‐1‐phenylcyclotrisiloxane ( I ) and tetramethyl‐1‐[3′,5′‐bis(trifluoromethyl)phenyl]‐1‐phenylcyclotrisiloxane ( II ), are reported. Anionic ring‐opening polymerization of I or II leads to copolymers with highly regular microstructures. Copolymers obtained by cationic polymerizations of I or II , initiated by triflic acid, have less regular microstructures characteristic of chemoselective polymerization processes. The composition and microstructure of copolymers have been characterized by ¹H and ²⁹Si‐NMR, the molecular weight distributions by GPC, and the thermal properties by DSC and TGA. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5235–5243, 2004     

“Printing” DNA Strand Patterns on Small Molecules with Control of Valency,Directionality, and Sequence

The incorporation of synthetic molecules as corner units in DNA structures has been of interest over the last two decades. In this work, we present a facile method for generating branched small molecule‐DNA hybrids with controllable valency, different sequences, and directionalities (5′–3′) using a “printing” process from a simple 3‐way junction structure. We also show that the DNA‐imprinted small molecule can be extended asymmetrically using polymerase chain reaction (PCR) and can be replicated chemically. This strategy provides opportunities to achieve new structural motifs in DNA nanotechnology and introduce new functionalities to DNA nanostructures.     

Synthesis of Some Novel Phenyl Substituted Oxothiazolidin- 1’’,3’’,4’’-thiadiazolo-[3’,4’-b]thiazoline of 3β-Substituted Cholestane

Three title compounds 4a—4c have been synthesized by the cyclodehydration of 1’-benzylidine-4’-(3β-substituted-5α-cholestane-6-yl)thiosemicarbazones 2a—2c with thioglycolic acid followed by the treatment with cold conc. H2SO4 in dioxane. The compounds 2a—2c were prepared by condensation of 3β-substituted-5α-cholestan- 6-one-thiosemicarbazones 1a—1c with benzaldehyde. These thiosemicarbazones 1a—1c were obtained by the reaction of corresponding 3β-substituted-5α-cholestan-6-ones with thiosemicarbazide in the presence of few drops of conc. HCl in methanol. The structures of the products have been established on the basis of their elemental, analytical and spectral data.     

A cationic dye triplet as a unique "glue" that can connect fully matched termini of DNA duplexes

In this study, we propose that three consecutive cationic p‐methylstilbazoles tethered on D ‐threoninols ( Z residues) at 5′ termini act as a unique “glue” connecting DNA duplexes by their interstrand cluster formation. Interstrand clustering of p‐methylstilbazoles ( ZZZ triplets) induces narrowing and hypsochromic shift of bands at 350 nm, which can be assigned to the absorption of p‐methylstilbazole. However, single‐stranded DNA conjugates involving a ZZZ triplet at the 5′ terminus of 8‐mer native nucleotides is found not to induce such large spectral changes, which implies that the intrinsic self‐assembling property of ZZZ triplets is weak. Interestingly, when this conjugate is hybridized with a complementary 8‐mer native oligonucleotide, a remarkable spectral change is observed, indicating the dimerization of a duplex through the interstrand clustering of ZZZ triplets. Dimerization of the duplex is also evidenced by cold‐spray ionization mass spectrometry. This interstrand clustering is observed only when a ZZZ triplet is tethered to a 5′ rather than 3′ terminus. Furthermore, the stability of the interstrand cluster increases by increasing the number of nucleobases of the DNA portion, and when mismatched base pairs are incorporated or when a base next to the Z residue is deleted, the stability substantially drops. When we apply the ZZZ triplet to the formation of a nanowire using two complementary DNA conjugates, each of which has a ZZZ triplet at the 5′ termini as overhang, we demonstrate the successful formation of a nanowire by native PAGE analysis. Since native sticky ends that have three nucleotides do not serve as “glue”, ZZZ triplets with their unique glue‐like properties are prime candidates for constructing DNA‐based nanoarchitectures.     

