Fluorescent 5-alkynyl-2'-deoxyuridines: high emission efficiency of a conjugated perylene nucleoside in a DNA duplex

Four fluorescent 5-alkynyl-2'-deoxyuridines were studied in DNA oligonucleotides and their duplexes. The fluorescence response to hybridization differs dramatically for nucleosides containing a perylene fluorochrome either conjugated or not conjugated to the nucleobase. The conjugated nucleoside, 5-(perylen-3-ylethynyl)-2'-deoxyuridine, shows enhanced long-wavelength emission in the DNA duplex, in contrast to the blue fluorescence of perylene on a flexible linker (in 5-[(perylen-3-yl)methoxyprop-1-ynyl]-2'-deoxyuridine), which is quenched upon duplex formation.     

Highly Efficient Fluorescent Interstrand Photo‐crosslinking of DNA Duplexes Labeled with 5‐Fluoro‐4‐thio‐2′‐O‐methyluridine

The formation of a fluorescent photoadduct between 5‐fluoro‐4‐thiouridine ( ^FS U ), in the sequence context 5′‐A ^FS U A‐3′ and incorporated into a synthetic oligonucleotide either at its 3′‐ or 5′‐end, and one of the thymines of the TAT motif in a complementary target DNA strand led to photo‐crosslinking of the two strands for several oligonucleotide constructs. Enzymatic digestion, MS, UV, and fluorescence spectral analyses of the interstrand crosslinked oligonucleotides revealed the identity of the thymidine that participates in the photo‐crosslinking reaction as well as the diastereomeric structures of the crosslinks. The proposed pathways of interstrand photo‐crosslinking are supported by experiments with isotopically labeled oligonucleotide constructs and visualized by means of molecular dynamics simulations.     

Triplexes with 8‐Aza‐2′‐Deoxyisoguanosine Replacing Protonated dC: Probing Third Strand Stability with a Fluorescent Nucleobase Targeting Duplex DNA

The fluorescent 8‐aza‐2′‐deoxyisoguanosine ( 4 ) as well as the parent 2′‐deoxyisoguanosine ( 1 ) were used as protonated dCH⁺ surrogates in the third strand of oligonucleotide triplexes. Stable triplexes were formed by Hoogsteen base pairing. In contrast to dC, triplexes containing nucleoside 1 or 4 in place of dCH⁺ are already formed under neutral conditions or even at alkaline pH values. Triplex melting can be monitored separately from duplex dissociation in cases in which the third strand contains the fluorescent nucleoside 4 . Third‐strand binding of oligonucleotides with 4 , opposite to dG, was selective as demonstrated by hybridisation experiments studying mismatch discrimination. Third‐strand binding is more efficient when the stability of the DNA duplex is reduced by mismatches, giving third‐strand binding more flexibility.     

An Isocytidine Derivative with a 2‐Amino‐6‐methylpyridine Unit for Selective Recognition of the CG Interrupting Site in an Antiparallel Triplex DNA

Sequence‐specific recognition of duplex DNA mediated by triple helix formation offers a potential basis for oligonucleotide therapy and biotechnology. However, triplex formation is limited mostly to homopurine strands, due to poor stabilization at CG or TA base pairs in the target duplex DNA sequences. Several non‐natural nucleosides have been designed for the recognition of CG or TA base pairs within an antiparallel triplex DNA. Nevertheless, problems including low selectivity and high dependence on the neighboring bases remain unsolved. We thus synthesized N²‐arylmethyl isodC derivatives and incorporated them into triplex‐forming oligonucleotides (TFOs) for the selective recognition of the CG base pair within antiparallel triplex DNA. It was shown that an isodC derivative bearing a 2‐amino‐6‐methylpyridine moiety (AP‐isodC) recognizes the CG base pair with high selectivity in antiparallel triplex DNA irrespective of the flanking base pairs.     

