Artificial metallo-DNA: a bio-inspired approach to metal array programming

Development of a novel carboxamide-based off–on switch fluorescence sensor: Hg2+, Zn2+ and Cd2+

Here, the carboxamide ligand N-(thiazole-2-yl) picolinamide (L) was synthesized in an ionic liquid tetrabutylammonium bromide (TBAB) as the benign reaction medium.

Role of the backbone of nucleic acids in the stability of Hg2+-mediated canonical base pairs and thymine–thymine mispair: a DFT study

Metal-mediated base pairs have attracted attention in nucleic acid research and molecular devices. Herein, we report a systematic computational study on Hg²⁺-mediated base pairs with canonical and TT mispair dimers. The computed results revealed that the model _DTT_D (thymine–thymine with DNA backbone) mispair is more energetically favored than the canonical base pairs. The _DTTTT_D mispair dimer is more energetically stable by ∼36.0 kcal mol⁻¹ than the corresponding canonical _DATGC_D base pairs. The Hg⋯Hg metallophilic interaction was observed with the _DTTTT_D mispair and not the canonical base pairs. The _DATGC_D (adenine: thymine, guanine: cytosine) base pairs were significantly perturbed upon interaction with the mercury ion; however, the TTTT mispairs were aligned upon interaction with the Hg²⁺ ion. The _DTTTT_D mispair adopts a B-type conformation with proper alignment of its nucleobases along the axis. The MESP calculations showed a larger V_min value for the interacting nitrogen centers of the thymine nucleobase, supporting its stronger binding with the Hg²⁺ ion compared to the other nucleobases. The role of the backbone is crucial in nucleic acids to determine many useful properties, and PNAs have been exploited extensively in the literature. Thus, this study was further extended to metal-mediated PNA-containing dimer mispairs such as _DTTTT_P (thymine–thymine dimer model with hybrid DNA and PNA backbone) and _PTTTT_P (thymine–thymine dimer model with PNA backbone). The calculated results showed that the _PTTTT_P PNA mispair is thermodynamically more stable than the canonical dimers. The enthalpy calculated for _DTTTT_D and _PTTTT_P at the B3LYP-D3/6-31G* level of theory showed that _PTTTT_P is ∼3.0 kcal mol⁻¹ more stable than _DTTTT_D. The metallophilic interaction of Hg²⁺ ions in the _PTTTT_P mispair was not observed; however, the metal ions interact with the nitrogen of the thymine bases, presumably enhancing the stability of this mispair by strong electrostatic interactions. These interactions arise due to the P-type conformations of PNAs, which lack metallophilic interactions between the metal ions and can adopt a wider and more unwounded helix. The interaction of the mispair dimers with the explicit water molecules also showed a similar stability trend to that observed with the implicit solvation model. The metallophilic interaction (Hg⋯Hg) was found to be conserved in _DTTTT_D. The AIM analysis performed for these dimers revealed that the interactions are primarily electrostatic in nature. The UV-vis absorption spectra of the mispair systems calculated at the B3LYP-D3/6-31G* level of theory using the TD-DFT method in the aqueous phase suggested that the absorption maximum is located at a longer wavelength in the case of _PTTTT_P compared to the corresponding _DTTTT_D and can be a signature to identify the formation of metal-mediated nucleic acid systems.

Hg²⁺-mediated PNA–PNA mispair duplex (_PTTTT_P) is more energetically favoured compared to DNA–DNA mispair duplex (_DTTTT_D).

Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications

Hydrogels are crosslinked hydrophilic polymers that can absorb a large amount of water. By their hydrophilic, biocompatible and highly tunable nature, hydrogels can be tailored for applications in bioanalysis and biomedicine. Of particular interest are DNA-based hydrogels owing to the unique features of nucleic acids. Since the discovery of the DNA double helical structure, interest in DNA has expanded beyond its genetic role to applications in nanotechnology and materials science. In particular, DNA-based hydrogels present such remarkable features as stability, flexibility, precise programmability, stimuli-responsive DNA conformations, facile synthesis and modification. Moreover, functional nucleic acids (FNAs) have allowed the construction of hydrogels based on aptamers, DNAzymes, i-motif nanostructures, siRNAs and CpG oligodeoxynucleotides to provide additional molecular recognition, catalytic activities and therapeutic potential, making them key players in biological analysis and biomedical applications. To date, a variety of applications have been demonstrated with FNA-based hydrogels, including biosensing, environmental analysis, controlled drug release, cell adhesion and targeted cancer therapy. In this review, we focus on advances in the development of FNA-based hydrogels, which have fully incorporated both the unique features of FNAs and DNA-based hydrogels. We first introduce different strategies for constructing DNA-based hydrogels. Subsequently, various types of FNAs and the most recent developments of FNA-based hydrogels for bioanalytical and biomedical applications are described with some selected examples. Finally, the review provides an insight into the remaining challenges and future perspectives of FNA-based hydrogels.

Pd(2+)-mediated base pairing in oligonucleotides

Two short glycol nucleic acid (GNA) oligonucleotides, having either a terminal or an intrachain nucleobase replaced by the pyridine-2,6-dicarboxamide chelate of Pd(2+), have been synthesized and their hybridization properties studied by melting temperature measurements. In the termini of a double-stranded oligonucleotide, the Pd(2+) chelates provided dramatic stabilization of the duplex relative to its metal-free counterpart, in all likelihood owing to formation of Pd(2+)-mediated base pairs between pyridine-2,6-dicarboxamide and the opposing nucleobase. In contrast, no stabilization was observed when the Pd(2+) chelate was placed in the middle of the chain. Furthermore, the results could not be reproduced by adding a Pd(2+) salt in situ to the dilute oligonucleotide solutions but the palladated oligonucleotides had to be synthesized and purified prior to the hybridization studies. This behavior, presumably attributable to the relatively slow ligand-exchange reactions of Pd(2+), differs greatly from what is usually observed with more labile metal ions. The present results offer an explanation for the failure of previous attempts to incorporate Pd(2+)-mediated base pairs into oligonucleotides.

Metal-ion-mediated base pairing between natural nucleobases and bidentate 3,5-dimethylpyrazolyl-substituted purine ligands

The potential of three modified purine bases, namely, 6-(3,5-dimethylpyrazol-1-yl)purine, 2-(3,5-dimethylpyrazol-1-yl)hypoxanthine, and 2-(3,5-dimethylpyrazol-1-yl)adenine, for metal-ion-mediated base pairing within an oligonucleotide environment has been investigated. The respective modified nucleosides were incorporated in the middle of 9-mer 2'-O-methyl oligonucleotides and the hybridization of these modified oligonucleotides with their unmodified counterparts studied by UV and CD spectrometry in the absence and presence of Cu(2+) or Zn(2+). All of the modified oligonucleotides formed more stable duplexes in the presence of divalent metal ions than in the absence thereof, but with different preferences for the complementary oligonucleotide. The oligonucleotide incorporating 2-(3,5-dimethylpyrazol-1-yl)hypoxanthine readily accepted any of the natural nucleobases opposite to this modified base regardless of whether Cu(2+) or Zn(2+) was used as the bridging metal ion. The other two oligonucleotides, on the other hand, were much more discriminating, exhibiting markedly elevated Tm values only in the presence of Cu(2+) and only when certain natural nucleobases were paired with the modified one. The origin of the selectivity (or promiscuity) of the metal-ion-mediated base pairing is discussed in terms of the ability of the modified nucleobases, as well as their natural counterparts, to serve as anionic ligands.

