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The Watson–Crick coding system depends on the molecular recognition of complementary purine and pyrimidine bases. Now, the construction of hybrid DNAs with Watson–Crick and purine–purine base pairs decorated with dendritic side chains was performed. Oligonucleotides with single and multiple incorporations of 5‐aza‐7‐deaza‐2′‐deoxyguanosine, its tripropargylamine derivative, and 2′‐deoxyisoguanosine were synthesized. Duplex stability decreased if single modified purine–purine base pairs were inserted, but increased if pyrene residues were introduced by click chemistry. A growing number of consecutive 5‐aza‐7‐deazaguanine–isoguanine base pairs led to strong stepwise duplex stabilization, a phenomenon not observed for the guanine–isoguanine base pair. Spacious residues are well accommodated in the large groove of purine–purine DNA tracts. Changes to the global helical structure monitored by circular dichroism spectroscopy show the impact of functionalization to the global double‐helix structure. This study explores new areas of molecular recognition realized by purine base pairs that are complementary in hydrogen bonding, but not in size, relative to canonical pairs., Fit in the groove: Hybrid DNAs with Watson–Crick and purine–purine base pairs decorated with dendritic side chains are prepared. Space‐demanding side chains introduced into the 7‐position of 5‐aza‐7‐deazaguanine–isoguanine base pairs are well accommodated in the large groove of purine–purine DNA and have a positive impact on helix stability.

Oxidation of nontraditional nucleobases 1-methylcytosine (hachimoji base S) and isoguanine (hachimoji base B) in gas-phase ternary complexes with CuII(terpyridine)2+ formed cation radicals that wer...

7-Functionalized 8-aza-7-deaza-2'-deoxyisoguanine and 8-aza-7-deaza-2-aminoadenine 2'-deoxyribonucleosides decorated with fluorescent pyrene or benzofuran sensor tags or clickable side chains with terminal triple bonds were synthesized. 8-Aza-7-deaza-7-iodo-2-amino-2'-deoxyadenosine was used as the central intermediate and was accessible by an improved two-step glycosylation/amination protocol. Functionalization of position-7 was performed either on 8-aza-7-deaza-7-iodo-2-amino-2'-deoxyadenosine followed by selective deamination of the 2-amino group or on 7-iodinated 8-aza-7-deaza-2'-deoxyisoguanosine. Sonogashira and Suzuki-Miyaura cross-coupling reactions were employed for this purpose. Octadiynyl side chains were selected as linkers for click reactions with azido pyrenes. KTaut values calculated from H2O/dioxane mixtures revealed that side chains have a significant influence on the tautomeric equilibrium. Photophysical properties (fluorescence, solvatochromism, and quantum yields) of the new 8-aza-7-deazapurine nucleosides with fluorescent side chains were determined. Remarkably, a strong excimer fluorescence in H2O was observed for pyrene dye conjugates of 8-aza-7-deazaisoguanine and 2-aminoadenine nucleosides with a long linker. In other solvents including methanol, excimer fluorescence was negligible. The 2-aminoadenine and isoguanine nucleosides with the 8-aza-7-deazapurine skeleton expand the class of nucleosides applicable to fluorescence detection with respect to diagnostic and therapeutic purposes.

Three new sulfated isoguanine alkaloid glycosides, locustoside A disulfate (1), saikachinoside B disulfate (2), and saikachinoside A trisulfate (3), have been isolated from the pupal case of the wild bruchid seed beetle Bruchidius dorsalis (Chrysomelidae, Bruchinae) infesting the seed of Gleditsia japonica Miquel (Fabaceae) along with the known compounds 9–11. The structures of the new compounds were determined through spectroscopic data and X-ray crystallographic analysis. The isolated compounds were evaluated for their inhibitory activity against starfish embryogenesis.

Revised geometrical parameters are proposed for the Watson–Crick pairs of nucleobases, for use as restraints in modeling and refinement of the structures of nucleic acids. Accurate values of these parameters were derived (and compared) from small-molecule Cambridge Structural Database structures, from super accurate ultrahigh-resolution nucleic acid structures in the Protein Data Bank, and from quantum mechanical calculations. The effect of base pairing on the molecular geometry of the nucleobases is also investigated., Geometrical restraints provide key structural information for the determination of biomolecular structures at lower resolution by experimental methods such as crystallography or cryo-electron microscopy. In this work, restraint targets for nucleic acids bases are derived from three different sources and compared: small-molecule crystal structures in the Cambridge Structural Database (CSD), ultrahigh-resolution structures in the Protein Data Bank (PDB) and quantum-mechanical (QM) calculations. The best parameters are those based on CSD structures. After over two decades, the standard library of Parkinson et al. [(1996), Acta Cryst. D52, 57–64] is still valid, but improvements are possible with the use of the current CSD database. The CSD-derived geometry is fully compatible with Watson–Crick base pairs, as comparisons with QM results for isolated and paired bases clearly show that the CSD targets closely correspond to proper base pairing. While the QM results are capable of distinguishing between single and paired bases, their level of accuracy is, on average, nearly two times lower than for the CSD-derived targets when gauged by root-mean-square deviations from ultrahigh-resolution structures in the PDB. Nevertheless, the accuracy of QM results appears sufficient to provide stereochemical targets for synthetic base pairs where no reliable experimental structural information is available. To enable future tests for this approach, QM calculations are provided for isocytosine, isoguanine and the iCiG base pair.