O6‐Alkylguanine‐DNA Alkyltransferase‐Mediated Repair of O4‐Alkylated 2′‐Deoxyuridines

O⁶‐Alkylguanine‐DNA alkyltransferases (AGTs) are responsible for the removal of O⁶‐alkyl 2′‐deoxyguanosine (dG) and O⁴‐alkyl thymidine (dT) adducts from the genome. Unlike the E. coli OGT (O⁶‐alkylguanine‐DNA‐alkyltransferase) protein, which can repair a range of O⁴‐alkyl dT lesions, human AGT (hAGT) only removes methyl groups poorly. To uncover the influence of the C5 methyl group of dT on AGT repair, oligonucleotides containing O⁴‐alkyl 2′‐deoxyuridines (dU) were prepared. The ability of E. coli AGTs (Ada‐C and OGT), human AGT, and an OGT/hAGT chimera to remove O⁴‐methyl and larger adducts (4‐hydroxybutyl and 7‐hydroxyheptyl) from dU were examined and compared to those relating to the corresponding dT species. The absence of the C5 methyl group resulted in an increase in repair observed for the O⁴‐methyl adducts by hAGT and the chimera. The chimera was proficient at repairing larger adducts at the O⁴ atom of dU. There was no observed correlation between the binding affinities of the AGT homologues to adduct‐containing oligonucleotides and the amounts of repair measured.     

Characterization of 2-Fluoro-2’-deoxyadenosine in Duplex,G-Quadruplex and i-Motif

Among various kinds of fluorine-substituted biomolecules, 2-fluoroadenine (2FA) and its derivatives have been actively investigated as therapeutic reagents, radio-sensitizers, and ¹⁹F NMR probes. In spite of their excellent properties, DNA containing 2FA has not been studied well. For fundamental understanding and future applications to the development of functional nucleic acids, we characterized 2FA-containing oligonucleotides for canonical right-handed DNA duplex, G-quadruplex, and i-motif structures. Properties of 2FA were similar to native adenine due to the small size of the fluorine atom, but it showed unique features caused by high electronegativity. This work provides useful information for future application of 2FA-modified DNA.     

Structural Insights into the Recognition of N2‐Aryl‐ and C8‐Aryl DNA Lesions by the Repair Protein XPA/Rad14

Aromatic amines are strongly carcinogenic. They are activated in the liver to give reactive nitrenium ions that react with nucleobases within the DNA duplex. The reaction occurs predominantly at the C8 position of the dG base, thereby giving C8‐acetyl‐aryl‐ or C8‐aryl‐dG adducts in an electrophilic aromatic substitution reaction. Alternatively, reaction with the exocyclic 2‐NH₂ group is observed. Although the C8 adducts retain base‐pairing properties, base pairing is strongly compromised in the case of the N² adducts. Here we show crystal structures of two DNA lesions, N²‐acetylnaphthyl‐dG and C8‐fluorenyl‐dG, within a DNA duplex recognized by the repair protein Rad14. The structures confirm that two molecules of the repair protein recognize the lesion and induce a 72 or 78° kink at the site of the damage. Importantly, the same overall kinked structure is induced by binding of the repair proteins, although the structurally different lesions result in distinct stacking interactions of the lesions within the duplex. The results suggest that the repair protein XPA/Rad14 is a sensor that recognizes flexibility. The protein converts the information that structurally different lesions are present in the duplex into a unifying sharply kinked recognition motif.     

Molecular Design of an Environmentally Sensitive Fluorescent Nucleoside, 3‐Deaza‐2′‐Deoxyadenosine Derivative: Distinguishing Thymine by Probing the DNA Minor Groove

An environmentally sensitive fluorescent nucleoside containing a 3‐deazaadenine skeleton has been developed, and its photophysical properties were investigated. Newly developed C3‐naphthylethynylated 3‐deaza‐2′‐deoxyadenosine (^3nzA, 1 ) exhibited dual fluorescence emission from an intramolecular charge‐transfer state and a locally excited state, depending upon molecular coplanarity. DNA probes containing 1 clearly discriminated a perfectly matched thymine base on the complementary strand by a distinct change in emission wavelength.     

Structure-function relationships of phenoxazine nucleosides for identification of mismatches in duplex DNA by fluorescence spectroscopy

The effects of the flanking sequence on the mismatch‐detection capabilities of the fluorescent nucleoside phenoxazine ( tC^O ) were examined in a systematic fashion, and compared to the previously reported fluorescent, phenoxazine‐based nucleoside Ç^f . We see some similarities for the two fluorescent nucleosides, for example, the emission intensity of the C‐mismatched duplex is always the highest, and a three‐peak pattern in the spectrum emerges when the fluorosides are base‐paired with A. However, phenoxazine was only able to distinguish a mismatch from the fully base‐paired duplex in 11 out of 16 flanking sequences, and was able to identify each of the mismatches in six of those sequences. Therefore, tC^O shows poorer discrimination of mismatches than was previously reported for Ç^f , which could be used to identify all base‐pairing partners in all immediately flanking sequences, albeit in some cases by using mercuric ions to selectively quench the emission of the T‐mismatched duplex. The mercuric titration might resolve the overlap of fluorescence curves of tC^O in some flanking sequences, but not for 5′‐d(C tC^O G) and 5′‐d(T tC^O A) due to overlap of A‐mismatch and G‐match fluorescence curves. A pH titration was performed on Ç^f , tC^O and a N5‐methylated derivative of tC^O , which showed that the emergence of the three‐peak pattern is associated with the de‐protonation of N5 in the fluorosides. We also show that neither the α‐ nor β‐anomer of the phenothiazine nucleoside ( tC ) was able to detect a mismatch in any of the flanking sequences examined.     

