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1.
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.  相似文献   

2.
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.  相似文献   

3.
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.  相似文献   

4.
There are numerous reports of coumarin ester derivatives, in particular phosphate esters, as photocleavable cages in biological systems. Despite the comprehensive analysis of the photocleavage mechanism, studies of 4-methylcoumarin caged phosphates and/or nucleotides were always performed at constant pH. In this work, we present the study of the pH effect on the photochemistry of (7-diethylaminocoumarin-4-yl)methyl phosphate (DEACM-P). Fluorescence and photocleavage quantum yields, as well as the fluorescence decay times were measured as a function of the pH. It was found that the pH produces significant changes in the overall photochemical quantum yield of DEACM-P, and the observed changes are complementary to those obtained from the fluorescence quantum yield. Deprotonation of DEACM-HPO(4)(-) to yield DEACM-PO(4)(2-), produces a decrease in the photochemical quantum yield (from 0.0045 to 0.0003) and an increase in the fluorescence quantum yield (from 0.072 to 0.092). Moreover, from the analysis of the decay times, we have also found that hydroxyl ion is not only relevant, but it is mechanistically involved in the photoreaction of DEACM-HPO(4)(-).  相似文献   

5.
Fluorescence excitation, multiphoton ionization, and dispersed fluorescence spectra of bare and hydrogen-bonded 2-fluoropyridine with water were measured in a supersonic free jet. For bare 2-fluoropyridine, fluorescence quantum yield decrease in the higher vibronic levels was observed even under collision-free conditions. The inter-system crossing channel was probed experimentally by two color R2PI and found to be negligible. The non-radiative relaxation process of 2-fluoropyridine is mainly governed by the relaxation to the electronic ground state. Electronic spectra of 2-fluoropyridine-(water)(n) (n=1 approximately 3) were also obtained. The hydrogen bond formation with water increases the quantum yield in the higher vibronic levels. Rather low frequency vibrations were observed in the hole burning spectrum of bare 2-fluoropyridine; however, these vibronic bands disappeared with the hydrogen bond formation with water. The appearance of low frequency vibronic bands observed for bare 2-fluoropyridine is ascribed to the existence of closely lying (n,pi) state.  相似文献   

6.
合成了两种双水杨醛缩环已二胺类西佛碱N,N’-(二羟苯次甲基)环已二胺(1)和N,N’-二(3,5-二叔丁基-2-羟苯次甲基)环已二胺(2),以及它们的金属锌配合物(3)和(4),通过核磁共振、元素分析和红外光谱确定了四种物质的结构,研究了它们的紫外吸收光谱、荧光光谱,测定了(3)和(4)的荧光量子效率.(4)中四个叔丁基的存在使其荧光量子效率提高.此类双西佛碱金属配合物可以应用于有机电致发光材料中.  相似文献   

7.
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.  相似文献   

8.
Excited-state dynamics of 4-thiothymidine (S4-TdR) and its photosensitization to molecular oxygen in solution with UVA irradiation were investigated. Absorption and emission spectra measurements revealed that UVA photolysis of S4-TdR gives rise to a population of T1(pipi*), following S2(pipi*) --> S1(npi*) internal conversion. In transient absorption measurement, the 355 nm laser photolysis gave broad absorption (380-600 nm) bands of triplet S4-TdR. The time-resolved thermal lensing (TRTL) signal of S4-TdR containing the thermal component due to decay of triplet S4-TdR was clearly observed by the 355 nm laser excitation. The quantum yield for S1 --> T1 intersystem crossing was estimated to be unity by a triplet quenching experiment with potassium iodide. In the presence of molecular oxygen, the photosensitization from triplet S4-TdR gave rise to singlet oxygen O2 (1Deltag) with a quantum yield of 0.50. Therapeutic implications of such singlet oxygen formation are discussed.  相似文献   

9.
A new 2,6-bis(5,6-dihydrobenzo[4,5]imidazo[1,2-c]quinazolin-6-yl)-4-methylphenol (1) serves as a highly selective and sensitive fluorescent probe for Zn(2+) in a HEPES buffer (50 mM, DMSO:water = 1:9 (v/v), pH = 7.2) at 25 °C. The increase in fluorescence in the presence of Zn(2+) is accounted for by the formation of dinuclear Zn(2+) complex [Zn(2)(C(35)H(25)N(6)O)(OH)(NO(3))(2)(H(2)O)] (2), characterized by X-ray crystallography. The fluorescence quantum yield of the chemosensor 1 is only 0.019, and it increases more than 12-fold (0.237) in the presence of 2 equiv of the zinc ion. Interestingly, the introduction of other metal ions causes the fluorescence intensity to be either unchanged or weakened. By incubation of cultured living cells (A375 and HT-29) with the chemosensor 1, intracellular Zn(2+) concentrations could be monitored through selective fluorescence chemosensing.  相似文献   

