以2-氨基嘌呤为荧光探针研究双链DNA分子内电荷传递机理

2-氨基嘌呤(2Ap)是腺嘌呤的结构类似物, 经常作为荧光探针分子用以研究DNA分子内电荷传递过程. 设计并合成了一系列2-氨基嘌呤和鸟嘌呤核苷酸重复序列GGG之间不同距离的双链DNA分子, 利用时间分辨荧光光谱手段研究了2Ap的荧光衰减动力学以及给体(…GGG…)与受体(2Ap)间的桥体(I, 次黄嘌呤)长度变化对双链DNA电荷传递过程的影响. 结果表明, DNA分子的荧光探针分子2-氨基嘌呤的荧光动力学呈三指数衰减. 其中几百皮秒的组分来源于2-氨基嘌呤和鸟嘌呤之间的电荷转移反应, 当两者间的距离不大于2.4 nm时, 衰减速率随距离的指数函数而减小, 衰减因子b值为1.3 nm^−1; 当两者间的距离大于2.4 nm时, 荧光衰减速率随距离增加而加快, 说明电荷转移过程还与桥体次黄嘌呤I的多重复序列能量匹配有关.     

给受共聚物链上与链间极化子的光谱特性

给受体共聚物具有重要的光伏效应,载流子在其中的传输机理一直备受关注. 近来聚（吡咯并吡咯二酮-噻吩[3,2-b]并噻吩联二噻吩）[poly（DPP-DTT）]在其场效应晶体管器件中表现出高达10.5 cm²/（V·s）的空穴迁移率,有实验表明链上的极化子传输是主要途径,但也有光谱数据表明链上与链间极化子共存. 单链或链间传输机制是目前大家关注的问题. 本工作从计算化学的角度给出单链与双链极化子的光谱特征,为澄清载流子传输的机制提供依据. 首先采用长程密度泛函理论计算不同结构的寡聚链的吸收光谱,通过与实验比较,找到能合理描述poly（DPP-DTT）单链中空穴/电子极化子及激子的有效模型. 然后,通过格点能修正的方法,计算不同堆积情况下链间的电荷转移积分,阐述poly（DPP-DTT）链间不同堆积方式对极化子离域性的影响. 转移积分大的空穴/电子双链极化子的理论吸收光谱与实验吻合. 计算结果表明,在poly（DPP-DTT）中同时存在一维极化子和不同堆积结构的二维极化子,同时也说明载流子的一维和二维传输是同时进行的,而不同堆积结构会影响载流子链间的传输特性.     

用生物质谱方法研究抗肿瘤双β-咔啉与DNA及核苷酸的非共价结合

利用电喷雾傅里叶变换离子回旋共振质谱研究一系列双β-咔啉化合物与DNA的非共价结合. 发现化合物1—5与5种不同序列的12-mer双链DNA均有明显的非共价结合, 并且有两个β-咔啉环之间连接碳链的长度对此类化合物与双链DNA的非共价结合活性有明显影响. 同时对此类化合物对于DNA非共价结合的序列选择性进行了讨论. 另外还利用电喷雾离子阱质谱研究了双β-咔啉化合物2和4与4种单核苷酸的非共价结合.     

基于CRISPR-Cas12a与G-四链体构建免标记电化学生物传感器检测microRNA

CRISPR-Cas12a是一种功能强大且可编程的分子诊断技术。本文基于CRISPR-Cas12a的附属切割活性与G-四链体/氯化血红素（Hemin）复合物,设计了一个免标记电化学生物传感器,实现对miRNA的强特异性检测。靶标miRNA-21与双链DNA探针上的Toehold区域结合并发生链置换反应,置换出双链DNA探针中较短的DNA。置换下来的DNA可以有效地激活CRISPR-Cas12a的附属切割活性。随后,具有附属切割活性的Cas12a切割电极表面上形成G-四链体/Hemin的DNA序列,导致电流信号减弱。在最优条件下,电流信号强度变化与10～100 pmol/L范围内的miRNA-21浓度呈良好的线性关系,检出限为4.2 pmol/L。该电化学生物传感器能够实现对单个碱基突变的miRNA-21或其它miRNA序列特异性识别,并可用于人血清样本（10%）中miRNA-21的检测。     

