Femtosecond electron-transfer reactions in mono- and polynucleotides and in DNA

Fluorescence Quenching Dynamics of 2-Amino-7-methyl-1,8-naphthyridine in Abasic-Site-Containing DNA Duplexes for Nucleobase Recognition

Dramatic fluorescence quenching of small heterocyclic ligands trapped in the abasic site (AP) of DNA has been implemented as an unprecedented strategy recognizing single-base mutations in sequence analysis of cancer genes. However, the key mechanisms governing selective nucleobase recognition remain to be disentangled. Herein, we perform fluorescence quenching dynamics studies for 2-amino-7-methyl-1,8-naphthyridine (AMND) in well-designed AP-containing DNA single/double strands. The primary mechanism is discovered, showing that AMND only targets cytosine to form a pseudo-base pair, and therefore, fluorescence quenching of AMND arises through the DNA-mediated electron transfer (ET) between excited state AMND* and flanking nucleobases, most favorably with flanking guanines. Subtle dynamic conformational variations induced by different flanking nucleobases are revealed and found to modulate efficiencies of electron transfer and fluorescence quenching. These findings provide critical mechanistic insights for guiding the design of photoinduced electron transfer (PET)-based fluorescent ligands as sensitive single-base recognition reporters.

Touch print smear of testicular tissue with thionine stain for intraoperative diagnosis in azoospermic men

PURPOSE

To compare the diagnostic value of testicular tissue touch print smear (TPS) conducted on azoospermic patients with results obtained from histopathology and in vitro fertility (IVF) lab findings.

METHODS

Microdissection testicular sperm extraction was performed on a group of 148 azoospermic patients and testicular samples obtained intraoperatively. Using TPS, the samples were smeared onto a sterile slide, followed with staining using thionine. The testis tissue bulk samples were also transferred to the IVF lab, and determinations of sperm presence or absence obtained from IVF lab tests were compared with the TPS sample results. Needle testis biopsy was separately performed on a group of 360 azoospermic patients, and results of pathohistology review on the biopsies were further compared with determinations of spermatogenesis stage obtained from TPS for those patients.

RESULTS

When compared with IVF lab results, TPS was found to have 100% (126/126) positive predictive value and 95.5% (25/26) negative predictive value for predicting sperm presence or absence, respectively. Furthermore, TPS was further found to have a 93.6% correlation (337 of 360 biopsies) with results of histological diagnoses performed by needle biopsy. Results from histology and TPS for the detection of sperm presence were concordant in 96.1% (346/360) of biopsies. Diagnosis of SCO by TPS shows the highest correlation with histopathology (98.6%), followed by complete spermatogenesis (97.5%), early maturation arrest (78.9%), and late maturation arrest (27.3%).

CONCLUSIONS

The results support the continued use of TPS in testicular tissue analysis for more rapid assessment of spermatogenesis and for detection of spermatozoa in azoospermic subjects.

Sequence-specific binding behavior of coralyne toward triplex DNA: An ultrafast time-resolved fluorescence spectroscopy study

Triplex DNA structure has potential therapeutic application in inhibiting the expression of genes involved in cancer and other diseases. As a DNA-targeting antitumor and antibiotic drug, coralyne shows a remarkable binding propensity to triplex over canonical duplex and thus can modulate the stability of triplex structure, providing a prospective gene targeting strategy. Much less is known, however, about coralyne-binding interactions with triplex. By combining multiple steady-state spectroscopy with ultrafast fluorescence spectroscopy, we have investigated the binding behaviors of coralyne with typical triplexes. Upon binding with a G-containing triplex, the fluorescence of coralyne is markedly quenched owing to the photoinduced electron transfer (PET) of coralyne with the G base. Systematic studies show that the PET rates are sensitive to the binding configuration and local microenvironment, from which the coexisting binding modes of monomeric (full and partial) intercalation and aggregate stacking along the sugar-phosphate backbone are distinguished and their respective contributions are determined. It shows that coralyne has preferences for monomeric intercalation within CGG triplex and pure TAT triplex, whereas CGC⁺ triplex adopts mainly backbone binding of coralyne aggregates due to charge repulsion, revealing the sequence-specific binding selectivity. The triplex-DNA-induced aggregation of coralyne could be used as a probe for recognizing the water content in local DNA structures. The strong π-π stacking of intercalated coralyne monomer with base-triplets plays an important role in stabilizing the triplex structure. These results provide mechanistic insights for understanding the remarkable propensity of coralyne in selective binding to triplex DNA and shed light on the prospective applications of coralyne-triplex targeted anti-gene therapeutics.

