Sonogashira alkynylation of unprotected 8-brominated adenosines and guanosines: fluorescence properties of compact conjugated acetylenes containing a purine ring

Bond Formation at C8 in the Nucleoside and Nucleotide Purine Scaffold: An Informative Selection

This paper presents methods for the introduction and exchange of substituents in a nucleobase and its nucleosides and nucleotides with emphasis on the C8-position in the purine skeleton. The nucleobase is open for electrophilic and nucleophilic chemistry. The nucleophilic chemistry consists mainly of displacement reactions when the C8-substituent is a good leaving group such as a halogen atom. The heteroatom in amines, sulfides, or oxides is a good nucleophile. Halides are good reaction partners. Metal-promoted cross-coupling reactions are important for carbylations. Direct oxidative metalation reactions using sterically hindered metal amides offer chemo- and regio-selectivity besides functional tolerance and simplicity. The carbon site is highly nucleophilic after metalation and adds electrophiles resulting in chemical bond formation. Conditions for metal-assisted reactions are described for nucleobases and their glycosides.

Probing the local structure and dynamics of nucleotides using vibrationally enhanced alkynyl stretching

Monitoring the site-specific local structure and dynamics of polynucleotides and DNA is important for understanding their biological functions. However, structurally characterizing these biomolecules with high time resolution has been known to be experimentally challenging. In this work, several 5-silylethynyl-2'-deoxynucleosides and 5-substituted phenylethynyl-2'-deoxynucleosides on the basis of deoxycytidine (dC) and deoxythymidine (dT) were synthesized, in which the alkynyl group shows intensified CC stretching vibration with infrared transition dipole moment magnitude close to that of typical CO stretching, and exhibits structural sensitivities in both vibrational frequency and spectral width. In particular, 5-trimethylsilylethynyl-2'-dC (^TMSEdC, molecule 1a) was examined in detail using femtosecond nonlinear IR spectroscopy. The solvent dependent CC stretching frequency of 1a can be reasonably interpreted mainly as the hydrogen-bonding effect between the solvent and cytosine base ring structure. Transient 2D IR and pump-probe IR measurements of 1a carried out comparatively in two aprotic solvents (DMSO and THF) and one protic solvent (MeOH) further reveal solvent dependent ultrafast vibrational properties, including diagonal anharmonicity, spectral diffusion, vibrational relaxation and anisotropy dynamics. These observed sensitivities are rooted in an extended π-conjugation of the base ring structure in which the CC group is actively involved. Our results show that the intensified CC stretching vibration can potentially provide a site-specific IR probe for monitoring the equilibrium and ultrafast structural dynamics of polynucleotides.

Diversely C8-functionalized adenine nucleosides via their underexplored carboxaldehydes

The potentially versatile N-unprotected 8-formyl derivatives of adenosine and 2'-deoxyadenosine are highly underexploited for C8 modifications of these nucleosides. Only in situ formation of 8-formyladenosine is known and a single application of an N-benzoyl derivative has been reported. On the other hand, 8-formyl-2'-deoxyadenosine and its applications remain unknown. Herein, we report straightforward, scalable syntheses of both N-unprotected 8-formyladenine nucleoside derivatives, and demonstrate broad diversification at the C8 position by hydroxymethylation, azidation, CuAAC ligation, reductive amination, as well as olefination and fluoroolefination with modified Julia and a Horner-Wadsworth-Emmons reagents.

Bright fluorescent purine analogues as promising probes

Modified bright fluorescent nucleosides that respond to the microenvironment have great potential as probes. A series of novel 8-(phenylethynyl)phenylated 2-amino-2'-deoxyadenosine and 2'-deoxyisoguanosine derivatives have been synthesized by Sonogashira-type coupling reaction and Suzuki reaction. The maximum emission of the new compounds is in the visible region, with strong solvatochromicity and pH-dependent fluorescent properties. Furthermore, some of them exhibit bright fluorescence emissions in various solvents (ε × Φ = 4000-39,000 cm-1 M-1). These consequences indicate that purine analogues could respond to the microenvironment and serve as promising fluorescent probes.Supplemental data for this article is available online at https://doi.org/10.1080/15257770.2021.2004418 .

