A Dinuclear Mercury(II)‐Mediated Base Pair in DNA

The first dinuclear metal‐mediated base pair containing divalent metal ions has been prepared. A combination of the neutral bis(monodentate) purine derivative 1,N⁶‐ethenoadenine (ϵA), which preferentially binds two metal ions with a parallel alignment of the N−M bonds, and the canonical nucleobase thymine (T), which readily deprotonates in the presence of Hg^II and thereby partially compensates the charge accumulation due to the two closely spaced divalent metal ions, yields the dinuclear T‐Hg^II₂‐ϵA base pair. This metal‐mediated base pair stabilizes the DNA oligonucleotide duplex as shown by an increase of 8 °C in its melting temperature. Formation of the base pair was demonstrated by temperature‐dependent UV spectroscopy as well as by titration experiments monitored by UV and CD spectroscopy.     

Highly Stable Double‐Stranded DNA Containing Sequential Silver(I)‐Mediated 7‐Deazaadenine/Thymine Watson–Crick Base Pairs

The oligonucleotide d(TX)₉, which consists of an octadecamer sequence with alternating non‐canonical 7‐deazaadenine (X) and canonical thymine (T) as the nucleobases, was synthesized and shown to hybridize into double‐stranded DNA through the formation of hydrogen‐bonded Watson–Crick base pairs. dsDNA with metal‐mediated base pairs was then obtained by selectively replacing W‐C hydrogen bonds by coordination bonds to central silver(I) ions. The oligonucleotide I adopts a duplex structure in the absence of Ag⁺ ions, and its stability is significantly enhanced in the presence of Ag⁺ ions while its double‐helix structure is retained. Temperature‐dependent UV spectroscopy, circular dichroism spectroscopy, and ESI mass spectrometry were used to confirm the selective formation of the silver(I)‐mediated base pairs. This strategy could become useful for preparing stable metallo‐DNA‐based nanostructures.     

Stable Copper(I)‐Mediated Base Pairing in DNA

A GNA (glycol nucleic acid) functionalized nucleoside analogue containing the artificial nucleobase 1H‐imidazo[4,5‐f][1,10]phenanthroline (P) was used to form a copper(I)‐mediated base pair within a DNA duplex. The geometrical constraints imposed by the artificial nucleobase play a pivotal role in this unprecedented stabilization of copper(I) in aqueous medium via metal‐mediated base pairing. The formation of the copper(I)‐mediated base pair was investigated by temperature‐dependent UV spectroscopy and CD spectroscopy. The metal‐mediated base pair stabilizes the DNA oligonucleotide duplex by 23 °C. A redox chemistry approach confirmed that this base pair formation was due to the incorporation of copper(I) into the duplex. This first report of a copper(I)‐mediated base pair adds metal‐based diversity to the field and consequently opens up the range of possible applications of metal‐modified nucleic acids.     

A Family of “Click” Nucleosides for Metal‐Mediated Base Pairing: Unravelling the Principles of Highly Stabilizing Metal‐Mediated Base Pairs

A family of artificial nucleosides has been developed by applying the Cu^I‐catalyzed Huisgen 1,3‐dipolar cycloaddition. Starting from 2‐deoxy‐β‐D ‐glycosyl azide as a common precursor, three bidentate nucleosides have been synthesized. The 1,2,3‐triazole involved in all three nucleobases is complemented by 1,2,4‐triazole ( TriTri ), pyrazole ( TriPyr ), or pyridine ( TriPy ). Molecular structures of two metal complexes indicate that metal‐mediated base pairs of TriPyr may not be fully planar. An investigation of DNA oligonucleotide duplexes comprising the new “click” nucleosides showed that they can bind Ag^I to form metal‐mediated base pairs. In particular the mispair formed from TriPy and the previously established imidazole nucleoside is significantly stabilized in the presence of Ag^I. A comparison of different oligonucleotide sequences allowed the determination of general factors involved in the stabilization of nucleic acids duplexes with metal‐mediated base pairs.     

Bifacial Base‐Pairing Behaviors of 5‐Hydroxyuracil DNA Bases through Hydrogen Bonding and Metal Coordination

A novel bifacial ligand‐bearing nucleobase, 5‐hydroxyuracil ( U^OH ), which forms both a hydrogen‐bonded base pair ( U^OH –A) and a metal‐mediated base pair ( U^OH –M– U^OH ) has been developed. The U^OH –M– U^OH base pairs were quantitatively formed in the presence of lanthanide ions such as Gd^III when U^OH – U^OH pairs were consecutively incorporated into DNA duplexes. This result established metal‐assisted duplex stabilization as well as DNA‐templated assembly of lanthanide ions. Notably, a duplex possessing U^OH –A base pairs was destabilized by addition of Gd^III ions. This observation suggests that the hybridization behaviors of the U^OH ‐containing DNA strands are altered by metal complexation. Thus, the U^OH nucleobase with a bifacial base‐pairing property holds great promise as a component for metal‐responsive DNA materials.     