Isoguanine (2-hydroxyadenine), considered to be a non-natural nucleobase has, however, been shown to occur in the croton bean, butterfly wings and a mollusk. For the first time, to the best of our knowledge, we report the identification of isoguanosine (2-hydroxyadenosine), the ribonucleoside, in humans and mouse. Isoguanosine is identified and quantified in RNA from mouse liver samples and in human urine and cerebrospinal fluid. Isoguanine could not be detected as the 2'-deoxyribonucleoside in mouse liver DNA. It could be speculated that the source of isoguanosine was formation from adenosine during oxidative stress in the body. However, the urinary concentrations of isoguanosine and the levels in the liver found here by using isotope dilution liquid chromatography-tandem mass spectrometry are identical to or exceed those of 8-oxo-7,8-dihydro-2'-deoxyguanosine and 8-oxo-7,8-dihydro-guanosine. Guanine is the nucleobase that is oxidized the easiest, so it appears spectacular that the levels of isoguanosine are higher than the levels of 8-oxo-7,8-dihydro-2'-deoxyguanosine and 8-oxo-7,8-dihydro-guanosine. It also appears intriguing that it was only possible to detect the ribonucleoside isoguanosine and not the 2'-deoxyribonucleoside. These observations could indicate that the isoguanosine found is not formed by oxidative stress and could have biological functions.

Evolution has yielded biopolymers that are constructed from exactly four building blocks and are able to support Darwinian evolution. Synthetic biology aims to extend this alphabet, and we recently showed that 8-letter (hachimoji) DNA can support rule-based information encoding. One source of replicative error in non-natural DNA-like systems, however, is the occurrence of alternative tautomeric forms, which pair differently. Unfortunately, little is known about how structural modifications impact free-energy differences between tautomers of the non-natural nucleo¬bases used in the hachimoji expanded genetic alphabet. Determining experimental tautomer ratios is technically difficult and so strategies for improving hachimoji DNA replication efficiency will benefit from accurate computational predictions of equilibrium tautomeric ratios. We now report that high-level quantum-chemical calculations in aqueous solution by the embedded cluster reference interaction site model (EC-RISM), benchmarked against free energy molecular simulations for solvation thermodynamics, provide useful quantitative information on the tautomer ratios of both Watson-Crick and hachimoji nucleobases. In agreement with previous computational studies, all four Watson-Crick nucleobases adopt essentially only one tautomer in water. This is not the case, however, for non-natural nucleobases and their analogs. For example, although the enols of isoguanine and a series of related purines are not populated in water, these heterocycles possess N1-H and N3-H keto tautomers that are similar in energy thereby adversely impacting accurate nucleobase pairing. These robust computational strategies offer a firm basis for improving experimental measurements of tautomeric ratios, which are currently limited to studying molecules that exist only as two tautomers in solution.

Isoguanine, an analogue of guanine, is of intrinsic interest as a noncanonical nucleobase. The crystal structure of isoguaninium chloride (systematic name: 6-amino-2-oxo-1H,7H-purin-3-ium chloride), C5H6N5O+·Cl−, has been determined by single-crystal X-ray diffraction. Structure analysis was supported by electrostatic interaction energy (E es) calculations based on charge density reconstructed with the UBDB databank. In the structure, two kinds of molecular tapes are observed, one parallel to (010) and the other parallel to (50\overline{4}). The tapes are formed by dimers of isoguaninium cations interacting with chloride anions. E es analysis indicates that cations in one kind of tape are oriented so as to minimize repulsive electrostatic interactions.

Three previously undescribed isoguanine glycosides with an N3-prenyl group, designated locustoside B, saikachinoside B, and saikachinoside C, have been isolated from the seed of Gleditsia japonica Miquel (Fabaceae) along with two known compounds, locustoside A and saikachinoside A. Their structures were determined from spectroscopic data and X-ray crystallographic analysis. The inhibitory activity against acid phosphatase was evaluated.