Fluorescent excimers and exciplexes of the purine base derivative 8-phenylethynyl-guanine in DNA hairpins

The ground- and excited-state electronic interactions between the nucleobase analog 8-(4'-phenylethynyl)deoxyguanosine, EG, with natural nucleobases and 7-deazaguanine, as well as between adjacent EG base analogs, have been characterized using a combination of steady-state spectroscopy and time-resolved fluorescence, absorption, and stimulated Raman spectroscopies. The properties of the nucleoside EG-H2 are only weakly perturbed upon incorporation into synthetic DNA hairpins in which thymine, cytosine or adenine are the bases flanking EG. Incorporation of the nucleoside to be adjacent to guanine or deazaguanine results in the formation of short-lived (40-80 ps) exciplexes, the charge transfer character of which increases as the oxidation potential of the donor decreases. Hairpins possessing two or three adjacent EG base analogs display exciton-coupled circular dichroism in the ground state and form long-lived fluorescent excited states upon electronic excitation. Incorporation of EG into the helical scaffold of the DNA hairpins places it adjacent to its neighboring nucleobases or a second EG, thus providing the close proximity required for the formation of exciplex or excimer intermediates upon geometric relaxation of the short-lived EG excited state. The three time-resolved spectroscopic methods employed permit both the characterization of the several intermediates and the kinetics of their formation and decay.

Synthesis of 8-Substituted 2'-Deoxyisoguanosines via Unprotected 8-Brominated 2-Amino-2'-deoxyadenosine

A variety of applications of 8-alkynylated nucleosides has prompted the synthesis of new purine analogues. Bromination of unprotected 2-amino-2'-deoxyadenosine with Br₂ /AcOH/AcONa gives 2-amino-8-bromo-2'-deoxyadenosine (87%). The brominated derivative is converted to 8-alkynylated 2-amino-2'-deoxyadenosines by palladium-catalyzed Sonogashira cross-coupling reaction via microwave assistance (81 - 95%). The resulting compounds are further transformed to 8-alkynylated 2'-deoxyisoguanosines (52 - 70%). The physical properties of new compounds are investigated.

Design and synthesis of fluorescent 7-deazaadenosine nucleosides containing π-extended diarylacetylene motifs

A novel series of C-modified π-extended 7-deazaadenosines exhibit promising fluorescence properties.

Analogues of uracil nucleosides with intrinsic fluorescence (NIF-analogues): synthesis and photophysical properties

Uridine cannot be utilized as fluorescent probe due to its extremely low quantum yield. For improving the uracil fluorescence characteristics we extended the natural chromophore at the C5 position by coupling substituted aromatic rings directly or via an alkenyl or alkynyl linker to create fluorophores. Extension of the uracil base was achieved by treating 5-I-uridine with the appropriate boronic acid under the Suzuki coupling conditions. Analogues containing an alkynyl linker were obtained from 5-I-uridine and the suitable boronic acid in a Sonogashira coupling reaction. The uracil fluorescent analogues proposed here were designed to satisfy the following requirements: a minimal chemical modification at a position not involved in base-pairing, resulting in relatively long absorption and emission wavelengths and high quantum yield. 5-((4-Methoxy-phenyl)-trans-vinyl)-2'-deoxy-uridine, 6b, was found to be a promising fluorescent probe. Probe 6b exhibits a quantum yield that is 3000-fold larger than that of the natural chromophore (Φ 0.12), maximum emission (478 nm) which is 170 nm red shifted as compared to uridine, and a Stokes shift of 143 nm. In addition, since probe 6b adopts the anti conformation and S sugar puckering favored by B-DNA, it makes a promising nucleoside analogue to be incorporated in an oligonucleotide probe for detection of genetic material.

Site-specific control of N7-metal coordination in DNA by a fluorescent purine derivative