Reversible metal-dependent destabilization and stabilization of a stem-chelate-loop probe binding to an unmodified DNA target

Herein, we report the discovery of a novel DNA probe with a stem-chelate-loop structure, wherein the stability of the probe-target duplex can be modulated lower or higher using a narrow concentration range of dilute transition metal ions (0.1-10 μM). Oligonucleotide probes containing two terpyridine (TPY) ligands separated by 15 bases of single-stranded DNA, with or without a flanking 5 base self-complementary DNA stem, were tested in thermal transition studies with linear target DNA and varying amounts of ZnCl(2). Without the stem, addition of Zn(2+) resulted only in reversible destabilization of the probe-target duplex, consistent with assembly (up to 1 equiv Zn(2+)) and disassembly (excess Zn(2+)) of the intramolecular Zn(2+)-(TPY)(2) chelate. Surprisingly, probes including both the intramolecular chelate and the stem gave a probe-target duplex that was reversibly destabilized and stabilized upon addition of Zn(2+) by ±5-7 °C, a phenomenon consistent with assembly and then disassembly of the entire stem-Zn(2+)-(TPY)(2) motif, including the DNA stem. Stem-chelate-loop probes containing dipicolylamine (DPA) ligands exhibited no metal-dependent stabilization or destabilization. The stem-Zn(2+)-(TPY)(2) motif is readily introduced with automated synthesis, and may have broad utility in applications where it is desirable to have both upward and downward, reversible metal-dependent control over probe-target stability involving an unmodified DNA target.

Detection of mercury-TpT dinucleotide binding by Raman spectra: a computational study

The Hg(2+) ion stabilizes the thymine-thymine mismatched base pair and provides new ways of creating various DNA structures. Recently, such T-Hg-T binding was detected by the Raman spectroscopy. In this work, detailed differences in vibrational frequencies and Raman intensity patterns in the free TpT dinucleotide and its metal-mediated complex (TpT·Hg)(2) are interpreted on the basis of quantum chemical modeling. The computations verified specific marker Raman bands indicating the effect of mercury binding to DNA. Although the B3LYP functional well-describes the Raman frequencies, a dispersion correction had to be added for all atoms including mercury to obtain realistic geometry of the (TpT·Hg)(2) dimer. Only then, the DFT complex structure agreed with those obtained with the wave function-based MP2 method. The aqueous solvent modeled as a polarizable continuum had a minor effect on the dispersion interaction, but it stabilized conformations of the sugar and phosphate parts. A generalized definition of internal coordinate force field was introduced to monitor covalent bond mechanical strengthening and weakening upon the Hg(2+) binding. Induced vibrational frequency shifts were rationalized in terms of changes in electronic structure. The simulations thus also provided reliable insight into the complex structure and stability.

Metal Ion Chelates as Surrogates of Nucleobases for the Recognition of Nucleic Acid Sequences: The Pd(2+) Complex of 2,6-Bis(3,5-dimethylpyrazol-1-yl)purine Riboside

A 2,6-bis(3,5-dimethylpyrazol-1-yl)purine ribonucleoside has been prepared and incorporated as a conventionally protected phosphoramidite into a 9-mer 2′-O-methyl oligoribonucleotide. According to 1H NMR spectroscopic studies, this nucleoside forms with Pd²⁺ and uridine a ternary complex that is stable at a micromolar concentration range. CD spectroscopic studies on oligonucleotide hybridization, in turn, suggest that the Pd²⁺ chelate of this artificial nucleoside, when incorporated in a 2′-O-methyl-RNA oligomer, is able to recognize thymine within an otherwise complementary DNA strand. The duplex containing thymidine opposite to the artificial nucleoside turned out to be somewhat more resistant to heating than its counterpart containing 2′-deoxycytidine in place of thymidine, but only in the presence of Pd²⁺. According to UV-melting measurements, replacement of 2′-O-methyladenosine with the artificial nucleoside markedly enhances hybridization with a DNA target, irrespective of the identity of the opposite base and the presence of Pd²⁺. With the thymidine containing DNA target, the T_m value is 2–4°C higher than with targets containing any other nucleoside opposite to the artificial nucleoside, but the dependence on Pd²⁺ is much less clear than in the case of the CD studies.

