Femtosecond fluorescence upconversion studies of excited-state proton-transfer dynamics in 2-(2′-hydroxyphenyl)benzoxazole (HBO) in liquid solution and DNA

A femtosecond fluorescence upconversion study is reported for HBO in solution, as well as for HBO incorporated in DNA. The typical time for the excited-state intramolecular proton-transfer reaction of the syn-enol tautomer in solution and in DNA has been determined to be 150 fs. In addition, the lifetimes of the keto, the anti-enol and the ‘solvated enol’ tautomer forms were determined in protic solvents, aprotic solvents and DNA. Picosecond rise and decay components in the fluorescence transients with characteristic times between 3 and 25 ps are also observed and attributed to the effects of vibrational cooling.     

Dimerization and double proton transfer-induced tautomerism of 4(3H)-pyrimidinone in solution studied by IR spectroscopy and quantum chemical calculations

The tautomerism and dimerization of 4(3H)-pyrimidinone (4(3H)Pyr) in carbon tetrachloride (CCl4) and chloroform (CHCl3) solutions were investigated using IR spectroscopy and quantum chemical calculations. The observed IR spectra in the NH and OH stretching regions clearly revealed the predominance of the keto tautomer in both solvent systems. The enol form only exists in a very small proportion in the CCl4 solution. The tautomeric constant for the two monomers KT[OH/NH] = 0.012 and DeltaE = 2.62 kcal/mol were estimated at 25 degrees C. This result was supported by the self-consistent reaction field/polarizable continuum (SCRF/PCM) calculation at the MP4(full, SDQ)/aug-cc-pVDZ level, which predicted DeltaE = 3.06 kcal/mol in CCl4. In the C=O stretching region, two bands were observed, suggesting the coexistence of two keto structures at equilibrium. The calculated IR spectra indicated that the bands at 1711 and 1675 cm(-1) arise from the keto monomer and keto-keto (KK) ring dimer, respectively. At elevated temperature, the populations of both the keto and enol monomers increased for the CCl4 solution. The present study revealed that the keto <--> enol tautomerization does not occur in the isolated monomer molecule. The double proton transfer (DPT) reaction in the KK ring dimer presumably plays a substantial role in the population increase of the enol monomer. To our knowledge, this may be the first observation of the tautomerization in a model base pair via the temperature-induced ground-state DPT reaction under a nonpolar liquid environment reported so far. This tautomerism can serve as a mimic circumstance for the spontaneous mutations induced by proton transfer in the DNA base pairs.     

The effect of minor-groove hydrogen-bond acceptors and donors on the stability and replication of four unnatural base pairs

The stability and replication of DNA containing self-pairs formed between unnatural nucleotides bearing benzofuran, benzothiophene, indole, and benzotriazole nucleobases are reported. These nucleobase analogues are based on a similar scaffold but have different hydrogen-bond donor/acceptor groups that are expected to be oriented in the duplex minor groove. The unnatural base pairs do not appear to induce major structural distortions and are accommodated within the constraints of a B-form duplex. The differences between these unnatural base pairs are manifest only in the polymerase-mediated extension step, not in base-pair stability or synthesis. The benzotriazole self-pair is extended with an efficiency that is only 200-fold less than a correct natural base pair. The data are discussed in terms of available polymerase crystal structures and imply that further modifications may result in unnatural base pairs that can be both efficiently synthesized and extended, resulting in an expanded genetic alphabet.     

Intramolecular Proton Transfer in 2‐(2′‐hydroxyphenyl)oxazolo[4,5‐b]pyridine: Evidence for Tautomer in the Ground State

The intramolecular proton transfer in a newly synthesized molecule, 2‐(2′‐hydroxyphenyl)oxazolo[4,5‐b]pyridine (HPOP) is studied using UV‐visible absorption, fluorescence emission, fluorescence excitation and time‐resolved fluorescence spectroscopy. In the ground state, the molecule exists as cis‐ and trans‐enol in all the solvents. However, in dioxane, alcohols, acetonitrile, dimethylformamide and dimethylsulfoxide the keto tautomer is also observed in the ground state. Dual fluorescence is observed in HPOP where the large Stoke shifted emission is due to emission from the excited‐state intramolecular proton transfer product, whereas the other emission is the normal emission from enol form. The fluorescence (both normal and tautomer emission) of HPOP is less than those of corresponding benzoxazole and imidazopyridine derivatives. This reveals that the nonradiative decay becomes more efficient upon substitution of electronegative atom on the charge acceptor group. The pH studies substantiate the conclusion that (unlike in its imidazole analog) the third ground state species is the keto tautomer and not the monoanion. The effect of temperature on cis‐enol‐trans‐enol‐keto equilibrium and the nonradiative deactivation from the excited state are also investigated.     

