Porphyrin substituted phosphoramidites: new building blocks for porphyrin-oligonucleotide syntheses

Preparation of porphyrin and phthalocyanine conjugates for biomedical applications

The aim of this review is to offer a succinct overview of the main synthetic techniques used in the preparation of conjugates containing porphyrins, including chlorins and bacteriochlorins and phthalocyanines for biomedical applications and photodynamic therapy (PDT). To illustrate the conjugation techniques representative examples from the literature will be presented.

Synthesis and Applications of Porphyrin-Biomacromolecule Conjugates

With potential applications in materials and especially in light-responsive biomedicine that targets cancer tissue selectively, much research has focused on developing covalent conjugation techniques to tether porphyrinoid units to various biomacromolecules. This review details the key synthetic approaches that have been employed in the recent decades to conjugate porphyrinoids with oligonucleotides and peptides/proteins. In addition, we provide succinct discussions on the subsequent applications of such hybrid systems and also give a brief overview of the rapidly progressing field of porphyrin-antibody conjugates. Since nucleic acid and peptide systems vary in structure, connectivity, functional group availability and placement, as well as stability and solubility, tailored synthetic approaches are needed for conjugating to each of these biomacromolecule types. In terms of tethering to ONs, porphyrins are typically attached by employing bioorthogonal chemistry (e.g., using phosphoramidites) that drive solid-phase ON synthesis or by conducting post-synthesis modifications and subsequent reactions (such as amide couplings, hydrazide-carbonyl reactions, and click chemistry). In contrast, peptides and proteins are typically conjugated to porphyrinoids using their native functional groups, especially the thiol and amine side chains. However, bioorthogonal reactions (e.g., Staudinger ligations, and copper or strain promoted alkyne-azide cycloadditions) that utilize de novo introduced functional groups onto peptides/proteins have seen vigorous development, especially for site-specific peptide-porphyrin tethering. While the ON-porphyrin conjugates have largely been explored for programmed nanostructure self-assembly and artificial light-harvesting applications, there are some reports of ON-porphyrin systems targeting clinically translational applications (e.g., antimicrobial biomaterials and site-specific nucleic acid cleavage). Conjugates of porphyrins with proteinaceous moieties, on the other hand, have been predominantly used for therapeutic and diagnostic applications (especially in photodynamic therapy, photodynamic antimicrobial chemotherapy, and photothermal therapy). The advancement of the field of porphyrinoid-bioconjugation chemistry from basic academic research to more clinically targeted applications require continuous fine-tuning in terms of synthetic strategies and hence there will continue to be much exciting work on porphyrinoid-biomacromolecule conjugation.

Synthesis and characterization of 5-(4-carboxyphenylspermine)-10,15,20-triphenylporphyrin

We synthetized and characterized a mono spermine porphyrin derivative by NMR, UV-vis and fluorescence spectroscopy. The photophysical properties and the protonation equilibria of 5-(4-carboxyphenylspermine)-10,15,20-triphenylporphyrin have been investigated, showing that porphyrin does not aggregate in acidic solutions, differently from what occurs as soon as the core of the porphyrin is deprotonated. These aggregation processes have been detected by the rising of new fluorescence band and a significant splitting of the Soret band.

Preparation of Ru(ii)@oligonucleotide nanosized polymers as potential tumor-imaging luminescent probes