10.
The photodynamics of the recombinant rhodopsin fragment of the histidine kinase rhodopsin HKR1 from Chlamydomonas reinhardtii was studied by absorption and fluorescence spectroscopy. The retinal cofactor of HKR1 exists in two Schiff base forms RetA and RetB. RetA is the deprotonated 13‐cis‐retinal Schiff base (RSB) absorbing in the UVA spectral region. RetB is the protonated all‐trans RSB absorbing in the blue spectral region. Blue light exposure converts RetB fully to RetA. UVA light exposure converts RetA to RetB and RetB to RetA giving a mixture determined by their absorption cross sections and their conversion efficiencies. The quantum efficiencies of conversion of RetA to RetB and RetB to RetA were determined to be 0.096 ± 0.005 and 0.405 ± 0.01 respectively. In the dark thermal equilibration between RetA and RetB with dominant RetA content occurred with a time constant of about 3 days at room temperature. The fluorescence emission behavior of RetA and RetB was studied, and fluorescence quantum yields of ?F(RetA) = 0.00117 and ?F(RetB) = 9.4 × 10?5 were determined. Reaction coordinate schemes of the photodynamics are developed.  相似文献   

11.
An absorption and emission spectroscopic characterisation of the combined wild-type LOV1-LOV2 domain string (abbreviated LOV1/2) of phot from the green alga Chlamydomonas reinhardtii is carried out at pH 8. A LOV1/2-MBP fusion protein (MBP=maltose binding protein) and LOV1/2 with a His-tag at the C-terminus (LOV1/2-His) expressed in an Escherichia coli strain are investigated. Blue-light photo-excitation generates a non-fluorescent intermediate photoproduct (flavin-C(4a)-cysteinyl adduct with absorption peak at 390 nm). The photo-cycle dynamics is studied by dark-state absorption and fluorescence measurement, by following the temporal absorption and emission changes under blue and violet light exposure, and by measuring the temporal absorption and fluorescence recovery after light exposure. The fluorescence quantum yield, phi(F), of the dark adapted samples is phi(F)(LOV1/2-His) approximately 0.15 and phi(F)(LOV1/2-MBP) approximately 0.17. A bi-exponential absorption recovery after light exposure with a fast (in the several 10-s range) and a slow component (in the near 10-min range) are resolved. The quantum yield of photo-adduct formation, phi(Ad), is extracted from excitation intensity dependent absorption measurements. It decreases somewhat with rising excitation intensity. The behaviour of the combined wildtype LOV1-LOV2 double domains is compared with the behaviour of the separate LOV1 and LOV2 domains.  相似文献   

12.
The effect of interaction with DNA and oligonucleotides on the photophysical properties of two thiazole orange (TO) derivatives, with different side chains (-(CH2)3-N+(CH3)3 and -(CH2)6-I)) linked to the nitrogen of the quinoline ring of the thiazole orange, is presented here. The first one called TO-PRO1 is a commercially available dye, whereas the second one called TO-MET has been specially synthesized for further covalent binding to oligonucleotides with the aim of being used for specific in situ detection of biomolecular interactions. Both photophysical measurements and molecular calculations have been done to assess their possible mode of interaction with DNA. When dissolved in buffered aqueous solutions both derivatives exhibit very low fluorescence quantum yields of 8 x 10(-5) and 2 x 10(-4), respectively. However, upon binding to double-stranded DNA, large spectroscopic changes result and the quantum yield of fluorescence is enhanced by four orders of magnitude, reaching values up to phi F = 0.2 and 0.3, respectively, as a result of an intercalation mechanism between DNA base pairs. A modulation of the quantum yield is observed as a function of the base sequence. The two derivatives also bind with single-stranded oligonucleotides, but the fluorescence quantum yield is not so great as that when bound to double-stranded samples. Typical fluorescence quantum yields of 7 x 10(-3) to 3 x 10(-2) are observed when the dyes interact with short oligonucleotides, whereas the fluorescence quantum yield remains below 10(-2) when interacting with single-stranded oligonucleotides. This slight but significant quantum-yield increase is interpreted as a folding of the single strand around the dye, which reduces the internal rotation of the two heterocycles around the central methine bridge that links the two moieties of the dye. From these properties, it is proposed to link monomer covalently to oligonucleotides for the subsequent detection of target sequences within cells.  相似文献   

