Quadracyclic adenine: a non-perturbing fluorescent adenine analogue

Fluorescent-base analogues (FBAs) comprise a group of increasingly important molecules for the investigation of nucleic acid structure and dynamics as well as of interactions between nucleic acids and other molecules. Here, we report on the synthesis, detailed spectroscopic characterisation and base-pairing properties of a new environment-sensitive fluorescent adenine analogue, quadracyclic adenine (qA). After developing an efficient route of synthesis for the phosphoramidite of qA it was incorporated into DNA in high yield by using standard solid-phase synthesis procedures. In DNA qA serves as an adenine analogue that preserves the B-form and, in contrast to most currently available FBAs, maintains or even increases the stability of the duplex. We demonstrate that, unlike fluorescent adenine analogues, such as the most commonly used one, 2-aminopurine, and the recently developed triazole adenine, qA shows highly specific base-pairing with thymine. Moreover, qA has an absorption band outside the absorption of the natural nucleobases (>300?nm) and can thus be selectively excited. Upon excitation the qA monomer displays a fluorescence quantum yield of 6.8?% with an emission maximum at 456?nm. More importantly, upon incorporation into DNA the fluorescence of qA is significantly less quenched than most FBAs. This results in quantum yields that in some sequences reach values that are up to fourfold higher than maximum values reported for 2-aminopurine. To facilitate future utilisation of qA in biochemical and biophysical studies we investigated its fluorescence properties in greater detail and resolved its absorption band outside the DNA absorption region into distinct transition dipole moments. In conclusion, the unique combination of properties of qA make it a promising alternative to current fluorescent adenine analogues for future detailed studies of nucleic acid-containing systems.     

Highly Fluorescent 2-Aminopurine Derivatives: Synthesis,Photo-physical Characterization,and Preliminary Cytotoxicity Evaluation

New fluorescent nucleobase analogues (FBAs) are emerging as extraordinarily useful tools for DNA labelling technologies. The highly fluorescent adenine analogue 2-aminopurine (2AP) is still the most used within the few hundreds of newly FBAs synthesized, but its excitation in the UV region demands for high energy sources endangering living cells. New and highly fluorescent 2AP derivatives, 2-amino-6-cyanopurines, were obtained using simpler but efficient synthesis method. All the new compounds exhibit advantageous photophysical properties over 2AP, showing absorption and emission bands ranging the visible region (blue-green region), high fluorescence quantum yields and Stokes’ shifts, especially in non-protic organic solvents. Density Functional Theory calculations (DFT) of electronic and vibrational structure were performed, allowing to predict absorption and emission spectra. In addition, these 2-amino-6-cyanopurines exhibit little to no toxicity in assays using yeast cells.     

Second‐Generation Fluorescent Quadracyclic Adenine Analogues: Environment‐Responsive Probes with Enhanced Brightness

Fluorescent base analogues comprise a group of increasingly important molecules for the investigation of nucleic acid structure, dynamics, and interactions with other molecules. Herein, we report on the quantum chemical calculation aided design, synthesis, and characterization of four new putative quadracyclic adenine analogues. The compounds were efficiently synthesized from a common intermediate through a two‐step pathway with the Suzuki–Miyaura coupling as the key step. Two of the compounds, qAN1 and qAN4, display brightnesses (εΦ_F) of 1700 and 2300, respectively, in water and behave as wavelength‐ratiometric pH probes under acidic conditions. The other two, qAN2 and qAN3, display lower brightnesses but exhibit polarity‐sensitive dual‐band emissions that could prove useful to investigate DNA structural changes induced by DNA–protein or –drug interactions. The four qANs are very promising microenvironment‐sensitive fluorescent adenine analogues that display considerable brightness for such compounds.     

Absorption Spectrum of A–T DNA Unraveled by Quantum Mechanical Calculations in Solution on the (dA)2⋅(dT)2 Tetramer

The absorption spectrum of A–T DNA is computed for the first time in aqueous solution by means of quantum mechanical calculations performed on realistic models, thereby accounting for both stacking and base pairing interactions and including solvent effects through the polarizable continuum model. The computed and experimental spectra are in close agreement. Our analysis allows the identification of all the electronic transitions hidden in the broad absorption spectrum of A–T DNA, thus determining their most relevant properties and providing an explanation for the most significant experimental features, such as the small blue shift of the band maximum and the appearance of a shoulder on the red wing of the absorption band. The lowest‐energy dark excited state corresponds to a charge‐transfer state between two stacked adenine bases.     