Detection of DNA hybridization by a pyrene-labeled polyelectrolyte prepared by ATRP

A novel pyrene-labeled polyelectrolyte (Py-PDMAEMA⁺) has been prepared by atom transfer radical polymerization (ATRP) for detection of DNA hybridization. The electrostatic and hydrophobic interactions between Py-PDMAEMA⁺ and ssDNA (hairpin or linear DNA) kept them forming a complex probe which could be used as a turn-off fluorescent sensor. The fluorescence intensity of the probe decreased upon adding the complementary strand, since the pyrene moiety could be intercalated into the duplex and thus the fluorescence quenching by nucleotide bases was strengthened. The proposed intercalation mode was confirmed by the circular dichroism spectra and the fluorescence quenching study with iodide. This pyrene-labeled polyelectrolyte combined with ssDNA may establish a novel fluorescence sensing system for DNA hybridization.     

O4‐Alkylated‐2‐Deoxyuridine Repair by O6‐Alkylguanine DNA Alkyltransferase is Augmented by a C5‐Fluorine Modification

Oligonucleotides containing various adducts, including ethyl, benzyl, 4‐hydroxybutyl and 7‐hydroxyheptyl groups, at the O⁴ atom of 5‐fluoro‐O⁴‐alkyl‐2′‐deoxyuridine were prepared by solid‐phase synthesis. UV thermal denaturation studies demonstrated that these modifications destabilised the duplex by approximately 10 °C, relative to the control containing 5‐fluoro‐2′‐deoxyuridine. Circular dichroism spectroscopy revealed that these modified duplexes all adopted a B‐form DNA structure. O⁶‐Alkylguanine DNA alkyltransferase (AGT) from humans (hAGT) was most efficient at repair of the 5‐fluoro‐O⁴‐benzyl‐2′‐deoxyuridine adduct, whereas the thymidine analogue was refractory to repair. The Escherichia coli AGT variant (OGT) was also efficient at removing O⁴‐ethyl and benzyl adducts of 5‐fluoro‐2‐deoxyuridine. Computational assessment of N1‐methyl analogues of the O⁴‐alkylated nucleobases revealed that the C5‐fluorine modification had an influence on reducing the electron density of the O⁴?C_α bond, relative to thymine (C5‐methyl) and uracil (C5‐hydrogen). These results reveal the positive influence of the C5‐fluorine atom on the repair of larger O⁴‐alkyl adducts to expand knowledge of the range of substrates able to be repaired by AGT.     

Triplex Crosslinking through Furan Oxidation Requires Perturbation of the Structured Triple‐Helix

Short oligonucleotides can selectively recognize duplexes by binding in the major groove thereby forming triplexes. Based on the success of our recently developed strategy for furan‐based crosslinking in DNA duplexes, we here investigated for the first time the use of the furan‐oxidation crosslink methodology for the covalent locking of triplex structures by an interstrand crosslink. It was shown that in a triplex context, although crosslinking yields are surprisingly low (to nonexistent) when targeting fully complementary duplexes, selective crosslinking can be achieved towards mismatched duplex sites at the interface of triplex to duplex structures. We show the promising potential of furan‐containing probes for the selective detection of single‐stranded regions within nucleic acids containing a variety of structural motifs.     