The development of Ru(ii) complexes as luminescent probes has attracted increasing attention in recent decades. In this study, the nanosized polymers of two Ru(ii) complexes [Ru(phen)₂(dppz)](ClO₄)₂ (1, phen = 1,10-phenanthrolin; dppz = dipyrido[3,2-a:2′,3′-c]phenazine) and [Ru(phen)₂(Br-dppz)](ClO₄)₂ (2, Br-dppz = 11-bromodipyrido[3,2-a:2′,3′-c]phenazine) with oligonucleotides were prepared and investigated as potential tumor-imaging probes. The formation of the nanosized polymers, which had an average width of 125–438 nm and an average height of 3–6 nm, for 1 and 2@oligonucleotides were observed through atomic force microscopy. The emission spectra indicated that the luminescence of 1 and 2 markedly increased after binding to oligonucleotides and double-strand DNA (calf thymus DNA), respectively. Moreover, further studies indicated that 1@oligonucleotides and 2@oligonucleotides can easily enter into tumor cells and selectively highlight the tumor area in the zebrafish bear xenograft tumor (MDA-MB-231). In summary, this study demonstrated that 1@oligonucleotides and 2@oligonucleotides could be developed as potential tumor-imaging luminescent probes for clinical diagnosis and therapy.

Ru(ii)@oligonucleotide nanoparticles can be developed as potential tumor selective tracker and have potential applications of tumor targeting imaging.

Self-assembly of porphyrin–DNA hybrids into large flat nanostructures

Two complementary 21-mer oligonucleotide/porphyrin hybrids were synthesized and assembled into nanostructures.

Increased duplex stabilization in porphyrin-LNA zipper arrays with structure dependent exciton coupling

Porphyrins were attached to LNA uridine building blocks via rigid 5-acetylene or more flexible propargyl-amide linkers and incorporated into DNA strands. The systems show a greatly increased thermodynamic stability when using as little as three porphyrins in a zipper arrangement. Thermodynamic analysis reveals clustering of the strands into more ordered duplexes with both greater negative ΔΔS and ΔΔH values, and less ordered duplexes with small positive ΔΔS differences, depending on the combination of linkers used. The exciton coupling between the porphyrins is dependent on the flanking DNA sequence in the single stranded form, and on the nature of the linker between the nucleobase and the porphyrin in the double stranded form; it is, however, also strongly influenced by intermolecular interactions. This system is suitable for the formation of stable helical chromophore arrays with sequence and structure dependent exciton coupling.

Structural Studies on Porphyrin-PNA Conjugates in Parallel PNA:PNA Duplexes: Effect of Stacking Interactions on Helicity

Parallel PNA:PNA duplexes were synthesized and conjugated with meso-tris(pyridyl)phenylporphyrin carboxylic acid at the N-terminus. The introduction of one porphyrin unit was shown to affect slightly the stability of the PNA:PNA parallel duplex, whereas the presence of two porphyrin units at the same end resulted in a dramatic increase of the melting temperature, accompanied by hysteresis between melting and cooling curves. The circular dichroism (CD) profile of the Soret band and fluorescence quenching strongly support the occurrence of a face-to-face interaction between the two porphyrin units. Introduction of a L-lysine residue at the C-terminal of one strand of the parallel duplex induced a left-handed helical structure in the PNA:PNA duplex if the latter contains only one or no porphyrin moiety. The left-handed helicity was revealed by nucleobase CD profile at 240-280 nm and by the induced-CD observed in the presence of the DiSC2 (5) cyanine dye at ~500-550 nm. Surprisingly, the presence of two porphyrin units led to the disappearance of the nucleobase CD signal and the absence of CD exciton coupling within the Soret band region. In addition, a dramatic decrease of induced CD of DiSC2 (5) was observed. These results are in agreement with a model where the porphyrin-porphyrin interactions cause partial loss of chirality of the PNA:PNA parallel duplex, forcing it to adopt a ladder-like conformation.

Synthesis of sulfonamide conjugates of Cu(ii), Ga(iii), In(iii), Re(v) and Zn(ii) complexes: carbonic anhydrase inhibition studies and cellular imaging investigations

New sulfonamides and their metal complexes are reported, with a focus on porphyrin derivatives for simultaneous cellular optical imaging, radiolabelling and Carbonic Anhydrase inhibition capabilities.