Dynamic interplay between thionine and DNA under carbon ion irradiation: a real-time first-principles study

Understanding the interactions between deoxyribonucleic acid (DNA) and photosensitizer under ion irradiation benefits the development of aptasensors, DNA biosensors and cancer diagnosis. Using real-time time-depended density functional theory, by simulating high-energy C ion passing through DNA with poly(dG)·poly(dC) sequence and that with embedded thionine (3,7-diamino-5-phenothiazinium, TH), we compared the electronic stopping power (ESP), evolution of the structure and charge, and absorption spectrum. TH inserting leads the increase in space charge density, a larger electron de-excitation and a larger ESP, but the speed corresponding to the maximum ESP is almost same. When C ion passes through TH-DNA, the structure of TH slightly changes and there still exists noncovalent interaction between TH and DNA, but the absorption coefficient depends on the electron occupied state of TH when the ion passes through. These results indicate that at low radiation doses, TH still can be a DNA detector, although its response wavelength and intensity have been slightly changed, and provide a theoretical reference to improve the possible application of phenothiazine dye in DNA biosensor under ion irradiation.

Visible-Light-Mediated Modification and Manipulation of Biomacromolecules

Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.

Photoinduced Electron Transfer between DNA and Water-Soluble Porphyrins

Photophysical properties of five kinds of porphyrins (H₂TMPyP, ZnTMPyP, PdTMPyP, H₂TPPS, and ZnTPPS) complexed with model DNAs (ctDNA and dGMP) have been investigated using steady-state absorption, circular dichroism (CD), and femtosecond transient absorption spectroscopy. Upon addition of ctDNA (or dGMP), larger hypochromism and red shifts are observed for H₂TMPyP and PdTMPyP compared to the other samples. The steady-state measurements have suggested that the binding modes of H₂TMPyP-ctDNA and PdTMPyP-ctDNA are partial intercalation and full intercalation, respectively, while ZnTMPyP-ctDNA shows outside groove binding. No significant interaction was observed between both H₂TPPS and ZnTPPS with two kinds of DNA. Upon excitation of the porphyrins into the higher excited state S₂ (Soret band), the appearance of the transient absorption from ∼500 to ∼620 nm at about 0.05 ps in H₂TMPyP-ctDNA, H₂TMPyP-dGMP, and PdTMPyP-dGMP indicates the occurrence of the electron transfer (ET) from guanine to H₂TMPyP and PdTMPyP. The forward ET are extremely fast (k_f ≥ 1.0 × 10¹³ s^-1), and the backward ET rates are ∼5.6 × 10¹² and ∼4.0 × 10¹² s^-1, respectively. The complexation with DNA may lead to the shorter lifetime of the fluorescence of H₂TMPyP and PdTMPyP.

Fluorescence quenching by photoinduced electron transfer between 7-methoxycoumarin and guanine base facilitated by hydrogen bonds: an in silico study

In this study, the effects of hydrogen bond (H-bond) formation on fluorescence quenching of 7-methoxycoumarin (7MC) via photo-induced electron transfer from a guanine base (Gua) are investigated using a combined quantum mechanics/molecular mechanics simulation. The electronic structure is calculated by the floating occupation molecular orbital complete active space configuration interaction modification on a semiempirical method. Then the full multiple spawning method is employed for the dynamics simulations on multiple electronic states. The methods employed here are validated by simulating direct dynamics of 7MC (without Gua) and compared with available experimental results. Our computational results are in good agreement with the previously reported experimental results in terms of spectroscopic properties of 7MC. In the case of a H-bonded 7MC-Gua complex, the results from constrained dynamics simulations and single-point calculations suggest that the electron transfer occurs on the second excited state and it depends not only on the H-bond length but also on the intermolecular planarity between 7MC and Gua. Moreover, a proton coupled electron transfer can occur at ≈1 Å of H-bond length, where a proton from Gua is also transferred together with the electron to 7MC. The obtained simulations are expected to be greatly beneficial for designing effective fluorescently labeled nucleotide probes as well as providing information for precise fluorescence signal interpretation.