A synthetic strategy that utilizes O6-protected 8-bromoguanosine gives broad access to C8-guanine derivatives with phenyl, pyridine, thiophene, and furan substituents. The resulting 8-substituted 2'-deoxyguanosines are push-pull fluorophores that can exhibit environmentally sensitive quantum yields (Φ=0.001-0.72) due to excited-state proton-transfer reactions with bulk solvent. Changes in nucleoside fluorescence were used to characterize metal-binding affinity and specificity of 8-substituted 2'-deoxyguanosines. One derivative, 8-(2-pyridyl)-2'-deoxyguanosine (2PyG), exhibits selective binding of Cu(II), Ni(II), Cd(II), and Zn(II) through a bidentate effect provided by the N7 position of guanine and the 2-pyridyl nitrogen atom. Upon incorporation into DNA, 2-pyridine-modified guanine residues selectively bind to Cu(II) and Ni(II) with equilibrium dissociation constants (K(d)) that range from 25 to 850 nM; the affinities depend on the folded state of the oligonucleotide (duplex>G-quadruplex) as well as the identity of the metal ion (Cu>Ni≫Cd). These binding affinities are approximately 10 to 1 000 times higher than for unmodified metal binding sites in DNA, thereby providing site-specific control of metal localization in alternatively folded nucleic acids. Temperature-dependent circular-dichroism studies reveal metal-dependent stabilization of duplexes, but destabilization of G-quadruplex structures upon adding Cu(II) to 2PyG-modified oligonucleotides. These results demonstrate how the addition of a single pyridine group to the C8 position of guanine provides a powerful new tool for studying the effects of N7 metalation on the structure, stability, and electronic properties of nucleic acids.

8-(p-CF3-cinnamyl)-modified purine nucleosides as promising fluorescent probes

Natural nucleotides are not useful as fluorescent probes because of their low quantum yields. Therefore, a common methodology for the detection of RNA and DNA is the application of extrinsic fluorescent dyes coupled to bases in oligonucleotides. To overcome the many limitations from which fluorescent nucleotide-dye conjugates suffer, we have developed novel purine nucleosides with intrinsic fluorescence to be incorporated into oligonucleotide probes. For this purpose we synthesized adenosine and guanosine fluorescent analogues 7-25, conjugated at the C8 position with aryl/heteroaryl moieties either directly, or via alkenyl/alkynyl linkers. Directly conjugated analogues 7-14, exhibited high quantum yields, φ >0.1, and short λ(em) (<385 nm). Alkynyl conjugated analogues 22-25, exhibited low quantum yields, φ <0.075, and λ(em)<385 nm. The alkenyl conjugated analogues 15-21, exhibited λ(em) 408-459 nm. While analogues 15,16, and 20 bearing an EDG on the aryl moiety, exhibited φ <0.02, analogues 17, and 21 with EWG on the aryl moiety, exhibited extremely high quantum yields, φ ≈ 0.8, suggesting better intramolecular charge transfer. We determined the conformation of selected adenosine analogues. Directly conjugated analogue 8 and alkynyl conjugated analogue 22, adapted the syn conformation, whereas alkenyl conjugated analogue 15 adapted the anti conformation. Based on the long emission wavelengths, high quantum yields, anti conformation and base-paring compatibility, we suggest analogues 17 and 21 for further development as fluorescent probes for the sensitive detection of genetic material.

Interrogation of a Sonogashira cross-coupling of 8-bromoguanosine with phenylacetylene on amberlite: evidence for Pd/Cu ion binding and propagation of Pd/Cu nanoparticles

The reactivity of Amberlite (IRA-67) base "heterogeneous" resin in Sonogashira cross-coupling of 8-bromoguanosine 1 with phenylacetylene 3 to give 2 has been examined. Both 1 and 2 coordinate to Pd and Cu ions, which explains why at equivalent catalyst loadings, the homogeneous reaction employing triethylamine base is poor yielding. X-ray photo-electron spectroscopy (XPS) has been used to probe and quantify the active nitrogen base sites of the Amberlite resin, and postreaction Pd and Cu species. The PdCl(2)(PPh(3))(2) precatalyst and CuI cocatalyst degrade to give Amberlite-supported metal nanoparticles (average size ∼2.7 nm). The guanosine product 2 formed using the Amberlite Pd/Cu catalyst system is of higher purity than reactions using a homogeneous Pd precatalyst, a prerequisite for use in biological applications.

Fluorescence properties of 8-(2-pyridyl)guanine "2PyG" as compared to 2-aminopurine in DNA