Electronic Modifications of Fluorescent Cytidine Analogues Control Photophysics and Fluorescent Responses to Base Stacking and Pairing

The rational design of fluorescent nucleoside analogues is greatly hampered by the lack of a general method to predict their photophysics, a problem that is especially acute when base pairing and stacking change fluorescence. To better understand these effects, a series of tricyclic cytidine (tC and tC^O) analogues ranging from electron-rich to electron-deficient was designed and synthesized. They were then incorporated into oligonucleotides, and photophysical responses to base pairing and stacking were studied. When inserted into double-stranded DNA oligonucleotides, electron-rich analogues exhibit a fluorescence turn-on effect, in contrast with the electron-deficient compounds, which show diminished fluorescence. The magnitude of these fluorescence changes is correlated with the oxidation potential of nearest neighbor nucleobases. Moreover, matched base pairing enhances fluorescence turn-on for the electron-rich compounds, and it causes a fluorescence decrease for the electron-deficient compounds. For the tC^O compounds, the emergence of vibrational fine structure in the fluorescence spectra in response to base pairing and stacking was observed, offering a potential new tool for studying nucleic acid structure and dynamics. These results, supported by DFT calculations, help to rationalize fluorescence changes in the base stack and will be useful for selecting the best fluorescent nucleoside analogues for a desired application.     

A microenvironment-sensitive fluorescent pyrimidine ribonucleoside analogue: synthesis, enzymatic incorporation, and fluorescence detection of a DNA abasic site

Base-modified fluorescent ribonucleoside-analogue probes are valuable tools in monitoring RNA structure and function because they closely resemble the structure of natural nucleobases. Especially, 2-aminopurine, a highly environment-sensitive adenosine analogue, is the most extensively utilized fluorescent nucleoside analogue. However, only a few isosteric pyrimidine ribonucleoside analogues that are suitable for probing the structure and recognition properties of RNA molecules are available. Herein, we describe the synthesis and photophysical characterization of a small series of base-modified pyrimidine ribonucleoside analogues derived from tagging indole, N-methylindole, and benzofuran onto the 5-position of uracil. One of the analogues, based on a 5-(benzofuran-2-yl)pyrimidine core, shows emission in the visible region with a reasonable quantum yield and, importantly, displays excellent solvatochromism. The corresponding triphosphate substrate is effectively incorporated into oligoribonucleotides by T7 RNA polymerase to produce fluorescent oligoribonucleotide constructs. Steady-state and time-resolved spectroscopic studies with fluorescent oligoribonucleotide constructs demonstrate that the fluorescent ribonucleoside photophysically responds to subtle changes in its environment brought about by the interaction of the chromophore with neighboring bases. In particular, the emissive ribonucleoside, if incorporated into an oligoribonucleotide, positively reports the presence of a DNA abasic site with an appreciable enhancement in fluorescence intensity. The straightforward synthesis, amicability to enzymatic incorporation, and sensitivity to changes in the microenvironment highlight the potential of the benzofuran-conjugated pyrimidine ribonucleoside as an efficient fluorescent probe to investigate nucleic acid structure, dynamics, and recognition events.     

Fluorescent Nucleobase Analogues with Extended Pi Surfaces Stabilize DNA Duplexes Containing O6‐Alkylguanine Adducts

Chemical alkylation of DNA produces potentially toxic and mutagenic damage such as O⁶‐alkylguanine (O⁶‐alkylG) adducts. Non‐natural nucleoside analogues that pair with DNA adducts provide a potential basis for studying damaged DNA. Herein, we evaluated the base pairing properties of elongated nucleoside analogues containing napthalene‐derived tricyclic nucleobases as DNA adduct‐pairing nucleoside analogues in DNA hybridization probes. DNA duplex melting studies revealed that the elongated nucleoside analogs formed more stable base pairs opposite O⁶‐alkylG than G and were better able to distinguish between G, O⁶‐alkylG, and an abasic site than any previously described nucleoside analogue. DNA duplexes containing an elongated base analogue exhibited different fluorescence intensities when paired opposite O⁶‐alkylG vs. G or abasic sites. Their selectivity for stabilizing alkylated DNA make the elongated hydrophobic base analogues improved candidates for incorporating into DNA hybridization probes targeting O⁶‐alkylG.     