We investigated the formation mechanisms of the nucleobases adenine and guanine and the nucleobase analogues hypoxanthine, xanthine, isoguanine, and 2,6-diaminopurine in a UV-irradiated mixed 10:1 H2O:NH3 ice seeded with precursor purine by using ab initio and density functional theory computations. Our quantum chemical investigations suggest that a multistep reaction mechanism involving purine cation, hydroxyl and amino radicals, together with water and ammonia, explains the experimentally obtained products in an independent study. The relative abundances of these products appear to largely follow from relative thermodynamic stabilities. The key role of the purine cation is likely to be the reason why purine is not functionalized in pure ammonia ice, where cations are promptly neutralized by free electrons from NH3 ionization. Amine group addition to purine is slightly favored over hydroxyl group attachment based on energetics, but hydroxyl is much more abundant due to higher abundance of H2O. The amino group is preferentially attached to the 6 position, giving 6-aminopurine, that is, adenine, while the hydroxyl group is preferentially attached to the 2 position, leading to 2-hydroxypurine. A second substitution by hydroxyl or amino group occurs at either the 6 or the 2 position depending on the first substitution. Given that H2O is far more abundant than NH3 in the experimentally studied ices (as well as based on interstellar abundances), xanthine and isoguanine are expected to be the most abundant bi-substituted photoproducts. Key Words: Astrophysical ice-Abiotic organic synthesis-Nucleic acids-Origin of life-RNA world. Astrobiology 17, 771-785.

Fluorescent tri-cyclic purine analogs, derivatives of isoguanine and adenine, were examined as potential substrates of purine-nucleoside phosphorylase. It was found previously that etheno- derivatives of both compounds are ribosylated in phosphate-free media, but ribosylation places in some instances differ from purine N9. New ribosides are examined as potential substrates of human blood PNP and indicators of this enzyme. Of these, N6-riboside of 1,N6-etheno-adenine was found the most promising.

Etheno-derivatives of guanine, O6-methylguanine, and isoguanine were prepared and purified using standard methods. The title compounds were examined as potential substrates of purine-nucleoside phosphorylases from various sources in the reverse (synthetic) pathway. It was found that 1,N2-etheno-guanine and 1,N6-etheno-isoguanine are excellent substrates for purine-nucleoside phosphorylase (PNP) from E. coli, while O6-methyl-N2,3-etheno-guanine exhibited moderate activity vs. this enzyme. The latter two compounds displayed intense fluorescence in neutral aqueous medium, and so did the corresponding ribosylation products. By contrast, PNP from calf spleens exhibited only modest activity towards 1,N6-etheno-isoguanine, the remaining compounds were not ribosylated by this enzyme. The enzymatic ribosylation of 1,N6-etheno-isoguanine using two forms of calf PNP (wild type and N243D) and E. coli PNP (wild type and D204N) gave three different products, which were identified on the basis of NMR analysis and comparison with the product of the isoguanosine reaction with chloroacetic aldehyde, which gave an essentially single compound, identified unequivocally as N9-riboside. With the wild-type E. coli enzyme as a catalyst, N9--d- and N7--d-ribosides are obtained in proportion ~1:3, while calf PNP produced another riboside, tentatively identified as N6--d-riboside. The potential application of various forms of PNP for synthesis of the tri-cyclic nucleoside analogs is discussed.

Purine isosteres present excellent opportunities in drug design and development. Using isosteres of natural purines as scaffolds for the construction of new therapeutic agents has been a valid strategy of medicinal chemistry. Inspired by the similarity to isoguanine, we attempted to develop a practical method for the preparation of 5-aza-isoguanines. Several synthetic approaches were explored to establish a robust general protocol for the preparation of these compounds. The significant difference in the reactivity of the C-5 and C-7 electrophilic centers of 1,2,4-triazolo[1,5-a][1,3,5]triazines (5-azapurines) towards nucleophiles was demonstrated. The most practical and general method for the preparation of 5-aza-isoguanines involved a regioselective reaction of ethoxycarbonyl isothiocyanate with a 5-aminotriazole. The intramolecular ring closure of the resulted product followed by the S-methylation afforded 7-methylthio-2-phenyl-1,2,4-triazolo[1,5-a][1,3,5]triazin-5-one, which could be effectively aminated with various amines. The resulted 5-aza-isoguanines resemble a known purine nucleoside phosphorylase inhibitor and could be interesting for further investigations as potential anticancer agents.

A DNA tetraplex, (isoG4)4-(K+)2-(Na+)12, has been studied at the BP86-D3(BJ)/def2-SVP level employing CPCM with water as solvent. The resulting optimized structure was found to contain two continuously hydrogen-bonded helical arrays of eight isoG nucleobases each. This structure is novel in the domain of oligonucleotide tetramerization, and could help further define molecular recognition by a classical nucleobase first reported by Fischer.

A series of 5 randomly designed in-house cyclometalated Ir(III) complexes were examined for their application in G-pentaplex probes and the "proof-of-principle" concept in G-pentaplex-based Cs(+) ions detection. The G-pentaplex-forming sequence (DNA1, 5'-T(iG)4T-3', where iG=isoguanine) is present in single strand DNA form ab initio, however, the addition of Cs(+) ions lead to formation of the intermolecular G-pentaplex structure which is identified by the novel Ir(III) complex 1 afterward and produce an enhanced luminescence signal for Cs(+) ions monitoring. To the best of our knowledge, this is the first G-pentaplex probe and also the first G-pentaplex-based label-free detection platform for Cs(+) ions reported in the literature. The monitoring of spiked Cs(+) ions in natural water samples demonstrates the potential application and technical sound of this "proof-of-principle" concept sensing platform.