Synthesis and properties of photosensitive poly(urethane‐acrylate) containing anil groups with application in the chemosensors area

Some aspects of the enol‐imine to keto‐enamine photoisomerism and fluorescent behavior of the new monomer with urethane and anil units in its structure, namely, methacryloyloxyethyl‐2‐carbamoyloxy(m‐methyl, o‐hydroxybenziliden)aniline (UAN), were studied comparatively with the corresponding copolymer poly (methacryloyloxyethyl‐2‐carbamoyloxy(m‐methyl, o‐hydroxybenziliden)aniline)‐co‐methyl methacrylate) (COP‐UAN). The structure, thermal properties, and morphology of the anil compounds were investigated by Fourier transform infrared, proton nuclear magnetic resonance, fluorescence spectroscopies, UV spectrophotometry, thermogravimetric analysis, differential scanning calorimetry, and atomic force microscopy. The photochromic behavior of salicylideneanil units was investigated by UV/laser irradiation, and an inspection of their photophysical properties suggested that such structures could function as fluorescent chemosensors for some transition metals, a fluorescence quenching in the presence of different metal cations (Fe³⁺, Fe²⁺, Cu²⁺, and Ni²⁺) being evidenced. The direct observation of an enhancement in the fluorescence emission caused of the presence of Zn²⁺ (solution) or Fe²⁺, Cu²⁺, and Zn²⁺ (thin film) would be rather suitable for the production of turn‐on fluorescent chemosensors. POLYM. ENG. SCI., 2011. © 2011 Society of Plastics Engineers     

NBD‐Based Green Fluorescent Ligands for Typing of Thymine‐Related SNPs by Using an Abasic Site‐Containing Probe DNA

The binding behavior of green fluorescent ligands, derivatives of 7‐nitrobenzo‐2‐oxa‐1,3‐diazole (NBD), with DNA duplexes containing an abasic (AP) site is studied by thermal denaturation and fluorescence experiments. Among NBD derivatives, N¹‐(7‐nitrobenzo[c][1,2,5]oxadiazol‐4‐yl)propane‐1,3‐diamine (NBD‐NH₂) is found to bind selectively to the thymine base opposite an AP site in a DNA duplex with a binding affinity of 1.52×10⁶ M ^?1. From molecular modeling studies, it is suggested that the NBD moiety binds to thymine at the AP site and a protonated amino group tethered to the NBD moiety interacts with the guanine base flanking the AP site. Green fluorescent NBD‐NH₂ is successfully applied for simultaneous G>T genotyping of PCR amplification products in a single cuvette in combination with a blue fluorescent ligand, 2‐amino‐6,7‐dimethyl‐4‐hydroxypteridine (diMe‐pteridine).     

Duplex Healing of Selectively Thiolated Guanosine Mismatches through a Cd2+ Chemical Stimulus

The on‐column selective conversion of guanosine to thioguanosine (tG) yields modified oligomers that exhibit destabilisation over the fully complementary duplex. Restoration to a stabilised duplex is induced through thio‐directed Cd²⁺ coordination; a route for healing DNA damage. Short oligomers are G‐specifically thiolated through a modified on‐column protocol without the need for costly thioguanosine phosphoramidites. Addition of Cd²⁺ ions to a duplex containing a highly disrupted tG central mismatch sequence, 3′‐A₆tG₄T₆‐5′, suggests a (tG)₈Cd₂ central coordination regime, resulting in increased base stacking and duplex stability. Equilibrium molecular dynamic calculations support the hypothesis of metal‐induced healing of the thiolated duplex. The 2 nm displacement of the central tG mismatched region is dramatically reduced after the addition of a chemical stimuli, Cd²⁺ ions, returning to a minimized fluctuational state comparable to the unmodified fully complementary oligomer.     

Templated Chemistry for Sequence‐Specific Fluorogenic Detection of Duplex DNA

We describe the development of templated fluorogenic chemistry for detection of specific sequences of duplex DNA in solution. In this approach, two modified homopyrimidine oligodeoxynucleotide probes are designed to bind by triple‐helix formation at adjacent positions on a specific purine‐rich target sequence of duplex DNA. One fluorescein‐labeled probe contains an α‐azidoether linker to a fluorescence quencher; the second (trigger) probe carries a triarylphosphine group that is designed to reduce the azide and cleave the linker. The data showed that at pH 5.6 these probes yielded a strong fluorescence signal within minutes on addition to a complementary homopurine duplex DNA target. The signal increased by a factor of about 60, and was completely dependent on the presence of the target DNA. Replacement of cytosine in the probes with pseudoisocytosine allowed the templated chemistry to proceed readily at pH 7. Single nucleotide mismatches in the target oligonucleotide slowed the templated reaction considerably; this demonstrated high sequence selectivity. The use of templated fluorogenic chemistry for detection of duplex DNAs has not been previously reported and could allow detection of double‐stranded DNA, at least for homopurine–homopyrimidine target sites, under native and nondenaturing conditions.     