Sequence‐Dependent Duplex Stabilization upon Formation of a Metal‐Mediated Base Pair

An artificial nucleoside surrogate with 1H‐imidazo[4,5‐f][1,10]phenanthroline ( P ) acting as an aglycone has been introduced into DNA oligonucleotide duplexes. This nucleoside surrogate can act as a bidentate ligand, and so is useful in the context of metal‐mediated base pairs. Several duplexes involving a hetero base pair with an imidazole nucleoside have been investigated. The stability of DNA duplexes incorporating the respective Ag^I‐mediated base pairs strongly depends on the sequence context. Quantum mechanical/molecular mechanical (QM/MM) calculations have been performed in order to gain insight into the factors determining this sequence dependence. The results indicated that, in addition to the stabilizing effect that results from the formation of coordinative bonds, destabilizing effects may occur when the artificial base pair does not fit optimally into the surrounding B‐DNA duplex.     

Structure Determination of an AgI‐Mediated Cytosine–Cytosine Base Pair within DNA Duplex in Solution with 1H/15N/109Ag NMR Spectroscopy

The structure of an Ag^I‐mediated cytosine–cytosine base pair, C–Ag^I–C, was determined with NMR spectroscopy in solution. The observation of 1‐bond ¹⁵N‐¹⁰⁹Ag J‐coupling (¹J(¹⁵N,¹⁰⁹Ag): 83 and 84 Hz) recorded within the C–Ag^I–C base pair evidenced the N3–Ag^I–N3 linkage in C–Ag^I–C. The triplet resonances of the N4 atoms in C–Ag^I–C demonstrated that each exocyclic N4 atom exists as an amino group (?NH₂), and any isomerization and/or N4–Ag^I bonding can be excluded. The 3D structure of Ag^I–DNA complex determined with NOEs was classified as a B‐form conformation with a notable propeller twist of C–Ag^I–C (?18.3±3.0°). The ¹⁰⁹Ag NMR chemical shift of C‐Ag^I‐C was recorded for cytidine/Ag^I complex (δ(¹⁰⁹Ag): 442 ppm) to completed full NMR characterization of the metal linkage. The structural interpretation of NMR data with quantum mechanical calculations corroborated the structure of the C–Ag^I–C base pair.     

Ag(I) ion mediated formation of a C-A mispair by DNA polymerases

Silver turns up the A-C: In the presence of Ag(I) ions, a DNA polymerase incorporated deoxyadenosine (from dATP) at the site opposite cytosine in the template strand to afford the full-length product (see scheme), meaning that DNA polymerases prefer a C-Ag(I)-A base pair to the more thermodynamically stable C-Ag(I)-C base pair.     

High‐Resolution Crystal Structure of a Silver(I)–RNA Hybrid Duplex Containing Watson–Crick‐like CSilver(I)C Metallo‐Base Pairs

Metallo‐base pairs have been extensively studied for applications in nucleic acid‐based nanodevices and genetic code expansion. Metallo‐base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo‐base pairs can be easily prepared from commercially available sources. Previously, we have reported a crystal structure of a DNA duplex containing T? Hg^II? T base pairs. Herein, we have determined a high‐resolution crystal structure of the second natural metallo‐base pair between pyrimidine bases C? Ag^I? C formed in an RNA duplex. One Ag^I occupies the center between two cytosines and forms a C? Ag^I? C base pair through N3? Ag^I? N3 linear coordination. The C? Ag^I? C base pair formation does not disturb the standard A‐form conformation of RNA. Since the C? Ag^I? C base pair is structurally similar to the canonical Watson–Crick base pairs, it can be a useful building block for structure‐based design and fabrication of nucleic acid‐based nanodevices.     

2,11-二硫代[3.3]二聚对二甲苯与线性氟代二羧酸银之配位聚合物的合成

本文主要描述了由配体2,11-二硫代[3.3]二聚对二甲苯与线性氟代二羧酸银反应制得的三个银配合物的结构。这些配合物的结构因氟代二羧酸银的不同,差别也很大。配体2,11-二硫代[3.3]二聚对二甲苯与氟代丁二酸银反应得到的配合物1是一维链状结构;将银盐换成氟代戊二酸银则获得了三维立体结构的配合物2;若使用氟代己二酸银,则得到了二维多孔的配合物3。在多孔配合物3中,每个孔中容纳了两个客体三甲苯分子,在150℃时这些客体分子可被完全脱除。     

Metal‐Ion Selectivity of Chemically Modified Uracil Pairs in DNA Duplexes

DNA duplexes containing 5‐modified uracil pairs (5‐bromo, 5‐fluoro, and 5‐cyanouracil) bind selectivity to metal ions. Their selectivity is sensitive to the pH value of the solution (see picture), as the acidities of the modified uracil bases vary according to the electron‐withdrawing properties of the substituents.