A dinuclear ruthenium(ii) phototherapeutic that targets duplex and quadruplex DNA

With the aim of developing a sensitizer for photodynamic therapy, a previously reported luminescent dinuclear complex that functions as a DNA probe in live cells was modified to produce a new iso-structural derivative containing RuII(TAP)2 fragments (TAP = 1,4,5,8-tetraazaphenanthrene). The structure of the new complex has been confirmed by a variety of techniques including single crystal X-ray analysis. Unlike its parent, the new complex displays Ru → L-based 3MLCT emission in both MeCN and water. Results from electrochemical studies and emission quenching experiments involving guanosine monophosphate are consistent with an excited state located on a TAP moiety. This hypothesis is further supported by detailed DFT calculations, which take into account solvent effects on excited state dynamics. Cell-free steady-state and time-resolved optical studies on the interaction of the new complex with duplex and quadruplex DNA show that the complex binds with high affinity to both structures and indicate that its photoexcited state is also quenched by DNA, a process that is accompanied by the generation of the guanine radical cation sites as photo-oxidization products. Like the parent complex, this new compound is taken up by live cells where it primarily localizes within the nucleus and displays low cytotoxicity in the absence of light. However, in complete contrast to [{RuII(phen)2}2(tpphz)]4+, the new complex is therapeutically activated by light to become highly phototoxic toward malignant human melanoma cell lines showing that it is a promising lead for the treatment of this recalcitrant cancer.

Monitoring guanine photo-oxidation by enantiomerically resolved Ru(II) dipyridophenazine complexes using inosine-substituted oligonucleotides

The intercalating [Ru(TAP)2(dppz)](2+) complex can photo-oxidise guanine in DNA, although in mixed-sequence DNA it can be difficult to understand the precise mechanism due to uncertainties in where and how the complex is bound. Replacement of guanine with the less oxidisable inosine (I) base can be used to understand the mechanism of electron transfer (ET). Here the ET has been compared for both Λ- and Δ-enantiomers of [Ru(TAP)2(dppz)](2+) in a set of sequences where guanines in the readily oxidisable GG step in {TCGGCGCCGA}2 have been replaced with I. The ET has been monitored using picosecond and nanosecond transient absorption and picosecond time-resolved IR spectroscopy. In both cases inosine replacement leads to a diminished yield, but the trends are strikingly different for Λ- and Δ-complexes.

Pump-Probe Spectroscopy Using the Hadamard Transform

A new method of performing pump-probe experiments is proposed and experimentally demonstrated by a proof of concept on the millisecond scale. The idea behind this method is to measure the total probe intensity arising from several time points as a group, instead of measuring each time separately. These measurements are multiplexes that are then transformed into the true signal via multiplication with a binary Hadamard S matrix. Each group of probe pulses is determined by using the pattern of a row of the Hadamard S matrix and the experiment is completed by rotating this pattern by one step for each sample excitation until the original pattern is again produced. Thus to measure n time points, n excitation events are needed and n probe patterns each taken from the n × n S matrix. The time resolution is determined by the shortest time between the probe pulses. In principle, this method could be used over all timescales, instead of the conventional pump-probe method which uses delay lines for picosecond and faster time resolution, or fast detectors and oscilloscopes on longer timescales. This new method is particularly suitable for situations where the probe intensity is weak and/or the detector is noisy. When the detector is noisy, there is in principle a signal to noise advantage over conventional pump-probe methods.