Synthesis of a multibranched porphyrin-oligonucleotide scaffold for the construction of DNA-based nano-architectures

The interest in the functionalization of oligonucleotides with organic molecules has grown considerably over the last decade. In this work, we report on the synthesis and characterization of porphyrin-oligonucleotide hybrids containing one to four DNA strands (P1-P4). The hybrid P4, which inserts one porphyrin and four DNA fragments, was combined with gold nanoparticles and imaged by transmission electron microscopy.

Comparative study of the interaction of meso-tetrakis (N-para-trimethyl-anilium) porphyrin (TMAP) in its free base and Fe derivative form with oligo(dA.dT)15 and oligo(dG.dC)15

Interaction between a cationic porphyrin and its ferric derivative with oligo(dA.dT)15 and oligo(dG.dC)15 was studied by UV-vis spectroscopy, resonance light scattering (RLS), and circular dichroism (CD) at different ionic strengths; molecular docking and molecular dynamics simulation were also used for completion. Followings are the observed changes in the spectral properties of meso-tetrakis (N-para-trimethyl-anilium) porphyrin (TMAP), as a free-base porphyrin with no axial ligand, and its Fe derivative (FeTMAP) upon interaction with oligo(dA.dT)15 and oligo(dG.dC)15: (1) the substantial red shift and hypochromicity at the Soret maximum in the UV-vis spectra; (2) the increased RLS intensity by increasing the ionic strength; and (3) an intense bisignate excitonic CD signal. All of them are the reasons for TMAP and FeTMAP binding to oligo(dA.dT)15 and oligo(dG.dC)15 with the outside binding mode, accompanied by the self-stacking of the ligands along the oligonucleotide helix. The CD results demonstrated a drastic change from excitonic in monomeric behavior at higher ionic strengths, which indicates the groove binding of the ligands with oligonucleotides. Molecular docking also confirmed the groove binding mode of the ligands and estimated the binding constants and energies of the interactions. Their interaction trend was further confirmed by molecular dynamics technique and structure parameters obtained from simulation. It showed that TMAP reduced the number of intermolecular hydrogen bonds and increased the solvent accessible surface area in the oligonucleotide. The self-aggregation of ligands at lower concentrations was also confirmed.

Highly sensitive and selective spectroscopic detection of mercury(II) in water by using pyridylporphyrin-DNA conjugates

Single-labeled pyridylporphyrin-DNA conjugates are reported as highly sensitive and selective spectroscopic sensors for mercury(II) ions in water. The effects of chemical structure (thymine versus adenine), number of nucleotides (monomer versus octamer), and porphyrin metalation (Zn versus free base) on the sensitivity and selectivity of mercury(II) detection are explored. The results indicated that pyridylporphyrin rather than the nucleobase plays a crucial role in mercury(II) sensing, because porphyrin conjugates with both adenosine and thymidine exhibited excellent mercury(II) detection. Mercury(II) recognition was shown in emission quenching, as well as in a redshift of the porphyrin Soret band absorption. The limit of detection (LOD, 3σ/slope) of zinc(II) pyridylporphyrin-5'-oligodeoxythymidine (ZnPorT8) obtained by fluorescence quenching was calculated to be 21.14 nM. Other metal cations (Zn(2+), Cd(2+), Pb(2+), Mn(2+), Ca(2+), Ni(2+), Mg(2+), Fe(2+), Cu(2+), and Na(+)) did not interfere with the emission and absorption sensing of mercury(II). Free-base porphyrin-oligothymine conjugate 2HPorT8 displayed similar sensitivity to ZnPorT8 but different selectivity. The results also implied that the sensing properties of porphyrin-deoxythymidine conjugates could potentially be tuned by porphyrin metalation.