Pyrenemethyl ara-uridine-2'-carbamate: a strong interstrand excimer in the major groove of a DNA duplex

The synthesis of new nucleoside derivatives, ara-uridine-2'-carbamates, and their incorporation into synthetic DNA oligomers is described. The modification directs ligands into the major groove of duplex DNA and somewhat destabilizes the duplexes of modified oligonucleotides with complementary DNA or RNA. In the case of pyrenemethyl carbamate modification in DNA-DNA duplexes, the destabilization is considerably reduced. The pyrenemethyl derivative also shows remarkable spectral properties: a "reversed" absorbance change for pyrene at 350 nm in the course of denaturation of the DNA duplex, as compared to the change seen in the nucleotide absorbance at 260 nm. This derivatization also causes pronounced sequence-dependent excimer formation in the major groove.     

Synthesis and photophysical behavior of a water‐soluble coumarin‐bearing polymer for proton and Ni2+ ion sensing

BACKGROUND: In recent years, many fluorescent chemosensors with various macromolecular structures have been prepared for the detection of protons or metal cations in the environment. Most of this research is focused on polymer sensors with fluorescent recognition sites in the main chain. In this case, the fluorescent recognition sites are covalently bonded to the polymer chain, and thus the polymer shows photophysical properties as a chemosensor for protons and metal ions. RESULTS: An acrylic monomer bearing coumarin moieties, 7‐hydroxy‐4‐methyl‐8‐(4′‐acryloylpiperazin‐1′‐yl)methylcoumarin, was synthesized. This was then copolymerized with N‐vinylpyrrolidone to obtain a blue fluorescent material. The fluorescent copolymer has good solubility in aqueous solution. Its main photophysical properties were determined in relation to its use as a sensor for protons and metal cations. It is an efficient ‘off‐on’ switcher for pH between 3.02 and 12.08. Additionally, the polymer sensor is selective to Ni²⁺ ions, with the increase in the fluorescence intensity depending on Ni²⁺ ion concentrations in the range 0.33 × 10^?5–7.67 × 10^?5 mol L^?1. CONCLUSION: The results suggest that this copolymer may offer potential as a reusable polymer sensor for protons and Ni²⁺ ions in aqueous solution. Copyright © 2009 Society of Chemical Industry     

Preparation of photoluminescence films containing rare earth complexes by UV photograft polymerization

To avoid the fluorescence quenching resulting from the uneven dispersion of fluorescent rare earth complexes in photoluminescence films, which were prepared by blending until recently, photoluminescence films were prepared in which the chemical bond combination occurs between the fluorescent rare earth complexes and the macromolecular material. Acrylic acid (AA) was grafted onto polyethylene (PE) film through liquid‐phase UV photograft polymerization. Then the grafted films (PAA‐g‐PE) were reacted with a solution of Eu³⁺ and thenoyltrifluoroacetone (TTA) in alcohol–water and with a solution of Tb³⁺ and acetylacetone (AcAc) in chloroform–water, respectively. Thus, red (Eu³⁺–TTA–PAA‐g‐PE) and green (Tb³⁺–ACAC–PAA‐g‐PE) photoluminescence films were obtained. The fluorescence and infrared spectra of the photoluminescence films were recorded. Compared with their corresponding solid fluorescent complexes, both the excitation and emission wavelengths of the photoluminescence films prepared in this way had been changed remarkably, indicating that the fluorescent rare earth complexes had been chemically bonded onto the PE film. Moreover, the effects of the conditions (including pH value, reaction time, and temperature) of the reaction of the grafted film with the solution containing Eu³⁺ and TTA on the fluorescence intensity of the red photoluminescence film were investigated. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 89: 662–667, 2003     

Enzymatic Polymerization of Phosphonate Nucleosides

5′‐O‐Phosphonomethyl‐2′‐deoxyadenosine (PMdA) proved to be a good substrate of the Therminator polymerase. In this article, we investigated whether the A, C, T and U analogues of this phosphonate nucleoside (PMdN) series can function as substrates of natural DNA polymerases. PMdT and PMdU could only be polymerized enzymatically to a limited extent. Nevertheless, PMdA and PMdC could be incorporated into a DNA duplex with complete chain elongation by all the DNA polymerases tested. A mixed sequence of four nucleotides containing modified C, T and A residues could be obtained with the Vent(exo^?) and Therminator polymerases. The kinetic values for the incorporation of PMdA by Vent(exo^?) polymerase were determined; a reduced K_M value was found for the incorporation of PMdA compared to the natural substrate. Future polymerase directed evolution studies will allow us to select an enzyme with a heightened capacity to process these modified DNA building blocks into modified strands.