The two-photon excitation cross section of 6MAP, a fluorescent adenine analogue

6MAP is a fluorescent analogue of adenine that undergoes Watson-Crick base pairing and base stacking in double-stranded DNA. The one-photon absorption spectrum of 6MAP is characterized by a maximum around 330 nm with moderate quantum yield fluorescence centered at about 420 nm. To take advantage of this probe for confocal and single-molecule microscopy, it would be advantageous to be able to excite the analogue via two photons. We report the first determination of the two-photon excitation cross section and spectrum for 6MAP from 614 to 700 nm. The power dependence of the fluorescence indicates that emission results from the absorption of two photons. The one-photon and two-photon emission line shapes are identical within experimental error. A study of the concentration dependence of the fluorescence yield for one-photon excitation shows no measurable quenching up to about 5 microM. The maximum in the two-photon excitation spectrum gives a two-photon cross section, delta(TPE), of 3.4 +/- 0.1 Goeppert-Mayer (G.M.) at 659 nm, which correlates well with the one-photon absorption maximum. This compares quite favorably with cross sections of various naturally fluorescent biological molecules such as flavins and nicotiamide. In addition, we have also obtained the two-photon-induced fluorescence emission spectrum of quinine sulfate. It is approximately the same as that for one-photon excitation, suggesting that two-photon excitation of quinine sulfate may be used for calibration purposes.     

Long‐Wavelength Fluorescence from 2‐Aminopurine‐Nucleobase Dimers in DNA

When 2‐aminopurine (2AP) is substituted for adenine in DNA, it is widely accepted that its fluorescence spectrum is essentially unchanged from that of the free fluorophore. We show that 2AP in DNA exhibits long‐wavelength emission and excitation bands, in addition to the familiar short‐wavelength spectra, as a result of formation of a ground‐state heterodimer with an adjacent, π‐stacked, natural base. The observation of dual emission from 2AP in a variety of oligodeoxynucleotide duplexes and single strands demonstrates the generality of this phenomenon. The photophysical and conformational properties of the long‐wavelength‐emitting 2AP‐nucleobase dimer are examined. Analogous long‐wavelength fluorescence is seen when 2AP π‐stacks with aromatic amino acid sidechains in the active sites of methyltransferase enzymes during DNA nucleotide flipping.     

Expanded-size bases in naturally sized DNA: evaluation of steric effects in Watson-Crick pairing

We describe physicochemical properties in DNA of altered-size nucleobases that retain Watson-Crick analogous hydrogen-bonding ability. Size-expanded analogues of adenine and thymine (xA and xT, respectively, which are expanded by benzo-fusion) were incorporated into natural DNA oligonucleotides, and their effects on helix stability were measured. Base stacking studies revealed that the two stretched analogues stack much more strongly than do their naturally sized counterparts. In contrast to this, pairing studies showed that single substitutions of the new bases are destabilizing to the natural helix as compared to A or T in standard A-T pairs in the same context, unless multiple adjacent substitutions are used. Interestingly, the size-expanded bases displayed selective recognition of the hydrogen-bonding complementary partners, suggesting that Watson-Crick analogous pairs were still formed despite local backbone strain. In an attempt to compensate for the added size of the expanded adenine, we tested a formamide deoxynucleoside, which Leonard proposed as a shortened thymine analogue (F(o)). Data showed, however, that this compound adopts a conformation unfavorable for pairing. On the basis of the combined thermodynamic data, we estimate the energetic cost of the 2.4 A stretching of an isolated base pair in DNA at ca. +1 to 2 kcal/mol. Notably, during the pairing studies, the two size-expanded nucleobases were found to display significant changes in fluorescence on formation of stacked versus unstacked structures, suggesting possible applications in probing nucleic acid structures and biochemical mechanisms.     

Photophysical characters of rationally designed hetero-ring-expanded guanine analogues and effect of cytosine pairing

We present the results of the CIS and TDB3LYP calculations of the optical absorption and emission spectra of some newly designed guanine (G) analogues and their Watson-Crick base pairs. Compared with natural G, the onset absorption peaks of these newly designed analogues are red-shifted, while the fluorescence peaks are blue-shifted. In general, the first excited singlet states (pipi*) of these analogues are nonplanar for all bases considered here. But, the Stokes shifts for the designed G-analogues are much smaller than that of natural G, suggesting that they have stronger molecular rigidity and higher fluorescence quantum yields than those of natural G. The first excited states of these Watson-Crick base pairs essentially originate from those of their isolated purine moieties, as demonstrated from the S1 geometries of their Watson-Crick base pairs. For G and its analogues, A1 and A2 (they are ring-expanded with one-bond intercalation at the C5 site), the pairing with cytosine reduces the oscillator strengths of both the first absorption peak (by 27%-60%) and the fluorescent emission (by 19%-23%), while for the analogues A3, A4, and xG in which G is ring-expanded with a two-bond intercalation at the C5 site, the pairing, in contrast, increases the oscillator strengths of both the first absorption peak (by 11%-15%) and the fluorescent emission (by 3%-20%). These observations indicate that the pairing with cytosine can quench the fluorescence for G, A1, and A2 but enhance the fluorescence quantum yields for A3, A4, and xG. The significant shifts induced by ring-expansion in the ring-expanded G with a two-bond intercalation at the C5 site reveal a possibility for their fluorescent detections.     