Theoretical investigation on DNA/RNA base pairs mediated by copper, silver, and gold cations

B3LYP density functional based computations were performed in order to characterize the interactions present in some Cu(+), Ag(+), and Au(+) metal ion-mediated DNA and RNA base pairs from both structural and electronic points of view. Examined systems involve as ligands canonical Watson-Crick, Hoogsteen and Wobble base pairs. Two artificial Hoogsteen base pairs were also taken into account. Binding energy values indicate that complexes involving silver cations are less stable than those in which copper or gold are present, and propose a similar behaviour for these two latter ions. The nature of the bond linking metal ions and bases was described by the NBO analysis that suggests metal coordinative interactions to be covalent. An evaluation of the dispersion contributions for the investigated systems was performed with the B3LYP-D3 functional.

Thermodynamic properties of the specific binding between Ag+ ions and C:C mismatched base pairs in duplex DNA

Metal-mediated base pairs formed by the interaction between metal ions and artificial bases in oligonucleotides have been developed for potential applications in nanotechnology. We recently found that a natural C:C mismatched base pair bound to an Ag(+) ion to generate a novel metal-mediated base pair in duplex DNA. Preparation of the novel C-Ag-C base pair involving natural bases is more convenient than that of metal-mediated base pairs involving artificial bases because time-consuming base synthesis is not required. Here, we examined the thermodynamic properties of the binding between the Ag(+) ion and each of single and double C:C mismatched base pair in duplex DNA by isothermal titration calorimetry. The Ag(+) ion specifically bound to the C:C mismatched base pair at a 1:1 molar ratio with 10(6) M(-1) binding constant, which was significantly larger than those for nonspecific metal ion-DNA interactions. The specific binding between the Ag(+) ion and the single C:C mismatched base pair was mainly driven by the positive dehydration entropy change and the negative binding enthalpy change. In the interaction between the Ag(+) ion and each of the consecutive and interrupted double C:C mismatched base pairs, stoichiometric binding at a 1:1 molar ratio was achieved in each step of the first and second Ag(+) binding. The binding affinity for the second Ag(+) binding was similar to that for the first Ag(+) binding. Stoichiometric binding without interference and negative cooperativity may be favorable for aligning multiple Ag(+) ions in duplex DNA for applications of the metal-mediated base pairs in nanotechnology.

Impact of histidine residue on chelating ability of 2'-deoxyriboadenosine

Copper(II) complexes with a new chelator-type nucleoside-histidine modified 2'-deoxyriboadenosine (N-[(9-β-D-2'-deoxyribofuranosylpurin-6-yl)-carbamoyl]histidine) were studied by potentiometric and spectroscopic (UV-visible, CD, EPR) techniques, in conjunction with computer modeling optimization. The ligand can act as bidentate or tridentate depending on pH range. In acidic pH a very stable dimeric complex Cu(2)L(2) predominates with coordination spheres of both metal ions composed of oxygen atoms from carboxylic groups, one oxygen atom from ureido group and two nitrogen atoms derived from purine base and histidine ring. Above pH 5, deprotonation of carbamoyl nitrogens leads to the formation of CuL(2), Cu(2)L(2)H(-1) and Cu(2)L(2)H(-2) species. The CuL(2)H(-1) and CuL(2)H(-2) complexes with three or four nitrogens in Cu(II) coordination sphere have been detected in alkaline medium. Our findings suggest that N-[(9-beta-D-2'-deoxyribofuranosylpurin-6-yl)-carbamoyl]histidine chelates copper(II) ions very efficiently. The resulting complex might be used as an alternative base-pairing mode in which hydrogen-bonded base pairs present in natural DNA are replaced by metal-mediated ones.

Metal-complex/DNA conjugates: a versatile building block for DNA nanoarrays

The use of DNA networks as templates for forming nanoarrays of metallic centres shows an exciting potential to generate addressable nanostructures. Inorganic units can be photoactive, electroactive and/or can possess magnetic and catalytic properties and can adopt different spatial arrangements due to their varied coordination nature. All these properties influence both the structure and function of passive DNA scaffolds and provide DNA nanostructures as a new platform for new materials in emerging technologies, such as nanotechnology, biosensing or biocomputing.