有机半导体Terazulene单晶双极电荷传输性质的理论研究

利用密度泛函方法计算Terazulene单晶的重组能和分子间电子耦合,结合Marcus电荷转移速率理论以及随机行走技术模拟电荷迁移率,分别研究Terazulene单晶中电子与空穴的角分辨各向异性迁移率及平均迁移率.结果表明,Terazulene单晶具有均衡的电子与空穴传输性质,并分析了具体原因.由于p型有机半导体Naphthodithiophene(NDT)的分子共轭长度与Terazulene接近,通过比较Terazulene单晶和NDT单晶中电荷传输的差异,从理论上理解分子结构对有机半导体材料电荷传输性能的影响.     

鸟苷的电子结构及其在碱基旋转过程中的变化

本文中我们计算了与 Z—DNA 和 B—DNA 相应的鸟苷的硷基原子净电荷,并研究了净电荷在硷基旋转过程中的变化,发现随着 DNA 种类不同或随着硷基的旋转,原子净电荷也发生不同程度的变化,其中以 N_7的净电荷变化最大.这可能影响重要的生物功能.     

利用对G-四链体环部的构型调节进行传感器的设计

对鸟嘌呤碱基G重复序列之间连接环结构对G-四链体形成的影响进行了研究。发现在连接环较长,DNA链不易形成G-四链体的情况下,可以通过将环序列设计成双链结构的方式促进G-四链体的重新形成。这就为传感器的设计提供了一个新途径,即可以利用目标分子对环部双链的调节作用控制G-四链体DNA酶的活性。为证明这一点,在双链区域引入T-T碱基错配,破坏双链结构使DNA链不能形成G-四链体。Hg2+对T-T错配的稳定作用可以促进双链结构的形成,DNA链重新折叠成G-四链体,得到的G-四链体与氯化血红素(Hemin)结合后形成具有过氧化物酶活性的G-四链体DNA酶,据此构建了Hg2+传感器。利用此传感器可在10~700 nmol/L范围内实现Hg2+的定量检测,检出限为8.7 nmol/L。在此基础上,利用半胱氨酸可以将Hg2+从T-Hg2+-T碱基对上竞争下来的能力,设计了一种半胱氨酸的检测方法。此方法可以在20~600 nmol/L范围内实现半胱氨酸的定量检测,检出限为14 nmol/L。     

腺嘌呤的氨基修饰增强DNA导电性的理论研究

利用密度泛函理论并结合非平衡态格林函数方法, 研究了腺嘌呤A的碳2位氨基修饰对DNA导电性的影响. 结果表明, 形成的双氨基嘌呤D可以与胸腺嘧啶T通过3个氢键进行配对, 由于氨基修饰形成了新的氢键, 使配对碱基D和T之间的结合比AT更紧密. 修饰后体系的能隙和电离能大大降低, 紫外吸收光谱在一定程度上会发生红移, 并增加了一些电荷转移跃迁. 计算的沿氢键方向的横向电荷输运和沿DNA链方向的纵向电荷输运性质, 证明了氨基的取代修饰可以很好地提高DNA的电荷输运性质. 揭示了DNA导电性增强是由于修饰调整了碱基对DT的最高占据轨道(HOMO)能级, 使之较天然碱基对AT更靠近GC的HOMO, 从而降低了空穴在DNA中迁移的势垒.     

类黄酮化合物对G-四链体及双链DNA选择性的电喷雾质谱研究

利用电喷雾质谱(ESI-MS)研究了4种常见的类黄酮化合物芦丁、 槲皮素、 葛根素和柚皮苷与2种不同形态结构的G-四链体DNA和3种双链DNA的非共价相互作用, 比较了这些小分子化合物与不同形态结构DNA结合的强弱及形成复合物的化学计量. 结果表明, 芦丁和槲皮素对G-四链体DNA具有一定的选择性, 同时它们对双链DNA的选择性也较高; 而葛根素和柚皮苷对G-四链体DNA仅显示了较低的选择性.     