Thrombin binding aptamer (TBA), is a short DNA 15-mer that forms G-quadruplex structure and possesses anticoagulant properties. Some chemical modifications, including unlocked nucleic acids (UNA), 2'-deoxy-isoguanosine and 2'-deoxy-4-thiouridine were previously found to enhance the biological activity of TBA. In this paper, we present thermodynamic and biological characteristics of TBA variants that have been modified with novel isoguanine derivative of UNA as well as isoguanosine. Additionally, UNA-4-thiouracil and 4-thiouridine were also introduced simultaneously with isoguanine derivatives. Thermodynamic analysis indicates that the presence of isoguanosine in UNA or RNA series significantly decreases the stability of G-quadruplex structure. The highest destabilization is observed for substitution at one of the G-tetrad position. Addition of 4-thiouridine in UNA or RNA series usually decreases the unfavorable energetic cost of the presence of UNA or RNA isoguanine. Circular dichroism and thermal denaturation spectra in connection with thrombin time assay indicate that the introduction of UNA-isoguanine or isoguanosine into TBA negatively affects G-quadruplex folding and TBA anticoagulant properties. These findings demonstrate that the highly-ordered structure of TBA is essential for inhibition of thrombin activity.

Guanine-rich, single-stranded, DNAs and RNAs are able to fold to form G-quadruplexes that are held together by guanine base quartets. G-quadruplexes are known to bind ferric heme [Fe(III)-protoporphyrin IX] and to strongly activate such bound hemes toward peroxidase (1-electron oxidation) as well as oxygenase/peroxygenase (2-electron oxidation) activities. However, much remains unknown about how such activation is effected. Herein, we investigated whether G-quadruplexes were strictly required for heme activation or whether related multi-stranded DNA/RNA structures such as isoguanine (iG) quadruplexes and pentaplexes could also bind and activate heme. We found that iG-pentaplexes did indeed bind and activate heme comparably to G-quadruplexes; however, iG-quadruplexes did neither. Earlier structural and computational studies had suggested that while the geometry of backbone-unconstrained iG-quintets templated by cations such as Na(+) or NH4 (+) was planar, that of iG-quartets deviated from planarity. We hypothesize that the binding as well as activation of heme by DNA or RNA is strongly supported by the planarity of the nucleobase quartet or quintet that interacts directly with the heme.

We report, herein, a new class of RNAi trigger molecules based on the unconventional parallel hybridization of two oligonucleotide chains. We have prepared and studied several parallel stranded (ps) duplexes, in which the parallel orientation is achieved through incorporation of isoguanine and isocytosine to form reverse Watson-Crick base pairs in ps-DNA:DNA, ps-DNA:RNA, ps-(DNA-2FANA): RNA, and ps-DNA:2F-RNA duplexes. The formation of these duplexes was confirmed by UV melting experiments, FRET and CD studies. In addition, NMR structural studies were conducted on a ps-DNA:RNA hybrid for the first time. Finally, we provide evidence for the unprecedented finding that ps-DNA:RNA and ps-DNA:2F-RNA hybrids can engage the RNAi pathway to silence gene expression in vitro.

Structure-based methods are powerful tools that are being exploited to unravel new functions with therapeutic advantage. Here, we report the discovery of a new class of deaminases, predominantly found in mycobacterial species that act on the commercially important s-triazine class of compounds. The enzyme Msd from Mycobacterium smegmatis was taken as a representative candidate from an evolutionarily conserved subgroup that possesses high density of Mycobacterium deaminases. Biochemical investigation reveals that Msd specifically acts on mutagenic nucleobases such as 5-azacytosine and isoguanine and does not accept natural bases as substrates. Determination of the X-ray structure of Msd to a resolution of 1.9 angstrom shows that Msd has fine-tuned its active site such that it is a hybrid of a cytosine as well as a guanine deaminase, thereby conferring Msd the ability to expand its repertoire to both purine and pyrimidine-like mutagens. Mapping of active site residues along with X-ray structures with a series of triazine analogues aids in deciphering the mechanism by which Msd proofreads the base milieu for mutagens. The genome location of the enzyme reveals that Msd is part of a conserved cluster that confers the organism with innate resistance: toward select xenobiotics by triggering their efflux.

The data presented here are related to the research paper entitled “Rare sulfated purine alkaloid glycosides from Bruchidius dorsalis pupal case” [1]. In this data article, we provide 1D and 2D nuclear magnetic resonance (NMR) spectroscopy and electrospray ionization mass spectrometry (ESIMS) data of three undescribed sulfated purine alkaloids, locustoside A disulfate, saikachinoside B disulfate, and saikachinoside A trisulfate isolated from the pupal case of the wild bruchid seed beetle Bruchidius dorsalis (Chrysomelidae, Bruchinae) infesting the seed of Gleditsia japonica Miquel (Fabaceae).