Supramolecular Stabilization of Metastable Tautomers in Solution and the Solid State

This work presents a successful application of a recently reported supramolecular strategy for stabilization of metastable tautomers in cocrystals to monocomponent, non‐heterocyclic, tautomeric solids. Quantum‐chemical computations and solution studies show that the investigated Schiff base molecule, derived from 3‐methoxysalicylaldehyde and 2‐amino‐3‐hydroxypyridine ( ap ), is far more stable as the enol tautomer. In the solid state, however, in all three obtained polymorphic forms it exists solely as the keto tautomer, in each case stabilized by an unexpected hydrogen‐bonding pattern. Computations have shown that hydrogen bonding of the investigated Schiff base with suitable molecules shifts the tautomeric equilibrium to the less stable keto form. The extremes to which supramolecular stabilization can lead are demonstrated by the two polymorphs of molecular complexes of the Schiff base with ap . The molecules of both constituents of molecular complexes are present as metastable tautomers (keto anion and protonated pyridine, respectively), which stabilize each other through a very strong hydrogen bond. All the obtained solid forms proved stable in various solid‐state and solvent‐mediated methods used to establish their relative thermodynamic stabilities and possible interconversion conditions.     

Solid-phase synthesis of positively charged deoxynucleic guanidine (DNG) tethering a Hoechst 33258 analogue: triplex and duplex stabilization by simultaneous minor groove binding

Deoxynucleic guanidine (DNG), a DNA analogue in which positively charged guanidine replaces the phosphodiester linkages, tethering to Hoechst 33258 fluorophore by varying lengths has been synthesized. A pentameric thymidine DNG was synthesized on solid phase in the 3' --> 5' direction that allowed stepwise incorporation of straight chain amino acid linkers and a bis-benzimidazole (Hoechst 33258) ligand at the 5'-terminus using PyBOP/HOBt chemistry. The stability of (DNA)(2).DNG-H triplexes and DNA.DNG-H duplexes formed by DNG and DNG-Hoechst 33258 (DNG-H) conjugates with 30-mer double-strand (ds) DNA, d(CGCCGCGCGCGCGAAAAACCCGGCGCGCGC)/d(GCGGCGCGCGCGCTTTTTGGGCCGCGCGCG), and single-strand (ss) DNA, 5'-CGCCGCGCGCGCGAAAAACCCGGCGCGCGC-3', respectively, has been evaluated by thermal melting and fluorescence emission experiments. The presence of tethered Hoechst ligand in the 5'-terminus of the DNG enhances the (DNA)(2).DNG-H triplex stability by a DeltaT(m) of 13 degrees C. The fluorescence emission studies of (DNA)(2).DNG-H triplex complexes show that the DNG moiety of the conjugates bind in the major groove while the Hoechst ligand resides in the A:T rich minor groove of dsDNA. A single G:C base pair mismatch in the target site decreases the (DNA)(2).DNG triplex stability by 11 degrees C, whereas (DNA)(2).DNG-H triplex stability was decreased by 23 degrees C. Inversion of A:T base pair into T:A base pair in the center of the binding site, which provides a mismatch selectively for DNG moiety, decreases the triplex stability by only 5-6 degrees C. Upon hybridization of DNG-Hoechst conjugates with the 30-mer ssDNA, the DNA.DNG-H duplex exhibited significant increase in the fluorescence emission due to the binding of the tethered Hoechst ligand in the generated DNA.DNG minor groove, and the duplex stability was enhanced by DeltaT(m) of 7 degrees C. The stability of (DNA)(2).DNG triplexes and DNA.DNG duplexes is independent of pH, whereas the stability of (DNA)(2).DNG-H triplexes decreases with increase in pH.     

Sequence specific fluorescence detection of double strand DNA

Methods for the fluorescent detection of specific sequences of double strand DNA in homogeneous solution may be useful in the field of human genetics. A series of hairpin polyamides with tetramethyl rhodamine (TMR) attached to an internal pyrrole ring were synthesized, and the fluorescence properties of the polyamide-fluorophore conjugates in the presence and absence of duplex DNA were examined. We observe weak TMR fluorescence in the absence of DNA. Addition of >/=1:1 match DNA affords a significant fluorescence increase over equimolar mismatch DNA for each polyamide-TMR conjugate. Polyamide-fluorophore conjugates offer a new class of sensors for the detection of specific DNA sequences without the need for denaturation. The polyamide-dye fluorescence-based method can be used to screen in parallel the interactions between aromatic ring pairs and the minor groove of DNA even when the binding site contains a non-Watson-Crick DNA base pair. A ranking of the specificity of three polyamide ring pairs-Py/Py, Im/Py, and Im/Im-was established for all 16 possible base pairs of A, T, G, and C in the minor groove. We find that Im/Im is an energetically favorable ring pair for minor groove recognition of the T.G base pair.     