Rapid naked-eye detection of mercury ions based on non-crosslinking aggregation of double-stranded DNA-carrying gold nanoparticles

Colorimetric detection of mercury ions (Hg(2+)) with the naked eye was accomplished within 1 min by a combination of non-crosslinking aggregation of double-stranded DNA-carrying gold nanoparticles and complex formation of thymine-Hg(2+)-thymine.

The crystal structure of non-modified and bipyridine-modified PNA duplexes

Peptide nucleic acid (PNA) is a synthetic analogue of DNA that commonly has an N-aminoethyl glycine backbone. The crystal structures of two PNA duplexes, one containing eight standard nucleobase pairs (GGCATGCC)(2), and the other containing the same nucleobase pairs and a central pair of bipyridine ligands, have been solved with a resolution of 1.22 and 1.10 Å, respectively. The non-modified PNA duplex adopts a P-type helical structure similar to that of previously characterized PNAs. The atomic-level resolution of the structures allowed us to observe for the first time specific modes of interaction between the terminal lysines of the PNA and the backbone and the nucleobases situated in the vicinity of the lysines, which are considered an important factor in the induction of a preferred handedness in PNA duplexes. Our results support the notion that whereas PNA typically adopts a P-type helical structure, its flexibility is relatively high. For example, the base-pair rise in the bipyridine-containing PNA is the largest measured to date in a PNA homoduplex. The two bipyridines bulge out of the duplex and are aligned parallel to the major groove of the PNA. In addition, two bipyridines from adjacent PNA duplexes form a π-stacked pair that relates the duplexes within the crystal. The bulging out of the bipyridines causes bending of the PNA duplex, which is in contrast to the structure previously reported for biphenyl-modified DNA duplexes in solution, where the biphenyls are π stacked with adjacent nucleobase pairs and adopt an intrahelical geometry. This difference shows that relatively small perturbations can significantly impact the relative position of nucleobase analogues in nucleic acid duplexes.

Unnatural nucleosides with unusual base pairing properties

Synthetic modified nucleosides designed to pair in unusual ways with natural nucleobases have many potential applications in biology and biotechnology. This overview lays the foundation for future protocol units on synthesis and application of unnatural bases, with particular emphasis on unnatural base analogs that mimic natural bases in size, shape, and biochemical processing. Topics covered include base pairs with alternative H-bonding schemes, dimensionally expanded base pairs, hydrophobic base pairs, metal-ligated bases, degenerate bases, universal nucleosides, and triplex constituents.

Polymerase amplification, cloning, and gene expression of benzo-homologous "yDNA" base pairs

A widened DNA base-pair architecture is studied in an effort to explore the possibility of whether new genetic system designs might possess some of the functions of natural DNA. In the "yDNA" system, pairs are homologated by addition of a benzene ring, which yields (in the present study) benzopyrimidines that are correctly paired with purines. Here we report initial tests of ability of the benzopyrimidines yT and yC to store and transfer biochemical and biological information in vitro and in bacterial cells. In vitro primer extension studies with two polymerases showed that the enzymes could insert the correct nucleotides opposite these yDNA bases, but with low selectivity. PCR amplifications with a thermostable polymerase resulted in correct pairings in 15-20 % of the cases, and more successfully when yT or yC were situated within the primers. Segments of DNA containing one or two yDNA bases were then ligated into a plasmid and tested for their ability to successfully lead the expression of an active protein in vivo. Although active at only a fraction of the activity of fully natural DNA, the unnatural bases encoded the correct codon bases in the majority of cases when singly substituted, and yielded functioning green fluorescent protein. Although the activities with native polymerases are modest with these large base pairs, this is the first example of encoding protein in vivo by an unnatural DNA base pair architecture.