Density functional study of tetraphenylporphyrin long-range exciton coupling

The performance of time-dependent density functional theory (TDDFT) for calculations of long-range exciton circular dichroism (CD) is investigated. Tetraphenylporphyrin (TPP) is used as a representative of a class of strongly absorbing chromophores for which exciton CD with chromophore separations of 50 Å and even beyond has been observed experimentally. A dimer model for TPP is set up to reproduce long-range exciton CD previously observed for a brevetoxin derivative. The calculated CD intensity is consistent with TPP separations of over 40 Å. It is found that a hybrid functional with fully long-range corrected range-separated exchange performs best for full TDDFT calculations of the dimer. The range-separation parameter is optimally tuned for TPP, resulting in a good quality TPP absorption spectrum and small DFT delocalization error (measured by the curvature of the energy calculated as a function of fractional electron numbers). Calculated TDDFT data for the absorption spectra of TPP are also used as input for a 'matrix method' (MM) model of the exciton CD. For long-range exciton CD, comparison of MM spectra with full TDDFT CD spectra for the dimer shows that the matrix method is capable of producing very accurate results. A MM spectrum obtained from TPP absorption data calculated with the nonhybrid Becke88-Perdew86 (BP) functional is shown to match the experimental brevetoxin spectrum 'best', but for the wrong reasons.

A novel sensor for monitoring of iron(III) ions based on porphyrins

Three A(3)B porphyrins with mixed carboxy-, phenoxy-, pyridyl-, and dimethoxy-substituent functionalization on the meso-phenyl groups were obtained by multicomponent synthesis, fully characterized and used as ionophores for preparing PVC-based membrane sensors selective to iron(III). The membranes have an ionophore:PVC:plasticizer composition ratio of 1:33:66. Sodium tetraphenylborate was used as additive (20 mol% relative to ionophore). The performance characteristics (linear concentration range, slope and selectivity) of the sensors were investigated. The best results were obtained for the membrane based on 5-(4-carboxyphenyl)-10,15,20-tris(4-phenoxyphenyl)-porphyrin plasticized with bis(2-ethylhexyl)sebacate, in a linear range from 1 × 10(-7)-1 × 10(-1) M with a slope of 21.6 mV/decade. The electrode showed high selectivity with respect to alkaline and heavy metal ions and a response time of 20 s. The influence of pH on the sensor response was studied. The sensor was used for a period of six weeks and the utility has been tested for the quantitative determination of Fe(III) in recovered solutions from spent lithium ion batteries and for the quantitative determination of Fe(III) in tap water samples.

Porphyrin-DNA conjugates: porphyrin induced adenine-guanine homoduplex stabilization and interduplex assemblies

DNA has found widespread uses as a nanosized scaffold for assembly of patterned multichomophoric nanostructures. Herein we report the synthesis, self-assembly, stability, and spectroscopic studies of short alternating non-self-complementary DNA sequences 5'-(dGdA)(4) and 5'-(dAdG)(4) with non-charged tetraarylporphyrins covalently linked to the 5' position of deoxyadenosine or deoxyguanosine via a phosphate or amide linker. The linker, the metal in the porphyrin coordination center, and the neighboring nucleobase have very distinct effects on the duplex formation of porphyrin-deoxyguanosine-deoxyadenosine oligodeoxynucleotides. At ionic strength between 5 mM and 40 mM, free base trispyridylphenylporphyrin appended to the 5' termini of 5'-(dAdG)(4) oligonucleotide via short non-polar amide linker served as a hydrophobic molecular cap inducing deoxyadenosine-deoxyguanosine antiparallel homoduplex. At ionic strength of ≥60 mM, the free base porphyrin functioned as a molecular 'glue' and induced the formation of porphyrin-DNA inter-homoduplex assemblies with characteristic tetrasignate CD Cotton effects in the porphyrin Soret band region. When the porphyrin cap was covalently attached to 5' position of deoxyguanosine or deoxyadenosine via charged phosphate linker, no significant deoxyadenosine-deoxyguanosine hybridization was observed even at elevated ionic strengths.