Ground and excited state interactions of metalloporphyrin PtTMPyP4 with polynucleotides [poly(dG-dC)]2 and [poly(dA-dT)]2

The ground- and excited-state interactions of Pt(ii) meso-tetrakis(4-N-methylpyridyl)porphyrin (PtTMPyP4) with polynucleotides [poly(dG-dC)]2 and [poly(dA-dT)]2 have been investigated using UV/visible, circular dichroism, and steady-state and time-resolved emission spectroscopy. PtTMPyP4 intercalates into [poly(dG-dC)]2 with K∼ 10(6) M(-1). When bound to [poly(dG-dC)]2 in aerated solution there is a six-fold emission enhancement with 18 nm red-shift in emission maximum. Emission lifetimes are biexponential. In the presence of [poly(dA-dT)]2 at least two distinct groove-binding modes are observed, depending on the binding ratio. In [poly(dA-dT)]2 the emission intensity increases by a maximum factor of 17 with no shift in the emission spectrum. Three exponentials were required for lifetime fitting. The lower extent of emission enhancement in the presence of [poly(dG-dC)]2 suggests that a slow electron transfer may take place to guanine, which is significantly less efficient than that previously observed for PtTMPyP4 in the presence of guanosine 5'-monophosphate (GMP). The results are compared to those previously recorded with free base H2TMPyP4.

Ultrafast Electron Transfer in Complexes of Doxorubicin with Human Telomeric G-Quadruplexes and GC Duplexes Probed by Femtosecond Fluorescence Spectroscopy

Doxorubicin (DOX) is a natural anthracycline widely used in chemotherapy; its combined application as a chemotherapeutic and photodynamic agent has been recently proposed. In this context, understanding the photoinduced properties of DOX complexes with nucleic acids is crucial. Herein, the study of photoinduced electron transfer in DOX-DNA complexes by femtosecond fluorescence spectroscopy is reported. The behaviour of complexes with two model DNA structures, a G-quadruplex (G4) formed by the human telomeric sequence (Tel21) and a d(GC) duplex, is compared. The DOX affinity for these two sequences is similar. Although both 1:1 and 2:1 stoichiometries have been reported for DOX-G4 complexes, only 1:1 complexes form with the duplex. The steady-state absorption indicates a strong binding interaction with the duplex due to drug intercalation between the GC base pairs. In contrast, the interaction of DOX with Tel21 is much weaker and arises from drug binding on the G4 external faces at two independent binding sites. As observed for DOX-d(GC) complexes, fluorescence of the drug in the first binding site of Tel21 exhibits decays within a few picoseconds following a biphasic pattern; this is attributed to the existence of two drug conformations. The fluorescence of the drug in the second binding site of Tel21 shows slower decays within 150 ps. These timescales are consistent with electron transfer from the guanines to the excited drug, as favoured by the lower oxidation potential of the stacked guanines of G4 with respect to those in the duplex.

Photoinduced Electron Transfer between Anionic Corrole and DNA

The interaction between a water-soluble anionic Ga(III) corrole [Ga(tpfc)(SO3Na)2] and calf thymus DNA (ct-DNA) has been investigated by using femtosecond transient absorption spectroscopy. A significant broadening from 570 to 585 nm of positive absorption band of the blend of Ga(tpfc)(SO3Na)2 and ct-DNA (Ga(tpfc)(SO3Na)2-ctDNA) has been observed from 0.15 to 0.50 ps after photoexcitation of Ga(tpfc)(SO3Na)2 into the Soret band. The control experiment has been performed on the model DNA ([poly(dG-dC)]2) rich in guanine bases, which exhibits a similar spectral broadening, whereas it is absent for [poly(dA-dT)]2 without guanine bases. The molecular orbital calculation shows that HOMO of Ga(tpfc)(SO3Na)2 is lower than that of guanine bases. The results of the electrochemical experiment show the reversible electron transfer (ET) between Ga(tpfc)(SO3Na)2 and guanine bases of ct-DNA is thermodynamically favorable. The dynamical analysis of the transient absorption spectra reveals that an ultrafast forward ET from the guanine bases to Ga(tpfc)(SO3Na)2 occurs within the pulse duration (156 fs), leading to the formation of an intermediate state. The following back ET to the ground state of Ga(tpfc)(SO3Na)2 may be accomplished in 520 fs.

Study of picosecond processes of an intercalated dipyridophenazine Cr(iii) complex bound to defined sequence DNAs using transient absorption and time-resolved infrared methods

Excited-state quenching of DNA intercalated [Cr(phen)₂(dppz)]³⁺ by guanine proceeds by rapid forward and back electron transfer of <3 ps.