Stabilization by extra-helical thymines of a DNA duplex with Hoogsteen base pairs

We present the crystal structure of the DNA duplex formed by d(ATATATCT). The crystals contain seven stacked antiparallel duplexes in the asymmetric unit with A.T Hoogsteen base pairs. The terminal CT sequences bend over so that the thymines enter the minor groove and form a hydrogen bond with thymine 2 of the complementary strand in the Hoogsteen duplex. Cytosines occupy extra-helical positions; they contribute to the crystal lattice through various kinds of interactions, including a unique CAA triplet. The presence of thymine in the minor groove apparently contributes to the stability of the DNA duplex in the Hoogsteen conformation. These observations open the way toward finding under what conditions the Hoogsteen duplex may be stabilized in vivo. The present crystal structure also confirms the tendency of A.T-rich oligonucleotides to crystallize as long helical stacks of duplexes.     

Visualisation of inter loop tertiary base pairing and stacking interactions in an unusual slipped loop DNA structure

The conformation of an unusual slipped loop DNA structure exhibited by the sequence d(GAATTCCCGAATTC)₂ is determined using a combination of geometrical and molecular mechanics methods. This sequence is known to form a B-DNA-like duplex with the central non-complementary cytosines extruded into single stranded loop regions. The unusual feature is that the interior guanine does not pair with the cytosine across, instead, it pairs with the cytosine upstream by skipping two cytosines, leading to a slipped loop DNA structure with the loops staggered by two base pairs. The two loops, despite being very small, can fold across minor or major groove symmetrically or asymmetrically disposed, with one of the loop bases partially blocking the major or minor groove. Most interestingly, for certain conformations, the loop bases approach one another at close proximity so as to engage even in base pairing as well as base stacking interactions across the major groove. While such pairing and stacking are common in the tertiary folds of RNA, this is the first time that such an interaction is visualized in a DNA. This observation demonstrates that a W-C pair can readily be accomplished in a typical slipped loop structure postulated for DNA. Such tertiary loop interaction may prevent access to regulatory proteins across the major groove of the duplex DNA, thus providing a structure-function relation for the occurrence of slipped loop structure in DNA. Contribution no. 839 from this department     

Excited-state intramolecular proton transfer in 2-(3'-hydroxy-2'-pyridyl)benzoxazole. Evidence of coupled proton and charge transfer in the excited state of some o-hydroxyarylbenzazoles

The influence of solvent, temperature, and viscosity on the phototautomerization processes of a series of o-hydroxyarylbenzazoles was studied by means of ultraviolet-visible (UV-vis) absorption spectroscopy and steady-state and time-resolved fluorescence spectroscopy. The compounds studied were 2-(2'-hydroxyphenyl)benzimidazole (HBI), 2-(2'-hydroxyphenyl)benzoxazole (HBO), 2-(2'-hydroxyphenyl)benzothiazole (HBT), 2-(3'-hydroxy-2'-pyridyl)benzimidazole (HPyBI), and the new derivative 2-(3'-hydroxy-2'-pyridyl)benzoxazole (HPyBO), this one studied in neutral and acid media. All of these compounds undergo an excited-state intramolecular proton transfer (ESIPT) from the hydroxyl group to the benzazole N3 to yield an excited tautomer in syn conformation. A temperature- and viscosity-dependent radiationless deactivation of the tautomer has been detected for all compounds except HBI and HPyBI. We show that this radiationless decay also takes place for 2-(3-methyl-1,3-benzothiazol-3-ium-2-yl)benzenolate (NMeOBT), the N-methylated analog of the tautomer, whose ground-state structure has anti conformation. In ethanol, the radiationless decay shows intrinsic activation energy for HPyBO and HBO; however, it is barrierless for HBT and NMeOBT and controlled instead by the solvent dynamics. The relative efficiency of the radiationless decay in the series of molecules studied supports the hypothesis that this transition is connected with a charge-transfer process taking place in the tautomer, its efficiency being related to the strength of the electron donor (dissociated phenol or pyridinol moiety) and electron acceptor (protonated benzazole). We propose that the charge transfer is associated with a large-amplitude conformational change of the tautomer, the process leading to a nonfluorescent charge-transfer intermediate. The previous ESIPT step generates the structure with the suitable redox pair to undergo the charge-transfer process; therefore, an excited-state intramolecular coupled proton and charge transfer takes place for these compounds.     