Synthesis, structure and physicochemical properties of a saddle-distorted porphyrin with a peripheral carboxyl group

A saddle-distorted porphyrin bearing a carboxyl group as a hydrogen-bonding site on a meso-phenyl group was synthesized and characterized. A supramolecular structure with intermolecular hydrogen bonding was revealed by X-ray diffraction analysis. The effects of the peripheral carboxyl group on the physicochemical properties of the porphyrin as well as on self-assembly were investigated by spectroscopic measurements in solutions. The redox properties of the porphyrin and its Zn(II) complex were also studied by electrochemical measurements and their application to dye-sensitized solar cells was examined.

Synthesis of β-pyrrolic-modified porphyrins and their incorporation into DNA

A synthetic methodology for the synthesis of various β-pyrrolic-functionalised porphyrins and their covalent attachment to 2'-deoxyuridine and DNA is described. Palladium(0)-catalysed Sonogashira and copper(I)-catalysed Huisgen 1,3-dipolar cycloaddition reactions were used to insert porphyrins into the structure of 2'-deoxyuridine and DNA. Insertion of a porphyrin into the middle of single-stranded CT oligonucleotides possessing a 5'-terminal run of four cytosines was shown to trigger the formation of pH- and temperature-dependent i-motif structures. Porphyrin insertion also led to the aggregation of single-stranded purine-pyrimidine sequences, which could be dissociated by heating at 90 °C for 5 min. Parallel triplexes and anti-parallel duplexes were formed in the presence of the appropriate complementary strand(s). Depending on the modification, porphyrins were placed in the major and minor grooves of duplexes and were used as bulged intercalating insertions in duplexes and triplexes. In general, the thermal stabilisation of parallel triplexes possessing porphyrin-modified triplex-forming oligonucleotide (TFO) strands was observed, whereas anti-parallel duplexes were destabilised. These results are compared and discussed on the basis of the results of molecular modelling calculations.

Highly polar carbohydrates stack onto DNA duplexes via CH/π interactions

Carbohydrate-nucleic acid contacts are known to be a fundamental part of some drug-DNA recognition processes. Most of these interactions occur through the minor groove of DNA, such as in the calicheamicin or anthracycline families, or through both minor and major groove binders such as in the pluramycins. Here, we demonstrate that carbohydrate-DNA interactions are also possible through sugar capping of a DNA double helix. Highly polar mono- and disaccharides are capable of CH/π stacking onto the terminal DNA base pair of a duplex as shown by NMR spectroscopy. The energetics of the carbohydrate-DNA interactions vary depending on the stereochemistry, polarity, and contact surface of the sugar involved and also on the terminal base pair. These results reveal carbohydrate-DNA base stacking as a potential recognition motif to be used in drug design, supramolecular chemistry, or biobased nanomaterials.

Functionalized nanostructures: redox-active porphyrin anchors for supramolecular DNA assemblies

We have synthesized and studied a supramolecular system comprising a 39-mer DNA with porphyrin-modified thymidine nucleosides anchored to the surface of large unilamellar vesicles (liposomes). Liposome porphyrin binding characteristics, such as orientation, strength, homogeneity, and binding site size, was determined, suggesting that the porphyrin is well suited as a photophysical and redox-active lipid anchor, in comparison to the inert cholesterol anchor commonly used today. Furthermore, the binding characteristics and hybridization capabilities were studied as a function of anchor size and number of anchoring points, properties that are of importance for our future plans to use the addressability of these redox-active nodes in larger DNA-based nanoconstructs. Electron transfer from photoexcited porphyrin to a lipophilic benzoquinone residing in the lipid membrane was characterized by steady-state and time-resolved fluorescence and verified by femtosecond transient absorption.