Cobalt(III)hexaammine-dependent photocrosslinks in the hairpin ribozyme

We have utilized the hairpin ribozyme, an RNA enzyme whose structure has been solved by high-resolution methods, to develop a new tool for mapping nucleobase-stacking interactions and potential metal-binding sites in RNA molecules. This tool involves the photoactivation of a specifically bound cobalt(III)hexaammine molecule at wavelengths corresponding to excitation of the metal ion complex only; no base excitation is involved. The photoexcitation initiates a process which strongly promotes the formation of a novel covalent bond or crosslink between one base (termed the "first base"), which is close in space to the excited cobalt(III)hexaammine complex, and another base upon which the first base is closely stacked. These crosslinked species can be isolated and sequenced; their activities can be analyzed to ensure that the crosslinked structures represent an active conformation of the molecule. We have shown that, as in electron transfer in DNA, several criteria must be met to result in the successful formation of these crosslinks. These include the appropriate oxidation potential of the first donor base, the stacking and close interaction of the two donor bases involved in the crosslink, and the binding of a specific cobalt(III)hexaammine molecule to the first donor base. Additionally, we have determined that this crosslinking is pH-sensitive, although the cause of this sensitivity remains unknown. This tool has proven useful in the past for the analysis of the hairpin ribozyme folded structure, and has been applied to identify potential metal-binding sites on the hairpin and extended hammerhead ribozymes.

Impact of a single base pair substitution on the charge transfer rate along short DNA hairpins

Numerical studies of hole migration along short DNA hairpins were performed with a particular emphasis on the variations of the rate and quantum yield of the charge separation process with the location of a single guanine:cytosine (G:C) base pair. Our calculations show that the hole arrival rate increases as the position of the guanine:cytosine base pair shifts from the beginning to the end of the sequence. Although these results are in agreement with recent experimental findings, the mechanism governing the charge migration along these sequences is revisited here. Instead of the phenomenological two-step hopping mechanism via the guanine base, the charge propagation occurs through a delocalization of the hole density along the base pair stack. Furthermore, the variations of the charge transfer with the position of the guanine base are explained by the impact of the base pair substitutions on the delocalized conduction channels.

Between superexchange and hopping: an intermediate charge-transfer mechanism in poly(A)-poly(T) DNA hairpins

We developed a model for hole migration along relatively short DNA hairpins with fewer that seven adenine (A):thymine (T) base pairs. The model was used to simulate hole migration along poly(A)-poly(T) sequences with a particular emphasis on the impact of partial hole localization on the different rate processes. The simulations, performed within the framework of the stochastic surrogate Hamiltonian approach, give values for the arrival rate in good agreement with experimental data. Theoretical results obtained for hairpins with fewer than three A:T base pairs suggest that hole transfer along short hairpins occurs via superexchange. This mechanism is characterized by the exponential distance dependence of the arrival rate on the donor/acceptor distance, k(a) ≃ e(-βR), with β = 0.9 Å(-1). For longer systems, up to six A:T pairs, the distance dependence follows a power law k(a) ≃ R(-η) with η = 2. Despite this seemingly clear signature of unbiased hopping, our simulations show the complete delocalization of the hole density along the entire hairpin. According to our analysis, the hole transfer along relatively long sequences may proceed through a mechanism which is distinct from both coherent single-step superexchange and incoherent multistep hopping. The criterion for the validity of this mechanism intermediate between superexchange and hopping is proposed. The impact of partial localization on the rate of hole transfer between neighboring A bases was also investigated.

Triplet-state dynamics of a metalloporphyrin photosensitiser (PtTMPyP4) in the presence of halides and purine mononucleotides

The photophysical properties of Pt(II) meso-tetrakis(4-N-methylpyridyl)porphyrin (PtTMPyP4) have been investigated in the presence of purine mononucleotides using emission and transient UV/visible/near-IR spectroscopy. While both adenosine 5'-monophosphate (AMP) and guanosine 5'-monophosphate (GMP) form 1:1 and 1:2 complexes with PtTMPyP4, the effect on the triplet lifetime is different. With AMP, complexation gives rise to an enhancement of lifetime and quantum yield due to shielding from dissolved oxygen and a slight decrease in the non-radiative decay rate. When complexed with GMP, quenching is observed consistent with photoinduced electron transfer from guanine to triplet-excited PtTMPyP4, due to both dynamic quenching of the porphyrin and to short-lived emission from 1:1 (67 ns) and 1:2 (400 ns) complexes. No charge-separated photoproducts are observed by transient UV/vis/near-IR absorption spectroscopy on the nanosecond timescale, suggesting that rapid reverse electron transfer may prevent type 1 DNA damage.