Free radical pathways for the synthesis of xanthine and isoguanine from formamide were studied using density functional theory (B3LYP/6-311G(d,p)). The proposed mechanisms are complex and appropriate for the non-aqueous scenario of prebiotic reactions. Formation of the carbonyl bond in the nucleobases proceeds through enol-keto tautomerization since the direct formation of the C O bond is a highly endothermic step. The mechanisms show 2-amino-imidazole as a precursor for nucleobases and polyazaporphyrin. The proposed mechanisms contribute to a further understanding of the origin of biomolecules.

3-Isopurine nucleosides, namely 3-(ribofuranosyl)purine nucleosides, are interesting owing to their potential biological activity and as components of modified oligonucleotides. A regio- and stereocontrolled method was developed for the synthesis of β-2′-deoxy-3-isopurine nucleosides using the intramolecular glycosylation protocol. The availability of this method was shown by the first chemical synthesis of 3-(2-deoxy-β- d -ribofuranosyl)xanthine and isoguanine.

Mechanisms of the deamination reactions of isoguanine with H2O, OH(-), and OH(-)/H2O and of protonated isoguanine (isoGH(+)) with H2O have been investigated by theoretical calculations. Eight pathways, paths A-H, have been explored and the thermodynamic properties (ΔE, ΔH, and ΔG), activation energies, enthalpies, and Gibbs energies of activation were calculated for each reaction investigated. Compared with the deamination reaction of isoguanine or protonated isoguanine (isoGH(+)) with water, the deamination reaction of isoguanine with OH(-) shows a lower Gibbs energy of activation at the rate-determining step, indicating that the deamination reaction of isoguanine is favorably to take place for the deprotonated form isoG(-) with water. With the assistance of an extra water, the reaction of isoguanine with OH(-)/H2O, pathways F and H, are found to be the most feasible pathways in aqueous solution due to their lowest Gibbs energy of activation of 174.7 and 172.6 kJ mol(-1), respectively, at the B3LYP/6-311++G(d,p) level of theory.

Recent studies have emphasized the benefits of increasing hydrophobic stacking area beyond that of a single nucleobase in nonenzymatic ligation reactions. We demonstrated that nucleic acid intercalators, with surface areas similar to that of a Watson–Crick base pair, dramatically increase the efficiency of ligation. [4a] von Kiedrowski and coworkers observed efficient ligation of oligonucleotides that form blunt-ended miniduplexes, which are also organized in solution by stacking surfaces defined by Watson–Crick base pairs. [12] In light of these results, and the proposal that purine–purine base pairs might have preceded purine–pyrimidine base pairs, we have investigated the nonenzymatic ligation of homopurine tetranucleotides. Here we show that homopurine miniduplexes exhibit a propensity for nonenzymatic ligation that is more than two orders of magnitude greater than that of analogous purine–pyrimidine oligonucleotides. These results provide additional support for the hypothesis that nucleic acid assembly in a pre-enzyme world is more probable if life began with a proto-RNA that contained alternative nucleobases, particularly those capable of greater stacking interactions. To investigate the potential for purine–purine miniduplexes to undergo nonenzymatic ligation, the self-complementary oligonucleotide bluntPuPu, with sequence d(p#DXG) (# = isoguanine; D = 2,6-diaminopurine; X = xanthine), was incubated with N-cyanoimidazole, a chemical activating agent for phospho

Several possible mechanisms underlying isoguanine formation when OH radical attacks the C2 position of adenine (AC2) are investigated theoreti- cally for the first time. Two steps are involved in this process. In the first step, one of two low-lying AC2 ···OH re- actant complexes is formed, leading to C2 � H2 bond cleavage. Between the two reactant complexes there is a small iso- merization barrier, which lies well below separated adenine plus OH radi- cal. The complex dissociates to free molecular hydrogen and an isoguanine tautomer (isoG 1 or isoG 2). The local and activation barriers for the two pathways are very similar. This evi- dence suggests that the two pathways are competitive. After dehydrogena- tion, there are two possible routes for the second step of the reaction. One is direct hydrogen transfer, via enol-keto tautomerization, which has high local barriers for both tautomers and is not favored. The other option is indirect hydrogen transfer involving microsol- vation by one water molecule. The water lowers the reaction barrier by over 20 kcal mol � 1 , indicating that water-mediated hydrogen transfer is much more favorable. Both A + OHC! isoG + HC reactions are exothermic and spontaneous. Among four isoguanine tautomers, isoG 1 has the lowest energy. Our findings explain why only the N1H and O2H tautomers of isolated isoguanine and isoguanosine have been observed experimentally.

A new purine derivative, 3-(3-methylbut-2-en-1-yl)isoguanine (1), and a new cleistanthane-type diterpenoid glucoside, 19-hydroxyspruceanol 19-O-β-D-glucopyranoside (2), together with eight known compounds were isolated from the whole plant of Phyllanthus reticulatus. The structures were elucidated by chemical and spectroscopic methods.