6MAP, a fluorescent adenine analogue, is a probe of base flipping by DNA photolyase

Cyclobutylpyrimidine dimers (CPDs) are formed between adjacent pyrimidines in DNA when it absorbs ultraviolet light. CPDs can be directly repaired by DNA photolyase (PL) in the presence of visible light. How PL recognizes and binds its substrate is still not well understood. Fluorescent nucleic acid base analogues are powerful probes of DNA structure. We have used the fluorescent adenine analogue 6MAP, a pteridone, to probe the local double helical structure of the CPD substrate when bound by photolyase. Duplex melting temperatures were obtained by both UV-vis absorption and fluorescence spectroscopies to ascertain the effect of the probe and the CPD on DNA stability. Steady-state fluorescence measurements of 6MAP-containing single-stranded and doubled-stranded oligos with and without protein show that the local region around the CPD is significantly disrupted. 6MAP shows a different quenching pattern compared to 2-aminopurine, another important adenine analogue, although both probes show that the structure of the complementary strand opposing the 5'-side of the CPD lesion is more destacked than that opposing the 3'-side in substrate/protein complexes. We also show that 6MAP/CPD duplexes are substrates for PL. Vertical excitation energies and transition dipole moment directions for 6MAP were calculated using time-dependent density functional theory. Using these results, the F?rster resonance energy transfer efficiency between the individual adenine analogues and the oxidized flavin cofactor was calculated to account for the observed intensity pattern. These calculations suggest that energy transfer is highly efficient for the 6MAP probe and less so for the 2Ap probe. However, no experimental evidence for this process was observed in the steady-state emission spectra.     

Solvent- and environment-dependent fluorescence of modified nucleobases

Fluorescent nucleosides with modified nucleobases are useful tools for detecting nucleic acids and probing their structures and functions. Nucleobases are suitable for modification because 1) intrinsically light-absorbing nucleobases can be converted to fluorescent chromophores by simple chemical modification, 2) attaching substituents to nucleobases at appropriately selected positions does not inhibit base pairing or duplex formation, and 3) duplex formation and protein interactions affect the environment of nucleobases, causing changes in their fluorescence intensities and/or wavelengths. This review summarizes recent fluorescent nucleosides and their photophysical properties, such as absorption wavelength, emission wavelength, and fluorescence quantum yield together with their solvent dependency.     

Furan Decorated Nucleoside Analogues as Fluorescent Probes: synthesis, photophysical evaluation and site-specific incorporation

The synthesis and photophysical evaluation of modified nucleoside analogues in which a five-membered heterocycle (furan, thiophene, oxazole, and thiazole) is attached to the 5-position of 2′-deoxyuridine are reported. The furan-containing derivative is identified as the most promising responsive nucleoside of this family due to its emission quantum efficiency and degree of sensitivity to its microenvironment. The furan moiety was then attached to the 5-position of 2′-deoxycytidine as well as the 8-position of adenosine and guanosine. Photophysical evaluation of these four furan-containing nucleoside analogues reveals distinct differences in the absorption, emission, and quantum efficiency depending upon the class of nucleoside (pyrimidine or purine). Comparing the photophysical properties of all furan-containing nucleosides, identifies the furan thymidine analogue, 5-(fur-2-yl)-2′-deoxyuridine, as the best candidate for use as a responsive fluorescent probe in nucleic acids. 5-(Fur-2-yl)-2′-deoxyuridine was then converted to the corresponding phosphoramidite and site specifically incorporated into DNA oligonucleotides with greater than 88% coupling efficiency. Such furan-modified oligonucleotides form stable duplexes upon hybridization to their complementary DNA strands and display favorable fluorescent features.     

4,4-Difluoro-4-bora-3a,4a-diaza-s-indacene as a bright fluorescent label for DNA

4,4-Difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) as a fluorescent label can be incorporated into DNA by two conceptually different ways: the non-nucleosidic DNA base surrogate Bo exhibits high brightness but no preferential base-pairing properties, whereas the BODIPY-modified uridine BodU has reduced quantum yields but shows preferred Watson-Crick base pairing with adenine.     