     

Influence of the Absolute Configuration of NPE‐Caged Cytosine on DNA Single Base Pair Stability

Photolabile protecting groups are a versatile tool to trigger reactions by light irradiation. In this study, we have investigated the influence of the absolute configuration of the 1‐(2‐nitrophenyl)ethyl (NPE) cage group on a 15‐base‐pair duplex DNA. Using UV melting, we determined the global stability of the unmodified and the selectively (S)‐ and (R)‐NPE‐modified DNA sequences, respectively. We observe a differently destabilizing effect for the two NPE stereoisomers on the global stability. Analysis of the temperature dependence of imino proton exchange rates measured by NMR spectroscopy reveals that this effect can be attributed to decreased base pair stabilities of the caged and the 3′‐neighbouring base pair, respectively. Furthermore, our NMR based structural models of the modified duplexes provide a structural basis for the distinct effect of the (S)‐ and the (R)‐NPE group.     

Silver Ions in Non‐canonical DNA Base Pairs: Metal‐Mediated Mismatch Stabilization of 2′‐Deoxyadenosine and 7‐Deazapurine Derivatives with 2′‐Deoxycytidine and 2′‐Deoxyguanosine

Novel silver‐mediated dA?dC, dA*?dC, and dA*?dG base pairs were formed in a natural DNA double helix environment (dA* denotes 7‐deaza‐dA, 7‐deaza‐7‐iodo‐dA, and 7‐cyclopropyl‐7‐deaza‐dA). 7‐Deazapurine nucleosides enforce silver ion binding and direct metal‐mediated base pair formation to their Watson–Crick face. New phosphoramidites were prepared from 7‐deaza‐dA, 7‐deaza‐7‐iodo‐dA, and 7‐cyclopropyl‐7‐deaza‐dA, which contain labile isobutyryl protecting groups. Solid‐phase synthesis furnished oligonucleotides that contain mismatches in near central positions. Increased thermal stabilities (higher T_m values) were observed for oligonucleotide duplexes with non‐canonical dA*?dC and dA?dC pairs in the presence of silver ions. The stability of the silver‐mediated base pairs was pH dependent. Silver ion binding was not observed for the dA?dG mismatch but took place when mismatches were formed between 7‐deazaadenine and guanine. The specific binding of silver ions was confirmed by stoichiometric UV titration experiments, which proved that one silver ion is captured by one mismatch. The stability increase of canonical DNA mismatches might have an impact on cellular DNA repair.     

A Simple and Highly Effective Ligand System for the Copper(I)‐Mediated Assembly of Rotaxanes

A [2]rotaxane was produced through the assembly of a picolinaldehyde, an amine, and a bipyridine macrocycle around a Cu^I template by imine bond formation in close‐to‐quantitative yield. An analogous [3]rotaxane is obtained in excellent yield by replacing the amine with a diamine, thus showing the suitability of the system for the construction of higher order interlocked structures. The rotaxanes are formed within a few minutes simply through mixing the components in solution at room temperature and they can be isolated through removal of the solvent or precipitation.     

Redox Sorption and Recovery of Silver Ions as Silver Nanocrystals on Poly(aniline‐co‐5‐sulfo‐2‐anisidine) Nanosorbents

Poly[aniline(AN)‐co‐5‐sulfo‐2‐anisidine(SA)] nanograins with rough and porous structure demonstrate ultrastrong adsorption and highly efficient recovery of silver ions. The effects of five key factors—AN/SA ratio, Ag^I concentration, sorption time, ultrasonic treatment, and coexisting ions—on Ag^I adsorbability were optimized, and AN/SA (50/50) copolymer nanograins were found to exhibit much stronger Ag^I adsorption than polyaniline and all other reported sorbents. The maximal Ag^I sorption capacity of up to 2034 mg g^?1 (18.86 mmol g^?1) is the highest thus far and also much higher than the maximal Hg‐ion sorption capacity (10.28 mmol g^?1). Especially at ≤2 mM Ag^I, the nanosorbents exhibit ≥99.98 % adsorptivity, and thus achieve almost complete Ag^I sorption. The sorption fits the Langmuir isotherm well and follows pseudo‐second‐order kinetics. Studies by IR, UV/Vis, X‐ray diffraction, polarizing microscopy, centrifugation, thermogravimetry, and conductivity techniques showed that Ag^I sorption occurs by a redox mechanism mainly involving reduction of Ag^I to separable silver nanocrystals, chelation between Ag^I and ? NH? /? N?/? NH₂/ ? SO₃H/? OCH₃, and ion exchange between Ag^I and H⁺ on ? SO₃^?H⁺. Competitive sorption of Ag^I with coexisting Hg, Pb, Cu, Fe, Al, K, and Na ions was systematically investigated. In particular, the copolymer nanoparticles bearing many functional groups on their rough and porous surface can be directly used to recover and separate precious silver nanocrystals from practical Ag^I wastewaters containing Fe, Al, K, and Na ions from Kodak Studio. The nanograins have great application potential in the noble metals industry, resource reuse, wastewater treatment, and functional hybrid nanocomposites.