水溶液中氨基酸侧链对G∶C碱基对间氢键影响的理论研究

利用量子化学方法研究了气相和水溶液下,氨基酸侧链与鸟嘌呤和胞嘧啶间的氢键作用.应用B3LYP/6-31+G(d,p)方法优化复合物几何结构,使用MP2/aug-cc-p VDZ方法进行复合物能量、自然键轨道(NBO)电荷和二阶稳定化能的计算.结果表明,水溶液可使氨基酸侧链与碱基或碱基对之间氢键键能显著减小;带电复合物气相和水溶液氢键键能之差范围为50.63~146.48 k J/mol,中性为0.17~24.94 k J/mol;电荷的转移量与氢键键能成正比,电荷转移量越多,复合物越稳定;二阶稳定化能与氢键键长成反比,与电荷转移量成正比,且气相与水溶液氢键二阶稳定化能之比约为两相的电荷转移量之比.水溶液对该类体系中氢键作用具有明显影响.     

Charge Transfer through the DNA Base Stack

Whether the DNA base pair stack might serve as a medium for efficient, long-range charge transfer has been debated almost since the first proposal of the double-helical structure of DNA. The consequences of long-range radical migration through DNA are important with respect to understanding carcinogenesis and mutagenesis. Double-helical DNA has in its core a stacked array of aromatic heterocyclic base pairs, and this molecular π stack represents a unique system in which to explore the chemistry of electron transfer. We designed a family of metal complexes which bind to DNA by intercalative stacking within the helix; these metallointercalators may be usefully applied in probing DNA-mediated electron transfer. Here we describe a range of electron transfer reactions we carried out which are mediated by the DNA base paired stack. In some cases, DNA serves as a bridge, and spectroscopic analyses permit us to probe how the π stack couples DNA-bound donors and acceptors. These studies point to the sensitivity of coupling to DNA intercalation. However, if the DNA π stack effectively bridges donors and acceptors, the base-pair stack itself might serve not only as a conduit for electron transfer in DNA, but also in reactions initiated from a remote position. We carried out a series of reactions involving oxidative damage to DNA arising from the remotely positioned oxidant on the helix. The implications of long-range charge migration through DNA to effect damage are substantial. As in other DNA-mediated charge transfers, these reactions are highly dependent on DNA intercalation and the integrity of the intervening base-pair stack, but not on molecular distance. Furthermore, a physiologically important DNA lesion, the thymine dimers, can be reversed in a reaction initiated by electron transfer. This repair reaction can also be promoted from a distance as a result of long-range charge migration through the DNA base pair stack.     

Recent developments of charge injection and charge transfer in DNA

The question of whether and how electrons migrate through DNA was a matter of controversial discussion over the last ten years. Today, there is no doubt that long distance charge migration through DNA exists and most scientists explain this process by a multistep hopping mechanism. This feature article presents recent developments of our group on the injection of a positive charge into DNA bases and the transfer of the charge between the DNA bases. The influence of the donor, the nature of the bridge, and the distance between the donor and the acceptor are discussed.     

Mechanism of intram olecular charge transfer in DNA helix as probed by the use of the fluorescent 2-aminopurine

~~Mechanism of intram olecular charge transfer in DNA helix as probed by the use of the fluorescent 2-aminopurine~~     

Energy and electron transfer in beta-alkynyl-linked porphyrin-[60]fullerene dyads