Solid-phase synthesis of oligonucleotide conjugates useful for delivery and targeting of potential nucleic acid therapeutics

Olignucleotide-based drugs show promise as a novel form of chemotherapy. Among the hurdles that have to be overcome on the way of applicable nucleic acid therapeutics, inefficient cellular uptake and subsequent release from endosomes to cytoplasm appear to be the most severe ones. Covalent conjugation of oligonucleotides to molecules that expectedly facilitate the internalization, targets the conjugate to a specific cell-type or improves the parmacokinetics offers a possible way to combat against these shortcomings. Since workable chemistry is a prerequisite for biological studies, development of efficient and reproducible methods for preparation of various types of oligonucleotide conjugates has become a subject of considerable importance. The present review summarizes the advances made in the solid-supported synthesis of oligonucleotide conjugates aimed at facilitating the delivery and targeting of nucleic acid drugs.

Synthesis and DNA-recognition and -cleavage properties of multiply charged porphyrin esters

A series of systematically modified porphyrin esters, compounds 1-6, with multiple, permanent positive charges introduced at the meso-positions via N-methylated 4-, 3-, or 2-pyridyl moieties, were prepared and characterized. Their singlet-oxygen production, CT-DNA-binding properties, and plasmid-DNA photocleavage propensities were determined spectroscopically and by gel electrophoresis, and compared to those of the known, fourfold-charged parent porphyrin 4,4',4'',4'''-porphyrin-5,10,15,20-tetrayltetrakis(1-methylpyridinium) (TMPyP4). Some interesting structure-activity relationships could be established to rationalize effects affecting DNA binding mode and cleavage ability.

Porphyrin conjugated to DNA by a 2'-amido-2'-deoxyuridine linkage

A porphyrin that contains a single carboxylic acid group was synthesized and coupled to 2'-amino-2'-deoxyuridine. The resultant product contained a free 3' hydroxyl group and a 4,4'-dimethoxytrityl (DMT) protecting group on the 5' hydroxyl of the uridine, making it suitable for use in oligonucleotide synthesis. The 3' H-phosphonate derivative of this molecule was synthesized and used to form a conjugate with a 19 nucleotide sequence of DNA (5'-CCTCCAGTGGAAATCAAGG-3'). This was carried out with the DNA attached at the 3' end to a control pore glass (CPG) substrate, allowing for rapid purification. After removal of the DMT group, an additional three nucleotides were added, leaving the porphyrin as an internal modification. This is the first report of porphyrin attached internally to an oligonucleotide using a hydrogen-bonding nucleoside analog. This allows oligonucleotides to be used as a scaffold for precise positioning of multiple porphyrins within biomimetic arrays.

Porphyrins as spectroscopic sensors for conformational studies of DNA

Molecular systems containing two or more interacting porphyrins show remarkable spectroscopic features that allow for a very sensitive detection of conformational changes on the microscale level by different methods, such as fluorescence and electronic circular dichroism (ECD). Covalent porphyrin-DNA assemblies can provide a CD profile (exciton couplet) within the porphyrin Soret band region which is very diagnostic for DNA conformational changes. Additionally, covalently linked porphyrins have been shown to function as DNA molecular caps and to stabilize the non-self-complementary non-Watson-Crick guanine-adenine DNA sequence via their strong π-π stacking.

5'-Porphyrin-oligonucleotide conjugates: neutral porphyrin-DNA interactions

[chemical reaction: see text]. Incorporation of hydrophilic tetraarylporphyrin phosphoramidites into the 5'-termimus of the DNA as well as noncharged porphyrin-DNA interactions have been studied. Porphyrin-modified oligonucleotides show lower melting temperatures than their unmodified analogues. Single-stranded DNA interacts more strongly with porphyrin and causes more intense chiral disturbance in the porphyrin environment than the corresponding double strand.

Porphyrins conjugated to DNA as CD reporters of the salt-induced B to Z-DNA transition

The porphyrin chromophore incorporated at the 5'-position of an oligonucleotide allows the simultaneous detection of the B- to Z-DNA transition via the porphyrin Soret band circular dichroism exciton couplet signal around 420 nm and the oligonucleotide CD region below 300 nm, at micromolar concentrations.