13.
Changes in the emission fluorescence intensity of pheophorbide-a (PHEO) in the presence of carboquone (CARBOQ) were used to obtain the association constant, the number of CARBOQ molecules interacting with PHEO, and the fluorescence quantum yield of the complex. Excitation spectra of mixtures of PHEO and CARBOQ in ethanol (EtOH) show an unresolved doublet in the red-most excitation band of PHEO, indicating the formation of a loose ground-state complex. The 1:1 CARBOQ-PHEO complex shows a higher fluorescence quantum yield in EtOH (0.41 ± 0.02) than in buffer solution (0.089 ± 0.002), which is also higher than that of the PHEO monomer (0.28). Quenching of the PHEO fluorescence by DNA nucleosides and double-stranded oligonucleotides was also observed and the bimolecular quenching rate constants were determined. The quenching rate constant increase as the oxidation potential of the DNA nucleoside increases. Larger quenching constants were obtained in the presence of CARBOQ suggesting that CARBOQ enhances DNA photo-oxidation, presumably by inhibiting the back-electron-transfer reaction from the photoreduced PHEO to the oxidized base. Thus, the enhanced DNA-base photosensitized oxidation by PHEO in the presence of CARBOQ may be related to the large extent by which this quinone covalently binds to DNA, as previously reported.  相似文献   

14.
Abstract— Three covalently-linked porphyrin hybrid dimers were synthesized, each containing a metallotetraarylporphyrin [Zn(II), Cu(II), or Ni(II)], and a free base tetraarylporphyrin. Transfer of singlet excitation energy from the metalloporphyrin center to the free base porphyrin center was determined by measuring fluorescence properties. The Zn hybrid dimer displayed excellent intramolecular transfer of energy ( 85%) from the excited singlet state of the Zn(II) chromophore to the free base chromophore. No evidence for such transfer of the excited singlet state energy was found in the Ni(II) or Cu(II) analogues. From our experimental data, the fluorescence quantum yield of the Zn hybrid dimer was the same as for the free base monomer porphyrin (0.11; Seybold and Gouterman, 1969). Thus, the covalent attachment of another fluorescent porphyrin center effectively doubled the antenna size without decreasing the quantum yield even though the fluorescence quantum yield of the Zn(II) containing monomer was substantially less (0.03, according to Seybold and Gouterman, 1969) than that of the free base porphyrin. The donor-acceptor distance and the rate constant for energy transfer were calculated using the Forster equation. Assuming random orientation, a donor-acceptor distance of 15 Å was calculated with an associated rate constant (kci) for energy transfer of 1.9 ± 109 s–1.  相似文献   

15.
[Pt(0)(binap)(2)] (binap = 2,2'-bis(diphenylphosphino)-1,1'-binaphthyl) is found to exhibit a luminescence from metal-to-ligand charge transfer state (MLCT) with a quantum yield of 0.12 and a lifetime of 1.2 micros in toluene at an ambient temperature. Prompt fluorescence with a quantum yield of 1.6 x 10(-)(4) is observed by means of a picosecond time-correlated single photon counting technique. The spectrum of the steady-state luminescence is almost identical to that of the prompt fluorescence, indicating that the intense luminescence is mainly delayed fluorescence from thermally activated (1)MLCT. The analysis of the temperature-dependent emission indicates that the energy difference between the (1)MLCT and (3)MLCT is 1.15 x 10(3) cm(-)(1). The lifetime of the prompt fluorescence is determined to be 3.2 ps from the decay of stimulated emission overlapped on subpicosecond transient absorption spectra. The lifetime of the (1)MLCT is much longer than expected from the large spin-orbit coupling constant of 5d (Pt) electrons (4000 cm(-)(1)). Theoretical analysis based on density functional theory reveals that structural distortion in the MLCT states causes large energy splitting between HOMO and HOMO - 1, which prevents a very fast ISC induced by strong spin-orbit interactions between these orbitals. The relatively slow ISC is therefore induced by weak spin-orbit interactions (ca. 50 cm(-)(1)) between ligand-centered molecular orbitals. Theoretical calculations indicate that the phosphorescence observed at lower temperatures is due to intensity borrowing from 4(1)B(2) --> GS transition. However, the large energy difference between HOMO and HOMO - 2 reduces the extent of mixing between the lowest (3)MLCT and 4(1)B(2) due to spin-orbit interaction, thereby decreasing the radiative rate of the phosphorescence.  相似文献   