Metal-mediated base pairing within the simplified nucleic acid GNA

Hydroxypyridone and pyridopurine homo- and hetero-base pairs have been investigated in the context of duplex GNA (glycol nucleic acid). Phosphoramidites for automated GNA solid phase synthesis were synthesized economically in a few steps starting from commercially available enantiopure glycidol. Similar to their behavior in DNA, the hydroxypyridone and pyridopurine homo-base pairs display a metal-dependent base pairing, with the hydroxypyridone base pair exhibiting a preference for copper(II) ions and the pyridopurine a preference for nickel(II) ions. However, these metallo-base pairs show modulated properties in GNA with respect to metal-dependent pairing stabilities and metal selectivities. Most interestingly, the hydroxypyridone homo-base pair and hydroxypyridone-pyridopurine hetero-base pair are particularly well accommodated in the GNA duplex and form copper(II)-dependent base pairs that are more stable compared to a Watson-Crick A:T base pair at the same position by nearly 20 degrees C and 24 degrees C, respectively. The structure of the copper(II)-hydroxypyridone homo-base pair is discussed based on a recent metallo-GNA duplex crystal structure.

Soft metal-mediated base pairing with novel synthetic nucleosides possessing an O,S-donor ligand

Metal-mediated base pairing with artificial ligand-bearing nucleosides allows site-selective metal incorporation inside DNA duplexes. In particular, this strategy has provided a general way of discrete, heterogeneous metal arrays in a programmable manner. To increase the kind of metallo-building blocks, we have newly synthesized two artificial nucleosides which have an O, S-donor ligand as the nucleobase moiety, mercaptopyridone ( M) and hydroxypyridinethione ( S). These nucleosides were found to efficiently form metal-mediated base pairs with soft transition metal ions such as Pd (2+) and Pt (2+).

Solution structure of a DNA duplex containing a guanine-difluorotoluene pair: a wobble pair without hydrogen bonding?

The incorporation of synthetic nucleoside analogues into DNA duplexes provides a unique opportunity to probe both structure and function of nucleic acids. We used 1H and 19F NMR and molecular dynamics calculations to determine the solution structures of two similar DNA decamer duplexes, one containing a central G-T mismatched or "wobble" base pair, and one in which the thymine in this base pair is replaced by difluorotoluene (a thymine isostere) creating a G-F pair. Here, we show that the non-hydrogen-bonding G-F pair stacks relatively well into the helix and that the distortions caused by each non-Watson-Crick G-T or G-F base pair are quite localized to a three base pair site around the mismatch. A detailed structural analysis reveals that the absence of hydrogen bonding introduces more dynamic motion into the G-F pair relative to G-T and permits the G-F pair to exhibit stacking and conformational features characteristic of both a Watson-Crick base pair (on the guanine containing strand) and a wobble base pair (on the strand containing the difluorotoluene). We used these results to posit a rationale for recognition and repair of mismatch sites in DNA.

X-ray crystallographic study of several 2'-deoxy-beta-D-ribonucleosides with 1-deazapurine-derived aglycones

The 2'-deoxy-beta-D-ribonucleosides of 1,3-deazapurine (benzimidazole (1)), 1-deazapurine (both 1H-imidazo[4,5-b]pyridine (2) and 3H-imidazo[4,5-b]pyridine (3)), and 6-benzoylamino-1-deazapurine (7-benzoylamino-3H-imidazo[4,5-b]pyridine (4)) have been prepared and structurally characterized by X-ray crystallography. Especially compounds 1-3 can serve as artificial nucleosides that may substitute 2'-deoxy adenosine because they lack the exocyclic amino group and one or two of the endocyclic nitrogen atoms and hence have a much smaller potential to engage in hydrogen bonds. In the latter respect, they are candidates for nucleosides in metal-ion mediated base pairs. The unit cell of compound 3 contains two crystallographically independent molecules. Compound 4 was crystallized from methanol and water, respectively, giving rise to two different solvates. Despite the closely related aglycones, the sugar conformations in 1-4 are found to be highly variable (1: (2)T(1); 2: (3)T(2); 3: (3)E and E(4); 4: (2)E and (2)T(3)). The structures reported here confirm that there is no simple correlation between the sugar conformation and the character of the nucleoside, and they will hopefully contribute to a better understanding of the complex interplay of different effects that are in control of the conformational equilibrium.