Three porphyrin-fullerene dyads, in which a diyne bridge links C(60) with a beta-position on a tetraarylporphyrin, have been synthesized. The free-base dyad was prepared, as well as the corresponding Zn(II) and Ni(II) materials. These represent the first examples of a new class of conjugatively linked electron donor-acceptor systems in which pi-conjugation extends from the porphyrin ring system directly to the fullerene surface. The processes that occur following photoexcitation of these dyads were examined using fluorescence and transient absorption techniques on the femtosecond, picosecond, and nanosecond time scales. In sharp contrast to the photodynamics associated with singlet excited-state decay of reference tetraphenylporphyrins (ZnTPP, NiTPP, and H(2)TPP), the diyne-linked dyads undergo ultrafast (<10 ps) singlet excited-state deactivation in toluene, tetrahydrofuran (THF), and benzonitrile (PhCN). Transient absorption techniques with the ZnP-C(60) dyad clearly show that in toluene intramolecular energy transfer (EnT) to ultimately generate C(60) triplet excited states is the dominant singlet decay mechanism, while intramolecular electron transfer (ET) dominates in THF and PhCN to give the ZnP(*+)/C(60)(*-) charge-separated radical ion pair (CSRP). Electrochemical studies indicate that there is no significant charge transfer in the ground states of these systems. The lifetime of ZnP(*+)/C(60)(*-) in PhCN was approximately 40 ps, determined by two different types of transient absorption measurement in two different laboratories. Thus, in this system, the ratio of the rates for charge separation (k(CS)) to rates for charge recombination (k(CR)), k(CS)/k(CR), is quite small, approximately 7. The fact that charge separation (CS) rates increase with increasing solvent polarity is consistent with this process occurring in the normal region of the Marcus curve, while the slower charge recombination (CR) rates in less polar solvents indicate that the CR process occurs in the Marcus inverted region. While photoinduced ET occurs on a similar time scale in a related dyad 15 in which a diethynyl bridge connects C(60) to the para position of a meso phenyl moiety of a tetrarylporphyrin, CR occurs much more slowly; i.e., k(CS)/k(CR) approximately equal to 7400. Thus, the position at which the conjugative linker is attached to the porphyrin moiety has a dramatic influence on k(CR) but not on k(CS). On the basis of electron density calculations, we tentatively conclude that unfavorable orbital symmetries inhibit charge recombination in 15 vis a vis the beta-linked dyads.     

Temperature dependence of charge separation and recombination in porphyrin oligomer-fullerene donor-acceptor systems

Electron-transfer reactions are fundamental to many practical devices, but because of their complexity, it is often very difficult to interpret measurements done on the complete device. Therefore, studies of model systems are crucial. Here the rates of charge separation and recombination in donor-acceptor systems consisting of a series of butadiyne-linked porphyrin oligomers (n = 1-4, 6) appended to C(60) were investigated. At room temperature, excitation of the porphyrin oligomer led to fast (5-25 ps) electron transfer to C(60) followed by slower (200-650 ps) recombination. The temperature dependence of the charge-separation reaction revealed a complex process for the longer oligomers, in which a combination of (i) direct charge separation and (ii) migration of excitation energy along the oligomer followed by charge separation explained the observed fluorescence decay kinetics. The energy migration is controlled by the temperature-dependent conformational dynamics of the longer oligomers and thereby limits the quantum yield for charge separation. Charge recombination was also studied as a function of temperature through measurements of femtosecond transient absorption. The temperature dependence of the electron-transfer reactions could be successfully modeled using the Marcus equation through optimization of the electronic coupling (V) and the reorganization energy (λ). For the charge-separation rate, all of the donor-acceptor systems could be successfully described by a common electronic coupling, supporting a model in which energy migration is followed by charge separation. In this respect, the C(60)-appended porphyrin oligomers are suitable model systems for practical charge-separation devices such as bulk-heterojunction solar cells, where conformational disorder strongly influences the electron-transfer reactions and performance of the device.     