Enol-keto tautomerism of aromatic photochromic Schiff base N,N'-bis(salicylidene)-p-phenylenediamine: ground state equilibrium and excited state deactivation studied by solvatochromic measurements on ultrafast time scale

A photochromic symmetric Schiff base, N,N'-bis(salicylidene)-p-phenylenediamine, is proposed as a probe for the study of solvent dependent enol-keto tautomerism in the ground and excited states. The ground state equilibrium between the enol-keto tautomers is found to depend mainly not on polarity but on the proton donating ability of the solvent. Upon selective excitation of each of these tautomers, the same excited state of a keto tautomer is created: in enol, after the ultrafast excited state intramolecular proton transfer (ESIPT), reaction, and in keto tautomer, directly. Then some part (<30%) of excited molecules are transferred to the photochromic form in its ground state. The evidence of another ultrafast deactivation channel in the excited enol tautomer competing with ESIPT has been found. The solvent does not influence the ESIPT dynamics nor the efficiency of the creation of the photochrome.     

Excited-state ab initio calculations and multidimensional Franck-Condon simulations on guanine

The guanine enol and keto N7H and N9H tautomers have been optimized at the CASSCF/cc-pVDZ levels of theory. Except for the enol N7H tautomer, CASSCF predicts distorted nonplanar S1 state geometries. Among the vibronic simulations carried out with the optimized structures only the enol N7H tautomer qualitatively mirrors the appearance of the experimental R2PI spectrum. Refined symmetry-adapted cluster configuration interaction (SACCI) geometries of the enol N7H tautomer produce simulations in good agreement with experiment and support the assignment of the first vibronic band and associated vibronic features of the R2PI spectrum to this tautomer. The sharp spectral features and the fact that Franck-Condon simulations based on the harmonic approximation allow for a faithful reproduction of the spectral signature associated with the enol N7H tautomer indicate that within the simulated energy window the S1 potential energy surface of this isomer is fairly harmonic and free from conical intersections involved in the S1 state lifetime-shortening relaxation processes of other DNA bases and possibly the remaining tautomers of guanine.     

Absorption and Emission Sensitivity of 2‐(2′‐Hydroxyphenyl)benzoxazole to Solvents and Impurities

2‐(2′‐Hydroxyphenyl)benzoxazole (HBO) is known for undergoing intramolecular proton transfer in the excited state to result in the emission of its tautomer. A minor long‐wavelength absorption band in the range 370–420 nm has been reported in highly polar solvents such as dimethylsulfoxide (DMSO). However, the nature of this species has not been entirely clarified. In this work, we provide evidence that this long‐wavelength absorption band might have been caused by base or metal salt impurities that are introduced into the spectral sample during solvent transport using glass Pasteur pipettes. The contamination by base or metal salt could be avoided by using borosilicate glass syringes or nonglass pipettes in sample handling. Quantum chemical calculations conclude that solvent‐mediated deprotonation is too energetically costly to occur without the aid of a base of an adequate strength. In the presence of such a base, the deprotonation of HBO and its effect on emission are investigated in dichloromethane and DMSO, the latter of which facilitates deprotonation much more readily than the former. Finally, the absorption and emission spectra of HBO in 13 solvents are reported, from which it is concluded that ESIPT is hindered in polar solvents that are also strong hydrogen bond acceptors.     

Ultrafast branching of reaction pathways in 2-(2'-hydroxyphenyl)benzothiazole in polar acetonitrile solution

In a combined study on the photophysics of 2-(2'-hydroxyphenyl)-benzothiazole (HBT) in polar acetonitrile utilizing ultrafast infrared spectroscopy and quantum chemical calculations, we show that a branching of reaction pathways occurs on femtosecond time scales. Apart from the excited-state intramolecular hydrogen transfer (ESIHT) converting electronically excited enol tautomer into the keto tautomer, known to be the dominating mechanism of HBT in nonpolar solvents such as cyclohexane and tetrachloroethene, in acetonitrile solution twisting also occurs around the central C-C bond connecting the hydroxyphenyl and benzothiazole units in both electronically excited enol and keto tautomers. The solvent-induced intramolecular twisting enables efficient internal conversion pathways to both enol and keto tautomers in the electronic ground state. Whereas relaxation to the most stable enol tautomer with twisting angle Θ = 0° implies full ground state recovery, a small fraction of HBT molecules persists as the keto twisting conformer with the twisting angle Θ = 180° for delay times extending beyond 120 ps.     