A new synthesis for 5,7-dichloroimidazo[4,5-b]pyridine is described. From this compound and 5-amino-7-chloroimidazo[4,5-b]pyridine a number of 5,7-disubstituted imidazo[4,5-b]pyridines are prepared, including 7-aminoimidazo[4,5-b]pyridin-5-one, the 1-deaza analogue of isoguanine.

Three new sulfated isoguanine alkaloid glycosides, designated as saikachinoside A monosulfate (1), saikachinoside A disulfate (2), and locustoside B disulfate (3), have been isolated from the pupal case of the wild bruchid seed beetle Bruchidius dorsalis (Chrysomelidae, Bruchinae) infesting the seed of Gleditsia japonica Miq. (Fabaceae). Their structures were determined by spectroscopic methods and the inhibitory activity of 2 and 3 against acid phosphatase was evaluated.

As with natural nucleic acids, pairing between artificial nucleotides can be influenced by tautomerism, with different placements of protons on the heterocyclic nucleobase changing patterns of hydrogen bonding that determine replication fidelity. For example, the major tautomer of isoguanine presents a hydrogen bonding donor-donor-acceptor pattern complementary to the acceptor-acceptor-donor pattern of 5-methylisocytosine. However, in its minor tautomer, isoguanine presents a hydrogen bond donor-acceptor-donor pattern complementary to thymine. Calculations, crystallography, and physical organic experiments suggest that this tautomeric ambiguity might be "fixed" by replacing the N-7 nitrogen of isoguanine by a CH unit. To test this hypothesis, we prepared the triphosphate of 2'-deoxy-7-deazaiso-guanosine and used it in PCR to estimate an effective tautomeric ratio "seen" by Taq DNA polymerase. With 7-deazaisoguanine, fidelity-per-round was ∼92%. The analogous PCR with isoguanine gave a lower fidelity-per-round of ∼86%. These results confirm the hypothesis with polymerases, and deepen our understanding of the role of minor groove hydrogen bonding and proton tautomerism in both natural and expanded genetic "alphabets", major targets in synthetic biology.

The binding of actinomycin D (C 1 , 1 ) and its analog actinomin ( 2 ) was studied on base-modified oligonucleotide duplexes with parallel chain orientation (ps) and with anti-parallel chains (aps) for comparison. Actinomycin D binds not only to aps duplexes containing guanine–cytosine base pairs but also to those incorporating modified bases such as 7-deazaguanine or its 6-deoxo derivative. For this, novel phosphoramidites were prepared. The new building block of 7-deaza-2′-deoxyguanosine is significantly more stable than the one currently used and allows normal oxidation conditions during solid-phase oligonucleotide synthesis. Actinomycin binds weakly to ps duplexes containing guanine–isocytosine base pairs but not to ps-DNA incorporating pairs of isoguanine–cytosine residues. On the contrary, the actinomycin D analog actinomin, which contains positively charged side chains instead of the chiral peptide rings, is strongly bound to both ps- and aps-DNA. Guanines, isoguanine, as well as other 7-deaza derivatives are accepted as nucleobases. Apparently, the pentapeptide lacton rings of actinomycin do not fit nicely into the groove of ps-DNA thereby reducing the binding strength of the antibiotic while the groove size of ps-DNA does not affect actinomin binding notably.

Nucleobase analogs 5-methylisocytosine ((Me)isoC) and isoguanine (isoG) form a non-natural base pair in duplex nucleic acids with base pairing specificity orthogonal to the natural nucleobase pairs. Sequencing reactions were conducted with oligodeoxyribonucleotides (ODNs) containing d(Me)isoC and disoG using modified pyrosequencing and dye terminator methods. Modified dye terminator sequencing was generally useful for the sequence identification of ODNs containing the non-natural nucleobases. The two sequencing methods were also used to monitor nucleotide incorporation and subsequent extension by Family A polymerases used in the sequencing methods with a six-nucleobase system that includes d(Me)isoC and disoG. Nucleic acids containing the six-nucleobase system could be replicated well, but not as well as natural nucleic acids, especially in regions of high d(Me)isoC-disoG content. Challenges in replication with d(Me)isoC-disoG are consistent with nucleobase tautomerism in the insertion step and disrupted minor groove nucleobase pair-polymerase contacts in subsequent extension.

The hydration Gibbs energies of adenine, cytosine, guanine, thymine, uracil and isoguanine are determined by the molecular dynamics-thermodynamic integration method (MD-TI) and using continuous COSMO and hybrid models. The role of solvents in the COSMO model is described by permittivity and by combining the permittivity and specific hydration of single water molecules placed on the energetically most probable position in the hybrid model. The hybrid model describes hydration similarly to the COSMO model; both the continuous methods are in good agreement with the MD-TI method. Differences are small and the use of both models can be recommended.