Excited state dependent electron transfer of a rhenium-dipyridophenazine complex intercalated between the base pairs of DNA: a time-resolved UV-visible and IR absorption investigation into the photophysics of fac-[Re(CO)3(F2dppz)(py)]+ bound to either [poly(dA-dT)]2 or [poly(dG-dC)]2

The transient species formed following excitation of fac-[Re(CO)(3)(F(2)dppz)(py)](+) (F(2)dppz = 11,12-difluorodipyrido[3,2-a:2',3'-c]phenazine) bound to double-stranded polynucleotides [poly(dA-dT)](2) or [poly(dG-dC)](2) have been studied by transient visible and infra-red spectroscopy in both the picosecond and nanosecond time domains. The latter technique has been used to monitor both the metal complex and the DNA by monitoring the regions 1900-2100 and 1500-1750 cm(-1) respectively. These data provide direct evidence for electron transfer from guanine to the excited state of the metal complex, which proceeds both on a sub-picosecond time scale and with a lifetime of 35 ps, possibly due to the involvement of two excited states. No electron transfer is found for the [poly(dA-dT)](2) complex, although characteristic changes are seen in the DNA-region TRIR consistent with changes in the binding of the bases in the intercalation site upon excitation of the dppz-complex.

Single-step charge transport through DNA over long distances

Quantum yields for charge transport across adenine tracts of increasing length have been measured by monitoring hole transport in synthetic oligonucleotides between photoexcited 2-aminopurine, a fluorescent analogue of adenine, and N(2)-cyclopropyl guanine. Using fluorescence quenching, a measure of hole injection, and hole trapping by the cyclopropyl guanine derivative, we separate the individual contributions of single- and multistep channels to DNA charge transport and find that with 7 or 8 intervening adenines the charge transport is a coherent, single-step process. Moreover, a transition occurs from multistep to single-step charge transport with increasing donor/acceptor separation, opposite to that generally observed in molecular wires. These results establish that coherent transport through DNA occurs preferentially across 10 base pairs, favored by delocalization over a full turn of the helix.

Excited state behaviour of substituted dipyridophenazine Cr(III) complexes in the presence of nucleic acids

The photophysics and photochemistry of [Cr(phen)(2)(dppz)](3+) and its 11,12-substituted derivatives [Cr(phen)(2)(X(2)dppz)](3+) {X = Me or F} have been studied in the presence of purine nucleotides or DNA using steady state and time-resolved absorption and luminescence spectroscopy. 5'-Adenosine monophosphate (5'-AMP) shows only a weak interaction with the excited states of each complex. By contrast they are efficiently quenched by 5'-guanosine monophosphate (5'-GMP), consistent with photo-induced electron transfer. Laser flash photolysis spectroscopy in the presence of 5'-GMP suggests that both forward and back electron-transfers are rapid. All complexes also display a strong affinity for DNA and evidence for both static and dynamic quenching mechanisms is provided.

Multiplex binding modes of toluidine blue with calf thymus DNA and conformational transition of DNA revealed by spectroscopic studies

It is noteworthy to understand the details of interactions between antitumor drugs and DNA because the binding modes and affinities affect their antitumor activities. Here, The interaction of toluidine blue (TB), a potential antitumor drug for photodynamic therapy of tumor, with calf thymus DNA (ctDNA) was explored by UV-vis, fluorescence, circular dichroism (CD) spectroscopy, UV-melting method and surface-enhance Raman spectroscopy (SERS). The experimental results suggest that TB could bind to ctDNA via both electrostatic interaction and partial intercalation. The fluorescence quenching of TB by ctDNA was static and due to electron transfer from bases to the excited singlet state of TB. At low [TB]/[DNA] ratio, TB mainly partially intercalated into ctDNA resulting in the slight increase of base stacking degree; at high [TB]/[DNA] ratio, excessive TB externally stacked along the helix surface via coupling with partially intercalated ones, thereby inducing B-A transition of ctDNA. The conformational transition of DNA was confirmed by the obvious improvement of the thermal stability of ctDNA. The SERS spectra suggest that TB could partially intercalate into DNA basepairs with its ring C(1)NC(1') side buried.