Because of their environment-sensitive fluorescence quantum yields, base analogues such as 2-aminopurine (2AP), 6-methylisoxanthopterin (6-MI), and 3-methylisoxanthopterin (3-MI) are widely used in nucleic-acid folding and catalysis assays. Emissions from these guanine mimics are quenched by base-stacking interactions and collisions with purine residues. Fluorescent base analogues that remain highly emissive in folded nucleic acids can provide sensitive means to differentiate DNA/RNA structures by participating in energy transfer from proximal ensembles of unmodified nucleobases. The development of new, highly emissive guanine mimics capable of proper base stacking and base-pairing interactions is an important prerequisite to this approach. Here we report a comparison of the most commonly used probe, 2-aminopurine (2AP), to 8-(2-pyridyl)-2'-deoxyguanosine (2PyG). The photophysical properties of these purine derivatives are very different. 2PyG exhibits enhanced fluorescence quantum yields upon its incorporation into folded nucleic acids--approximately 50-fold brighter fluorescence intensity than 2AP in the context of duplex DNA. Due to its bright fluorescence and compatibility with proper DNA folding, 2PyG can be used to accurately quantify energy-transfer efficiencies, whereas 2AP is much less sensitive to structure-specific trends in energy transfer. When using nucleoside monomers, Stern-Volmer plots of 2AP fluorescence revealed upward curvature of F(0) /F upon titration of guanosine monophoshate (GMP), whereas 2PyG exhibited unusual downward curvature of F(0) /F that resulted in a recovery of fluorescence at high GMP concentrations. These results are consistent with the trends observed for 2PyG- and 2AP-containing oligonucleotides, and furthermore suggest that solutions containing high concentrations of GMP can, in some ways, mimic the high local nucleobase densities of folded nucleic acids.

Highly fluorescent guanosine mimics for folding and energy transfer studies

Guanosines with substituents at the 8-position can provide useful fluorescent probes that effectively mimic guanine residues even in highly demanding model systems such as polymorphic G-quadruplexes and duplex DNA. Here, we report the synthesis and photophysical properties of a small family of 8-substituted-2′-deoxyguanosines that have been incorporated into the human telomeric repeat sequence using phosphoramidite chemistry. These include 8-(2-pyridyl)-2′-deoxyguanosine (2PyG), 8-(2-phenylethenyl)-2′-deoxyguanosine (StG) and 8-[2-(pyrid-4-yl)-ethenyl]-2′-deoxyguanosine (4PVG). On DNA folding and stability, 8-substituted guanosines can exhibit context-dependent effects but were better tolerated by G-quadruplex and duplex structures than pyrimidine mismatches. In contrast to previously reported fluorescent guanine analogs, 8-substituted guanosines exhibit similar or even higher quantum yields upon their incorporation into nucleic acids (Φ = 0.02–0.45). We have used these highly emissive probes to quantify energy transfer efficiencies from unmodified DNA nucleobases to 8-substituted guanosines. The resulting DNA-to-probe energy transfer efficiencies (η_t) are highly structure selective, with η_t(duplex) < η_t(single-strand) < η_t(G-quadruplex). These trends were independent of the exact structural features and thermal stabilities of the G-quadruplexes or duplexes containing them. The combination of efficient energy transfer, high probe quantum yield, and high molar extinction coefficient of the DNA provides a highly sensitive and reliable readout of G-quadruplex formation even in highly diluted sample solutions of 0.25 nM.

A sequential direct arylation/Suzuki-Miyaura cross-coupling transformation of unprotected 2'-deoxyadenosine affords a novel class of fluorescent analogues

Novel rigid 8-biaryl-2'-deoxyadenosines with tuneable fluorescent properties can be accessed by an efficient sequential catalytic Pd(0)-coupling approach.

Design of environmentally sensitive fluorescent 2'-deoxyguanosine containing arylethynyl moieties: distinction of thymine base by base-discriminating fluorescent (BDF) probe

We have synthesized various substituted 8-arylethynylated 2'-deoxyguanosine derivatives. Among them, acetyl substituted deoxyguanosine analogue 4c showed a remarkable solvent dependent fluorescence property, that is, an intense fluorescence in non-polar solvents but extremely weak fluorescence in polar solvents like methanol. By using solvatofluorochromic deoxyguanosine analogue 4c, we have developed highly thymine (T) selective fluorescent DNA probes that can sense T opposite 4c in a target DNA regardless of the flanking sequences. We were able to demonstrate that 4c can be used as a T specific base-discriminating fluorescent (BDF) nucleoside in homogeneous fluorescence assay.