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

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

2-(2-巯苯基)苯并噁唑分子内质子转移取代基电子效应的密度泛函理论研究

在B3LYP/6-31G(d,p)和TDB3LYP/6-31++G(d,p)//CIS/6-31G(d,p)水平上研究了2-(2-巯苯基)苯并噁唑及其衍生物基态和激发态分子内质子转移现象,并探讨取代基电子效应对分子内质子转移的影响,研究结果表明,在基态时,硫醇式异构体为优势构象,供电子取代基使基态分子内正向质子转移能垒(烯醇式→酮式)升高;而吸电子取代基则可降低能垒,有利于基态分子内质子转移并有助于硫酮式异构体的稳定.在激发态时,硫酮式结构为优势构象,所研究的2-(2-巯苯基)苯并噁唑化合物及衍生物均可以发生无能垒或低能垒(≤1.5kJ/mol)的激发态分子内质子转移.巯苯基部分是激发态失活的主要活性部分,供电子基团有利于激发态的质子转移,吸电子基团使激发态跃迁困难,不利于激发态的质子转移.     

Sequence-specific recognition and cleavage of DNA by anti-tumour antibiotics

Abstract

DNA cleavage by a bleomycin—iron complex occurs preferentially at guanine-pyrimidine (5′ → 3′) sequences, in particular at G-C sites. Metallobleomycin binds in the minor groove of B-DNA and the bithiazole moiety probably plays an important role as an anchor on DNA duplex. The 2-amino group of guanine adjacent to the 5′-side of the cleaved pyrimidine base is one key element of the specific 5′-GC recognition by the bleomycin-metal complex. Endiyne anti-tumour antibiotics such as esperamicin A₁ and dynemicin A also interact with the minor groove of DNA, and their strong DNA splitting activity is due to phenylene diradical formation from the enediyne core. A possible binding mode between these antibiotics and B-DNA has been proposed by computer-constructed model building.     

Minor Groove Binding between Norfloxacin and DNA Duplexes in Solution： A Molecular Dynamics Study

Quinolones,a series of nalidixic acid analogues,represent a class of extremely potent antibacterial drugs.Although the functional target of these agents such as norfloxacin has been identified as the enzyme DNA gyrase,the direct binding site of the drug is the DNA itself1.Interactions between quinolones and diversified DNA have been studied by several biochemical,spectroscopic and computational methods2-8.Shen et al.proposed a cooperative drug-DNA binding model.The essential feature of th…     

Λ-、Δ-[Rh(bpy)2chrysi]3+对含C:T错配的DNA序列识别作用的分子模拟研究

通过分子模拟方法研究了手性金属配合物[Rh(bpy)2Chrysi]3 (bpy=2,2’- bipyridine;Chrysi=5,6-chrysenequinonediimine)对包含C:T错配碱基对的B-DNA序列的识别作用。结合类似的针对含G:A错配的和正常的B-DNA序列的识别作用研究,发现配合物[Rh(bpy)2Chrysi]3 可以对错配B-DNA序列进行序列特异性的识别．能量对比计算结果表明,该经典插入识别作用倾向于在错配碱基对附近进行,其中Δ-[Rh(bpy)2charysi]3 比其手性异构体更占优势．这同Barton教授工作组的实验结果是一致的。另外插入作用倾向于在错配序列中的正常双碱基对C3A4／G374(错配碱基对附近)中从小沟进行．与该配合物对含G:A错配的和正常的B-DNA序列的识别作用不同的是,对包含C:T错配碱基对的B-DNA序列的识别作用倾向于从小沟进行．这一点可能源于C:T碱基对结构的不同．     

寡聚酰胺为探针的电化学DNA生物传感器

DNA分子中的碱基对可以长程传递电荷, DNA分子中的碱基π堆积结构为电荷的长程传递提供了良好的通道. 电荷在DNA分子中的传递受碱基序列的影响, 利用这种性质可以构建DNA碱基错配检测的电化学传感器. 寡聚酰胺能和DNA以小沟绑定方式高亲和力地结合, 并且具有序列识别功能, 本文以带有硝基官能团的寡聚酰胺分子为电化学探针, 设计了电化学DNA生物传感器. 结果显示, 寡聚酰胺与DNA修饰电极作用后, 电化学响应显著增强, 并且可以作为检测DNA碱基错配的电化学探针分子.