Back-electron transfer suppresses the periodic length dependence of DNA-mediated charge transport across adenine tracts

DNA-mediated charge transport (CT) is exquisitely sensitive to the integrity of the bridging pi-stack and is characterized by a shallow distance dependence. These properties are obscured by poor coupling between the donor/acceptor pair and the DNA bridge, or by convolution with other processes. Previously, we found a surprising periodic length dependence for the rate of DNA-mediated CT across adenine tracts monitored by 2-aminopurine fluorescence. Here we report a similar periodicity by monitoring N 2-cyclopropylguanosine decomposition by rhodium and anthraquinone photooxidants. Furthermore, we find that this periodicity is attenuated by consequent back-electron transfer (BET), as observed by direct comparison between sequences that allow and suppress BET. Thus, the periodicity can be controlled by engineering the extent of BET across the bridge. The periodic length dependence is not consistent with a periodicity predicted by molecular wire theory but is consistent with a model where multiples of four to five base pairs form an ideal CT-active length of a bridging adenine domain.

Photosensitized oxidation of hypoxanthine and xanthine by aluminum phthalocyanine tetrasulfonate. Role of the alkylating quinone 2,5-dichloro-diaziridinyl-1,4-benzoquinone

Photoirradiation of nitrogen-saturated aqueous solutions containing aluminum phthalocyanine tetrasulfonate (AlPcS4) at 675 nm in the presence of 2,5-dichloro-diaziridinyl-1,4-benzoquinone (AZDClQ) and hypoxanthine (HX) produces the oxidized HX derivatives, xanthine (X) and uric acid (UA). Concentrations of the AZDClQ semiquinone, X and UA increase at the expense of HX with an increase in irradiation time. Almost negligible decomposition of HX, as well as very low amounts of X, are detected if photolysis occurs under identical conditions but in the absence of AZDClQ. Addition of calf-thymus DNA produces quinone-DNA covalent adducts after photolysis of anaerobic samples containing quinone, DNA and AlPcS4, in the presence or absence of HX and at pH 5.5. However, larger amounts of quinone-DNA adducts are detected if HX is present. The results presented here could have applications in the photodynamic treatment of hypoxic tissues such as solid tumors, under conditions of high HX concentration, where Type-I pathways could be more important than singlet oxygen generation.

Photooxidation of guanine by a ruthenium dipyridophenazine complex intercalated in a double-stranded polynucleotide monitored directly by picosecond visible and infrared transient absorption spectroscopy

Transient species formed by photoexcitation (400 nm) of [Ru(dppz)(tap)2]2+ (1) (dppz = dipyrido[3,2-a:2',3'-c]phenazine; tap=1,4,5,8-tetraazaphenanthrene) in aqueous solution and when intercalated into a double-stranded synthetic polynucleotide, [poly(dG-dC)]2, have been observed on a picosecond timescale by both visible transient absorption (allowing monitoring of the metal complex intermediates) and transient infrared (IR) absorption spectroscopy (allowing direct study of the DNA nucleobases). By contrast with its behavior when free in aqueous solution, excitation of 1 when bound to [poly(dG-dC)]2 causes a strong increase in absorbance at 515 nm due to formation of the reduced complex [Ru(dppz)(tap)2]+ (rate constant=(2.0+/-0.2) x 10(9) s(-1)). The subsequent reformation of 1 proceeds with a rate constant of (1.1+/-0.2) x 10(8) s(-1). When the process is carried out in D2O, the rates of formation and removal of [Ru(dppz)(tap)2]+ are reduced (rate constants (1.5+/-0.3) x 10(9) and (0.7+/-0.2) x 10(8) s(-1) respectively) consistent with proton-coupled electron transfer processes. Picosecond transient IR measurements in the 1540-1720 cm(-1) region in D2O solution confirm that the reduction of 1 intercalated into [poly(dG-dC)]2 is accompanied by bleaching of IR ground-state bands of guanine (1690 cm(-1)) and cytosine (1656 cm(-1)), each with similar rate constants.