Conformational change induced by metal-ion-binding to DNA containing the artificial 1,2,4-triazole nucleoside

A conformational switch can be induced upon the addition of transition-metal ions to oligonucleotides that contain a row of successive artificial nucleobases flanked by complementary sequences of natural nucleobases, provided that the artificial bases cannot undergo self-pairing via hydrogen bonding but only via the formation of metal-ion-mediated base pairs. Such oligonucleotides adopt a hairpin structure in the absence of transition-metal ions, yet they show a preference for the formation of a regular double helix if the appropriate metal ions are present. We report here our experimental data on the structure of the oligonucleotide d(A7X3T7) (A=adenine, T=thymine, X=1,2,4-triazole) in the absence and presence of silver(I). This study comprising temperature-dependent UV spectroscopy, CD spectroscopy, MALDI-TOF measurements, fluorescence spectroscopy, and dynamic light scattering opens up a new approach to the generation of a large variety of metal-ion sensors with the possibility of fine-tuning their sensing capabilities, depending on the artificial nucleoside that is used.

DNA-based phosphane ligands

In order to expand the repertoire of DNA sequences specifically interacting with transition metals, we report here the first examples of DNA sequences carrying mono- and bidentate phosphane ligands as well as P,N-ligands. Aminoalkyl-modified oligonucleotides have been reacted at predetermined internal sites with carboxylate derivatives of pyrphos, BINAP and phosphinooxazoline (PHOX) 2 b-d. Carbodiimide coupling in the presence of N-hydroxysuccinimide provided the DNA-ligand conjugates in 38-78 % yield. Phosphane-containing oligonucleotides and their phosphane sulfide analogues were characterized by mass spectrometry (MALDI-TOF and FT-ICR-ESI) and their stability after purification and isolation was systematically investigated. While DNA-appended pyrphos ligand was quickly oxidized, BINAP and PHOX conjugates showed high stabilities, making them useful precursors for incorporation of transition metals into DNA.

Symmetry Selection in Artificial DNA Base Pairs

We report the results of density functional theory (DFT) studies on the formation of the complex H1--Cu2+-H1- consisting of two deprotonated hydroxypyridone ligands (H1-) and a Cu2+ ion. We compare the total energies of three possible structures with different symmetries and show that the structure with plane reflection symmetry has the lowest energy. The electronic structure of the periodic extended DNA-like double helix consisting of stacked H1--Cu2+-H1- units is then calculated within the density functional method, and the double helix is found to be an insulating ferromagnet.

DFT Energy Surfaces for Aminopurine Homodimers and Their Conjugate Acid Ions

Dimers of free nucleobases with their conjugate acid ions can be assigned to either of two categories: protonated dimers or proton-bound dimers. In the former, the extra proton attaches to a lone pair of a neutral dimer. In the latter, the extra proton is situated between two lone pairs and participates in a proton bridge. In general, proton-bound dimers are found to be more tightly held together than protonated dimers. While neutral adenine and its isomer 8-aminopurine (C(5)H(5)N(5)) are substantially more stable than their 7H tautomers, their conjugate acid ions and those of their respective 7H tautomers have nearly the same heats of formation. Correspondingly, the most stable (C(5)H(5)N(5))2H+ structures contain 7H tautomers as the neutral partner. Proton transit from one partner to the other within the most stable protonated dimer of 8-aminopurine has a low barrier (6 kJ mol(-1)). The potential energy curve for the NH stretch in that case is better fitted as a double minimum rather than as a harmonic potential. Purine-purine mismatches have been observed in nucleic acids, to which calculated (C(5)H(5)N(5))2H+ dimer geometries appear nearly isosteric.