Isoguanine (isoG) trimers have been theoretically studied using the density functional theory to reveal the role of H-bonding in the formation of different base aggregations. Similar to the isoG tetrads, the isoG trimer also adopts diverse conformations. Cooperative effects for the H-bonding in the cyclic isoG trimers have been found to be important. As a result of the strong cooperativity, the conformer characterized by the highest symmetry is the most stable among the possible trimers. Vibration mode analysis reveals the influence of the cooperative effects on the H-bond stretching motion. An atoms-in-molecules study of the H-bonds in the isoG trimers suggests that the electronic density topology of the bifurcated H-bond is insensitive to the cooperative effects. The values of the binding energy, the vibration frequency, and the electronic density topology of the noncyclic isoG trimers demonstrate that there is no cooperativity in these open ring structures.

Organic chemistry has made possible the synthesis of molecules that expand on Nature's genetic alphabet. Using the previously described nonstandard DNA base pair constructed from isoguanine and 5-methylisocytosine, we report a highly specific and sensitive method that allows for the fast and specific quantitation of genetic sequences in a closed tube format. During PCR amplification, enzymatic site-specific incorporation of a quencher covalently linked to isoguanine allows for the simultaneous detection and identification of multiple targets. The specificity of method is then established by analysis of thermal denaturation or melting of the amplicons. The appropriate functions of all reactions are further verified by incorporation of an independent target into the reaction mixture. We report that the method is sensitive down to the single copy level, and specificity is demonstrated by multiplexed end-point genotypic analysis of four targets simultaneously using four separate fluorescent reporters. The method is general enough for quantitative and qualitative analysis of both RNA and DNA using previously developed primer sets. Though the method described employs the commonly used PCR, the enzymatic incorporation of reporter groups into DNA site-specifically should find broad utility throughout molecular biology.

Five different isoguanine (isoG) base pairs and five isoG tetrads have been located as the local minima on the potential energy surfaces at the B3LYP/6-311G(d,p) level of theory. An analysis of the isoG base pair enables us to evaluate the hydrogen bond energy in isoG−iosG interactions which is useful in the study of the energy properties of the isoG tetrad. All isoG tetrads in cyclic form are more stable than guanine tetrads. The difference in the stabilization energy between the planar and nonplanar conformers of the isoG tetrad is negligible. With the bond energy assignment, we are able to investigate the cooperative effect of hydrogen bonding in the cyclic tetrads. The cooperative effects of hydrogen bonding are crucial for the highly stabilized isoG tetrads. The balance between proton donation and the accepting of protons in the isoG tetrad governs the cooperative effects. Bifurcated H-bonding is important in the formation of isoG tetrads. They provide alternatives for isoG to develop various stable ...

Isoguanine (2-oxo-6-aminoguanine, isoG) quintet and its cation (Na + and K + ) complexes have been investigated by density functional theory (DFT) in order to understand the formation and stability of the high-order self-pairing of isoG systems. The comparison of the relative stability of the quintet with that of the tetrad indicates preferential formation of the isoG tetrad in the absence of metal ions. This preference is governed by the entropy of the system as revealed in this study. The large interaction energy evaluated for complexes of cations with the isoG quintet suggests that metal ions are crucial for regulating the strand association. This study also provides direct evidence for the orbital interaction between K + and the surrounding oxygen atoms in the tetrad and quintet complexes.

Assuming that the efficiency of the incorporation of 5-methyl-2'-deoxyisocytosine-5' triphosphate (dMiCTP) and dTTP opposite isoguanine (iG) is a measure of the proportion of the keto and enol tautomers of iG in the Thermus aquaticus DNA polymerase active centre, we studied the influence of temperature and iG-neighbouring bases in the template on base-pairing of iG. On the basis of experiments with four sequences (3'-TXT-5', 3'-GXG-5', 3'-CXC-5', 3'-CXT-5', where X=iG) at 37, 50, 65 and 80 degrees C, we found that 3'-neighbours decrease the fraction of the keto tautomer in the order C>G>or=T, whereas temperature apparently does not influence the tautomeric equilibrium of iG. The variability of the ratio of incorporation of dMiCTP versus dTTP (5-20) primarily reflects the variability of K (m) values, since V (max) values are roughly similar, which indicates that the iG.MiC and iG.T pairs fit the polymerase active centre equally well. The altering of the base-pairing of iG by sequence context is discussed in relation to tautomerism and miscoding of this oxidized adenine derivative. A key derivative for preparation oligodeoxynucleotides, O (2)-diphenylcarbamoyl- N (6)-[(dimethylamino)ethylidene]-2'-deoxyisoguanosine, is extremely labile (t (1/2)=3.5 min) in 3% trichloroacetic acid/dichloromethane, i.e. under the conditions of automated DNA synthesis, which results in low yield and length heterogeneity of templates.