Electronic coupling between base pair dimers of LNA:DNA oligomers

We calculated ab initio electronic coupling elements between neighboring base-pair dimers in a set of LNA:DNA oligomers with different numbers of locked nucleotides and compared them by averaging the values over ensembles of snapshots from molecular dynamics trajectories. Averaging was based on coupling elements for various ensembles comprising of 33,000 structures. The known pronounced variations of coupling elements on the nanosecond timescale due to thermal fluctuations of the DNA structure were confirmed. We found significant differences in electronic coupling at the dimer level between a non-modified DNA:DNA duplex and the corresponding duplex containing one fully LNA-substituted strand. We rationalized these differences by very dissimilar overlap in the pi-stack as a consequence of the LNA-modified system approximating an A-DNA-type helix. The calculated coupling elements for the non-modified reference duplex were similar to those of standard B-DNA and those for the fully modified oligomer resembled the matrix elements estimated for standard A-DNA.

Electron-transfer oxidation properties of DNA bases and DNA oligomers

Kinetics for the thermal and photoinduced electron-transfer oxidation of a series of DNA bases with various oxidants having the known one-electron reduction potentials (E(red)) in an aqueous solution at 298 K were examined, and the resulting electron-transfer rate constants (k(et)) were evaluated in light of the free energy relationship of electron transfer to determine the one-electron oxidation potentials (E(ox)) of DNA bases and the intrinsic barrier of the electron transfer. Although the E(ox) value of GMP at pH 7 is the lowest (1.07 V vs SCE) among the four DNA bases, the highest E(ox) value (CMP) is only 0.19 V higher than that of GMP. The selective oxidation of GMP in the thermal electron-transfer oxidation of GMP results from a significant decrease in the pH dependent oxidation potential due to the deprotonation of GMP*+. The one-electron reduced species of the photosensitizer produced by photoinduced electron transfer are observed as the transient absorption spectra when the free energy change of electron transfer is negative. The rate constants of electron-transfer oxidation of the guanine moieties in DNA oligomers with Fe(bpy)3(3+) and Ru(bpy)3(3+) were also determined using DNA oligomers containing different guanine (G) sequences from 1 to 10 G. The rate constants of electron-transfer oxidation of the guanine moieties in single- and double-stranded DNA oligomers with Fe(bpy)3(2+) and Ru(bpy)3(3+) are dependent on the number of sequential guanine molecules as well as on pH.

Luminescence of a Pt(II) complex in the presence of DNA. Dependence of luminescence changes on the interaction binding mode

Luminescence intensity changes of a Pt(II) complex which is known to bind externally to DNA at low [DNA]/[complex] ratio and to intercalate at high [DNA]/[complex] ratio are studied in the presence of calf thymus DNA. External binding is demonstrated to induce luminescence enhancement whereas intercalation leads to luminescence quenching. The reasons for this behaviour are discussed.

Adsorption characteristics of thionine on gold nanoparticles

Adsorption characteristics of thionine on gold nanoparticles have been studied by using UV-vis absorption spectroscopy, fluorescence spectroscopy, transmission electron microscopy (TEM), cyclic voltammetry and Fourier transform infrared spectroscopy. With the increasing concentration of gold nanoparticles, the absorption peak intensity of H-type dimers of thionine increases continuously, whereas that of monomers of thionine first increases and then decreases. The addition of gold nanoparticles makes the equilibrium between the monomer and H-type dimer forms of thionine move toward the dimer forms. Furthermore, the adsorption behavior of thionine on gold nanoparticles is also influenced by temperature. TEM images show that the addition of thionine results in an obvious aggregation, and further support the absorption spectral results. The fluorescence intensity of adsorbed thionine is quenched by gold nanoparticles due to the electronic interaction between thionine molecules and gold nanoparticles. Cyclic voltammetric and infrared spectroscopic studies show that the nitrogen atoms of both of the NH2 moieties of thionine strongly bind to the gold nanoparticle surfaces through the electrostatic interaction of thionine with gold nanoparticles. For 15-20 nm particles, the number of adsorbed thionine molecules per gold nanoparticle is about 7.66 x 10(4). Thionine molecules can not only bind to a particle to form a compact monolayer via both of the NH2 moieties, but they can also bind to two particles via their two NH(2) moieties, respectively.