Quantum chemical characterization of the cytosine: 2‐Aminopurine base pair

The nature of the base pairing between cytosine and 2‐aminopurine is investigated by means of quantum mechanical calculations including electron correlation and accounting for the effects of aqueous solvation. At neutral pH, both a neutral wobble base pair and a Watson–Crick‐like base pair having a protonated 2‐aminopurine are predicted to be close to one another in energy; other previously proposed forms are found to be too high in energy to be of significant chemical interest. Accounting for the energetics of helix embedding suggests that the equilibrium between the two low‐energy motifs is quite sensitive to local environment. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1167–1179, 2001     

Synthesis of Triazole‐linked Homonucleoside Polymers through Topochemical Azide–Alkyne Cycloaddition

There is a great deal of interest in developing stable modified nucleic acids for application in diverse fields. Phosphate‐modified DNA analogues, in which the phosphodiester group is replaced with a surrogate group, are attractive because of their high stability and resistance to nucleases. However, the scope of conventional solution or solid‐phase DNA synthesis is limited for making DNA analogues with unnatural linkages. Other limitations associated with conventional synthesis include difficulty in making larger polymers, poor yield, incomplete reaction, and difficult purification. To circumvent these problems, a single‐crystal‐to‐single‐crystal (SCSC) synthesis of a 1,5‐triazole‐linked polymeric ssDNA analogue from a modified nucleoside through topochemical azide–alkyne cycloaddition (TAAC) is reported. This is the first solvent‐free, catalyst‐free synthesis of a DNA analogue that proceeds in quantitative yield and does not require any purification.     

Monitoring the site-specific incorporation of dual fluorophore-quencher base analogues for target DNA detection by an unnatural base pair system

We developed intramolecular dual fluorophore-quencher base analogues for site-specific incorporation into DNA by an unnatural base pair replication system. An unnatural base pair between 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px) exhibits high fidelity in PCR amplification, and the 2-nitropyrrole moiety of Px acts as a quencher. Deoxyribonucleoside triphosphates of Px linked with a fluorophore (Cy3, Cy5 or FAM) were chemically synthesized, and the fluorescent properties and the enzymatic incorporation of the fluorophore-linked dPxTPs into DNA were examined in PCR amplification. The fluorophore-linked dPxTPs were site-specifically incorporated by PCR into DNA, opposite Ds in templates, with high selectivity. Furthermore, we found that the fluorescence of the triphosphates was partially quenched, but increased upon their incorporation into DNA. These dual fluorophore-quencher base analogues would be useful for site-specific DNA labeling and for monitoring the amplification products of target nucleic acid molecules with a specific sequence. We have demonstrated the utility of the fluorophore-linked Px substrates and the Ds-Px pairing in real-time quantitative PCR for target DNA molecule detection.     

Rational design of outer‐expanded purine analogues as building blocks of DNA‐based nanowires with enhanced electronic properties

Due to the fact that natural DNA may lack sufficient conductance for direct application in molecular electronics, a novel design of outer‐expanded purine analogues was proposed by incorporating an aromatic ring at the N7‐C8 site into natural G and A bases from the outside. The effect of the outer‐expansion modification on electronic properties of DNA was investigated by density functional theory and molecular dynamics. The analyses revealed that these purine analogues not only preserve the same sizes of natural purine bases, thus avoiding distortions of DNA skeleton induced by the normal ring‐inner‐expansion modification, but also keep the selectivity of pairing with their natural counterpart C and T bases. More importantly, their electronic properties are enhanced, indicated by the narrowed HOMO–LUMO gaps, the lowered ionization potentials and the improved ultraviolet absorption spectra. This work may provide helpful information for designing of artificial bases as promising building blocks of biomolecular nanowires. © 2014 Wiley Periodicals, Inc.     

Stable Copper(I)‐Mediated Base Pairing in DNA

A GNA (glycol nucleic acid) functionalized nucleoside analogue containing the artificial nucleobase 1H‐imidazo[4,5‐f][1,10]phenanthroline (P) was used to form a copper(I)‐mediated base pair within a DNA duplex. The geometrical constraints imposed by the artificial nucleobase play a pivotal role in this unprecedented stabilization of copper(I) in aqueous medium via metal‐mediated base pairing. The formation of the copper(I)‐mediated base pair was investigated by temperature‐dependent UV spectroscopy and CD spectroscopy. The metal‐mediated base pair stabilizes the DNA oligonucleotide duplex by 23 °C. A redox chemistry approach confirmed that this base pair formation was due to the incorporation of copper(I) into the duplex. This first report of a copper(I)‐mediated base pair adds metal‐based diversity to the field and consequently opens up the range of possible applications of metal‐modified nucleic acids.