The formation of both isoguanine tetrad and isoguanine pentad alkali metal ion complexes has been reported in experimental studies. We have performed B3LYP hybrid density functional calculations on complexes between alkali metal ions and cyclic isoguanine tetrads and pentads to study a possible preference of specific ions for either pentads or tetrads. All tetrad cation complexes are strongly nonplanar, except for Li + complexes. Pentads form planar complexes with K + and Rb + . For all investigated model systems, the polyad alkali ion interaction is the dominant contribution to the interaction energy. In tetrads, the hydrogen bond pattern changes when passing from the tetrad to the metal-ion-containing complexes. In general, the interaction energy between polyads and alkali metal ions decreases with the size of the ion. For Li + , the interaction with the tetrad is stronger, whereas for ions with larger radii the pentad alkali metal ion interaction energy exceeds the corresponding energy for tetrads. A comparison of the interaction energies per base also indicates that the formation of tetrad ion complexes is generally favored for smaller ions, whereas for large ions the difference of the interaction energy per base in tetrads and pentads vanishes. To estimate the performance of the density functional approach for hydrogen-bonded systems, dimers of 6-amino-1H-pyrimidin-2-one, a substructure of isoguanine, have been studied by B3LYP and Moller-Plesset perturbation theory.

Noncanonical parallel-stranded DNA double helices (ps-DNA) comprising natural nucleotide sequences are usually second in stability to antiparallel-stranded (aps) canonical DNA structures, which ensures reliable cell functioning. However, recent data indicate a possible role of ps-DNA in DNA loops or in trinucleotide repeats connected with neurodegenerative diseases. The review surveys recent studies on the effect of nucleotide sequence on preference of one or other type of DNA duplex. (1) Ps-DNA with mixed AT/GC composition was found to have conformational and thermodynamic properties drastically different from those of Watson-Crick double helix. Its stability depends strongly on the specific sequence in a manner peculiar to the ps double helix, because of the energy disadvantage of the AT/GC contacts. The AT/GC boundary facilitated flipping of A and T out of the ps double helix. Proton acceptor groups of bases are exposed into the both grooves of the ps-DNA and are accessible to solvent and ligands, including proteins. (2) DNA regions containing natural minor bases isoguanine and isomethylcytosine were shown to form ps-DNA with transAT-, trans isoGC, and trans iso5meCG pairs exceeding in stability a related aps duplex. (3) Nucleotide sequence dG(GT)4G from yeast telomeres and microsatellites was demonstrated to form novel ps-DNA with GG and TT base pairing. Unlike d(GT)n and d(GnTm) sequences able to form quadruplexes, the dG(GT)4G sequence formed no alternative double- or multistranded structures in a wide range of experimental conditions, thus suggesting that the nucleotide context governs the observed structural polymorphism of the d(GT)n sequence. The possible biological role of ps-DNA and the prospects of its study are discussed.

As a follow-up on our previous study of a series of purines (purine, 6-chloropurine, purine-6-thiol, hypoxanthine, theobromine, theophylline, caffeine, and uric acid), we have investigated six additional biologically important purines (adenine, guanine, isoguanine, thioguanine, xanthine, and kinetin). Their ground-state dipole moments were measured in dioxane at 293 K. The first excited singlet-state dipole moments were obtained using the solvatochromic shift equations (McRae, Suppan, Bakhshiev, and Kawski-Chamma-Viallet). The theoretical dipole moments were calculated as a combination of the π-moment (PPP method) and the σ-moment (vector sum of the σ-bond and σ-group moments). The same approach was used to obtain their first excited singlet-state dipole moments (excited state π-moment; σ-moment assumed to be the same as in the ground state). Ab initio HF 6-31G** calculations were also used to obtain ground-state dipole moments for all the fourteen purines under study. In addition, a DFT/B3PW91/6311++(2df,2p) calculation has been carried out for purine for comparison. The different sets of theoretical dipole moments were compared with the respective experimental values. There is an approximately equally good agreement among the experimental dipole moments and the PPP + σ dipole moments (±6.9%) and the ab initio dipole moments (±7.4%). The effect of structure on the dipole moments is discussed.

The phosphoramidites of 8-aza-7-deaza-2'-deoxyisoguanosine (1a) and its bromo derivative 1b as well as of 6-aza-2'-deoxyisocytidine and its 5-methyl derivative (3a,b) were synthesized. Parallel-stranded duplexes containing the nucleosides 1a,b show a significantly enhanced duplex stability compared to those containing 2'-deoxyisoguanosine.

The incorporation of alternative functional components into nucleic acids can provide insight into what molecular features are necessary for an informational macromolecule to be successful. It can also provide a means to improve particular physical characteristics of nucleic acids for diagnostic and therapeutic purposes, or probe mechanisms. By testing the fitness of nucleic acid-like molecules derived by structural permutations of RNA, it may also prove possible to trace a path from simple prebiotic precursors to biotic molecules. This article describes the applications of 2′,5′-phosphodiester linked, zwitterionic, and base-permuted nucleic acid derivatives.