16.
Three disubstituted N-confused porphyrins (2-4) were prepared in ca. 4% yield using a one-pot synthesis. These porphyrins bear 3,5-di-tert-butylphenyl groups substituted at the C(5) and C(20) meso positions and para-substituted (Br, NO(2), ethynyl) phenyl groups at the C(10) and C(15) meso positions. The specific orientation of the aryl rings around the macrocycle in porphyrin 2 was definitively determined using a combination of 1D ((1)H and (13)C) and 2D (gHMQC and gHMBC) NMR spectroscopy. The absorption spectra of 2-4 in CH(2)Cl(2) and dimethylacetamide are similar to those of N-confused tetraphenylporphyrin in the same solvents but have Soret and Q-bands that are shifted to lower energies. Steady-state fluorescence measurements revealed Q(x)(0,0) and Q(x)(0,1) bands similar in energy to the unsubstituted NCPs 1i and 1e. The fluorescence quantum yield results for two of these NCPs (2, 4) are atypical of porphyrin behavior and are being further investigated by time-resolved spectroscopy.  相似文献   

17.
A 13mer DNA duplex containing the artificial 4‐aminophthalimide:2,4‐diaminopyrimidine (4AP:DAP) base pair in the central position was characterized by optical and NMR spectroscopy. The fluorescence of 4AP in the duplex has a large Stokes shift of Δλ =124 nm and a quantum yield of Φ F=24 %. The NMR structure shows that two interstrand hydrogen bonds are formed and confirms the artificial base pairing. In contrast, the 4‐N ,N ‐dimethylaminophthalimide moiety prefers the syn conformation in DNA. The fluorescence intensity of this chromophore in DNA is very low and the NMR structure shows no significant interaction with DAP. Primer‐extension experiments with DNA polymerases showed that not only is the 4AP C nucleotide incorporated at the desired position opposite DAP in the template, but also that the polymerase is able to progress past this position to give the full‐length product. The observed selectivity supports the NMR results.  相似文献   

18.
The formation of cyclobutane pyrimidine dimers between adjacent thymines by UV radiation is thought to be the first event in a cascade leading to skin cancer. Recent studies showed that thymine dimers are fully formed within 1 ps of UV irradiation, suggesting that the conformation at the moment of excitation is the determining factor in whether a given base pair dimerizes. MD simulations on the 50 ns time scale are used to study the populations of reactive conformers that exist at any given time in T18 single-strand DNA. Trajectory analysis shows that only a small percentage of the conformations fulfill distance and dihedral requirements for thymine dimerization, in line with the experimentally observed quantum yield of 3%. Plots of the pairwise interactions in the structures predict hot spots of DNA damage where dimerization in the ssT18 is predicted to be most favored. The importance of hairpin formation by intra-strand base pairing for distinguishing reactive and unreactive base pairs is discussed in detail. The data presented thus explain the structural origin of the results from the ultrafast studies of thymine dimer formation.  相似文献   

19.
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 tCO) 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 tCO 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.  相似文献   

20.
四-β-(邻苯二甲酰亚胺甲基)酞菁锌(ZnPcP4)与85%水合肼反应得到四-β-(氨甲基)酞菁锌(ZnPcN4,分子式C36H28N12Zn),其盐酸盐为ZnPcN4.HCl。测试合成得到的标题化合物紫外-可见电子吸收光谱,荧光光谱和单线态氧生成速率。标题化合物在水中聚集,在90%1,2-丙二醇/水中主要以单体形式存在。目标酞菁锌配合物在90%DMF/水的中性溶液存在聚集体,在弱酸性条件下,随酸度增大,675 nm处Q带单体吸收峰升高,在DMF/water(10%,V/V)/HCl(1.2 mmol·L-1)溶液中10-5 mol·L-1的酞菁配合物基本上没有聚集;在强酸性条件下,随酸度增大,675 nm处Q带单体吸收峰下降的同时,在713 nm处酞菁单质子化吸收峰强度有所增加。ZnPcN4.HCl在DMF体系中聚集,荧光量子产率和单线态氧量子产率变小,但其在DMF/water(10%,V/V)/HCl(1.2mmol·L-1)体系中主要以单体形式存在,荧光量子产率为0.19,单线态氧量子产率0.58,光敏活性与标准无取代酞菁锌相近。  相似文献   

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