Coherent effects in energy transport in model dendritic structures investigated by ultrafast fluorescence anisotropy spectroscopy

Measurements of ultrafast fluorescence anisotropy decay in model branched dendritic molecules of different symmetry are reported. These molecules contain the fundamental branching center units of larger dendrimer macromolecules with either three (C(3))- or four (T(d), tetrahedral)-fold symmetry. The anisotropy for a tetrahedral system is found to decay on a subpicosecond time scale (880 fs). This decay can be qualitatively explained by F?rster-type incoherent energy migration between chromophores. Alternatively, for a nitrogen-centered trimer system, the fluorescence anisotropy decay time (35 fs) is found to be much shorter than that of the tetramers, and the decay cannot be attributed to an incoherent hopping mechanism. In this case, a coherent interchromophore energy transport mechanism should be considered. The mechanism of the ultrafast energy migration process in the branched systems is interpreted by use of a phenomenological quantum mechanical model, which examines the two extreme cases of incoherent and coherent interactions.     

双链DNA分子内电荷转移超交换机理

设计并合成了一系列寡聚核苷酸组成的双链DNA分子,通过检测样品中二氨基嘌呤(Ap)荧光峰强度和相对荧光量子产率来研究DNA分子内电荷转移.实验中直接分辨和观测到双链DNA分子内电荷转移超交换机理,超交换机理在近距离起作用；而电荷转移跳跃机理,可能是通过极子运动形式体现.     

DNA mediated charge transport: characterization of a DNA radical localized at an artificial nucleic acid base

DNA assemblies containing 4-methylindole incorporated as an artificial base provide a chemically well-defined system in which to explore the oxidative charge transport process in DNA. Using this artificial base, we have combined transient absorption and EPR spectroscopies as well as biochemical methods to test experimentally current mechanisms for DNA charge transport. The 4-methylindole radical cation intermediate has been identified using both EPR and transient absorption spectroscopies in oxidative flash-quench studies using a dipyridophenazine complex of ruthenium as the intercalating oxidant. The 4-methylindole radical cation intermediate is particularly amenable to study given its strong absorptivity at 600 nm and EPR signal measured at 77 K with g = 2.0065. Both transient absorption and EPR spectroscopies show that the 4-methylindole is well incorporated in the duplex; the data also indicate no evidence of guanine radicals, given the low oxidation potential of 4-methylindole relative to the nucleic acid bases. Biochemical studies further support the irreversible oxidation of the indole moiety and allow the determination of yields of irreversible product formation. The construction of these assemblies containing 4-methylindole as an artificial base is also applied in examining long-range charge transport mediated by the DNA base pair stack as a function of intervening distance and sequence. The rate of formation of the indole radical cation is >/=10(7) s(-)(1) for different assemblies with the ruthenium positioned 17-37 A away from the methylindole and with intervening A-T base pairs primarily composing the bridge. In these assemblies, methylindole radical formation at a distance is essentially coincident with quenching of the ruthenium excited state to form the Ru(III) oxidant; charge transport is not rate limiting over this distance regime. The measurements here of rates of radical cation formation establish that a model of G-hopping and AT-tunneling is not sufficient to account for DNA charge transport. Instead, these data are viewed mechanistically as charge transport through the DNA duplex primarily through hopping among well stacked domains of the helix defined by DNA sequence and dynamics.     

PNA versus DNA: effects of structural fluctuations on electronic structure and hole-transport mechanisms

The effects of structural fluctuations on charge transfer in double-stranded DNA and peptide nucleic acid (PNA) are investigated. A palindromic sequence with two guanine bases that play the roles of hole donor and acceptor, separated by a bridge of two adenine bases, was analyzed using combined molecular dynamics (MD) and quantum-chemical methods. Surprisingly, electronic structure calculations on individual MD snapshots show significant frontier orbital electronic population on the bridge in approximately 10% of the structures. Electron-density delocalization to the bridge is found to be gated by fluctuations of the covalent conjugated bond structure of the aromatic rings of the nucleic bases. It is concluded, therefore, that both thermal hopping and superexchange should contribute significantly to charge transfer even in short DNA/PNA fragments. PNA is found to be more flexible than DNA, and this flexibility is predicted to produce larger rates of charge transfer.