Characterization of the interaction between 8-bromoadenosine with human serum albumin and its analytical application

This study was designed to examine the interaction of 8-bromoadenosine with human serum albumin (HSA) by fluorescence spectroscopy in combination with molecular modeling under simulative physiological conditions. The results of fluorescence measurements indicate that 8-bromoadenosine has a strong ability to quench the intrinsic fluorescence of HSA through static quenching procedure. The binding constants (K) at different temperatures and thermodynamic parameters, enthalpy changes (DeltaH) and entropy changes (DeltaS) were calculated according to the fluorescence data. The results showed that the hydrophobic force played the major role in the binding of 8-bromoadenosine to HSA. The fluorescence experimental results were in agreement with the results obtained by molecular modeling study. The effects of some normal positive and negative ions on the binding constants were also discussed. Moreover, the synchronous fluorescence technique was used to characterize the interaction of 8-bromoadenosine to HSA and successfully applied to determine the total proteins in human serum, urine and saliva samples at room temperature under the optimum conditions with a wide linear range and satisfactory results.

Rigid rod and tetrahedral hybrid compounds featuring nucleobase and nucleoside end-capped structures

Being aimed at a new type of porous solids, a moduled design strategy of molecular tectons, making use of the conjugation between a shape defined artificial backbone and the bioinspired molecular fragments of nucleobases or nucleobase derivatives as functional end-caps, has been developed. This led to the formation of the new hybrid compounds 1-13 of linear and tetrahedral geometry, containing uracil, adenine, adenosine, guanosine and its acylated analogs as the sticky end-cap sites. The compounds were synthesized from a halogen or ethynyl substituted nucleobase component and the corresponding ethynylated spacer unit following a metal assisted coupling process as the key reaction step. X-Ray crystal structure analysis demonstrates that the parent compound 1 is a solvent complex with DMSO (1:2), showing the DMSO molecules incorporated in a hydrogen bonded layer structure. Specific dependencies of the fluorescence properties of the new compounds in solution on the structure of the molecules are reported. A selection of solid compounds has been studied in respect of their ability to adsorb organic vapours. They revealed significant differences both in the sorption capacity and the selectivity towards particular solvent vapours.

Nucleobase-containing transition metal complexes as building blocks for biological markers and supramolecular structures

The incorporation of metal complexes into nucleobases, nucleosides and nucleotides has provided a focus for the development of many novel compounds with a wide range of applications. In this perspective article the different methods to incorporate transition metal complexes into these species will be described. Applications of these compounds as biological markers, catalysts and how the hydrogen bonding properties may be employed in directing supramolecular assembly in both the solid state and solution will be discussed.

Microwave-Assisted Direct Amination: Rapid Access to Multi-Functionalized N6-Substituted Adenosines

Analogues of adenosine have a range of interesting biological activities and potential therapeutic applications. A method for the efficient preparation of highly functionalized N6-substituted adenosines has been developed from the corresponding tert-butyldimethylsilyl-protected inosine. The key step in this procedure is a microwave-assisted amination reaction between an appropriately substituted inosine and an amine in the presence of PyBroP. High yields of desired N6-substituted adenosines were achieved with hindered amines and the reaction was also found to accommodate a range of substituents on the inosine precursor.

A fast synthetic route to GDP-sugars modified at the nucleobase

The direct structural modification of GDP-mannose via the bromination and Suzuki-Miyaura cross-coupling of the unprotected sugar-nucleotide, to produce 8-substituted fluorescent analogues of GDP-mannose.

Structure-activity relationship studies on anti-HCV activity of ring-expanded ('fat') nucleobase analogues containing the imidazo[4,5-e][1,3]diazepine-4,8-dione ring system

In continuation of our structure-activity relationship studies on anti-HCV activity of the title imidazo[4,5-e][1,3]diazepine ring system, we report here the synthesis and effect on biological activity of introducing hydrophobic substituents at the 2-position of the heterocycle. Our results suggest that there is no particular advantage to that end as the observed antiviral activity of the test compounds was lower than that of the unmodified 2-bromo derivative used for comparison. The activity/toxicity profile of all target compounds, however, was still better than that of the reference compound ribavirin used in the antiviral assay, but not as good as that of interferon-alpha, the other reference compound used in the assay.

A facile two-step synthesis of 8-arylated guanosine mono- and triphosphates (8-aryl GXPs)

We report a simple and high-yielding two-step procedure for the preparation of 8-arylated guanosine mono- and triphosphates (8-aryl GXPs). The key step of our synthesis is the Suzuki-Miyaura coupling of unprotected 8-bromo GMP and 8-bromo GTP with various arylboronic acids in aqueous solution. The 8-bromoguanosine 5'-phosphates required as cross-coupling substrates were prepared from 8-bromoguanosine via an optimised Yoshikawa procedure.