Selenium‐substituted carbonates as mediators for controlled radical polymerization

A series of selenium‐substituted carbonates, S,Se‐dibenzyl dithioselenocarbonate (DTSC), S,Se‐dibenzyl thiodiselenocarbonate (TDSC), and Se,Se‐dibenzyl triselenocarbonate (TSC), were synthesized and used as mediators in radical polymerization. The results indicate that these selenium‐substituted carbonates can control the polymerization of styrene (St) and methyl acrylate, as evidenced by the number‐average molecular weight that increased linearly with the monomer conversion, molecular weights that agreed well with the predicted values, and successful chain extensions. The treatment of the resultant polystyrene by hydrogen peroxide generated polymers with approximately half‐reduced molecular weights, and the absence of carbonate groups and vinyl double bond‐terminated chain ends. The polymerization with these selenium‐substituted carbonates was the same polymerization mechanism as their analogue, the widely used S,S‐dibenzyl trithiocarbonate. This work provided a flexible protocol to incorporate selenium into the polymer chain backbone. Specifically, the treatment of these polymers by oxidation produced “clickable” vinyl‐terminated chain ends, which provided possibilities for further functionalization, for example, via a thiol‐ene click reaction. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 2606–2613     

Preparation of High‐Loading Polymer Supports by Polymerization Reaction Useful for Oligonucleotide Synthesis

A simple protocol based on polymerization reactions has been developed for the preparation of high‐loading polymer supports, useful for large‐scale synthesis of oligonucleotides. Polymer supports of different pore sizes have been employed in the present investigation to improve the functional‐group density on them. A ten‐ to twelvefold increase in the loading of the functional groups, after the polymerization reaction, has been observed. The support was then used in the subsequent reaction to attach the leader nucleoside to obtain fully functionalized supports 6a – 6c by oligonucleotide synthesis in an automated DNA synthesizer. The aminoalkylated‐supports 5a – 5c were directly employed for the synthesis of oligonucleotide 3′‐phosphates. The oligonucleotides and oligonucleotide 3′‐phosphates synthesized on these supports were compared with the corresponding standard oligomers with respect to their retention time on HPLC. These were further characterized on MALDI‐TOF mass spectrometry.     

The amplified circularly polarized luminescence emission response of chiral 1,1′‐binaphthol‐based polymers via Zn(II)‐coordination fluorescence enhancement

Two kinds of chiral 1,1′‐binaphthol (BINOL)‐based polymer enantiomers were designed and synthesized by the polymerization of 5,5′‐((2,2′‐bis (octyloxy)‐[1,1′‐binaphthalene]‐3,3′‐diyl)bis(ethyne‐2,1‐diyl))bis(2‐hydroxybenzaldehyde) ( M1 ) with alkyl diamine ( M2 ) via nucleophilic addition–elimination reaction. The resulting chiral polymers can exhibit mirror image cotton effects either in the absence or in the presence of Zn²⁺ ion. Almost no fluorescence or circularly polarized luminescence (CPL) emission could be observed for two chiral BINOL‐based polymer enantiomers in the absence of Zn²⁺. Interestingly, the chiral polymers can show strong fluorescence and CPL response signals upon the addition of Zn²⁺, which can be attributed to Zn²⁺‐coordination fluorescence enhancement effect. This work can develop a new strategy on the design of the novel CPL materials via metal‐coordination reaction. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2018 , 56, 1282–1288     

“Printing” DNA Strand Patterns on Small Molecules with Control of Valency,Directionality, and Sequence

The incorporation of synthetic molecules as corner units in DNA structures has been of interest over the last two decades. In this work, we present a facile method for generating branched small molecule‐DNA hybrids with controllable valency, different sequences, and directionalities (5′–3′) using a “printing” process from a simple 3‐way junction structure. We also show that the DNA‐imprinted small molecule can be extended asymmetrically using polymerase chain reaction (PCR) and can be replicated chemically. This strategy provides opportunities to achieve new structural motifs in DNA nanotechnology and introduce new functionalities to DNA nanostructures.