分子模拟及光谱法研究2-乙基-3-(3-硝基苯基)喹唑啉-4-酮与小牛胸腺DNA的相互作用

合成了2-乙基-3-(3-硝基苯基)喹唑啉-4-酮(ENPQO),用紫外光谱法、荧光光谱法、荧光偏振法、离子强度法及分子模拟法研究了ENPQO与小牛胸腺DNA(ct DNA)的相互作用。紫外光谱法显示ct DNA与ENPQO作用后,引起ENPQO紫外吸收光谱的增色效应;在以吖啶橙(AO)为荧光探针的实验中,随着ENPQO浓度的增加,ct DNA-AO体系的荧光被猝灭,其猝灭过程主要是静态猝灭,ENPQO对ct DNA-AO体系的荧光偏振基本无影响;不同浓度的Na Cl溶液未削弱ENPQO对ct DNA-AO的猝灭程度。以上结果均表明ENPQO与ct DNA之间的作用方式主要为沟槽结合。利用分子模拟对接技术预测了ENPQO与ct DNA的结合最优构象,与光谱实验结果一致。     

9-(3-氨基苯胺基)吖啶与核酸作用的荧光光谱及其分析应用

报道了荧光试剂9-（3-氨基苯胺基）吖啶（简称：m-APAA）的合成,产品经多次重结晶提纯,用IR、^1HNMR和元素分析确证了结构。研究了该物质与DNA作用的荧光光谱,随着DNA的加入观察到418nm（λex=256nm）处的荧光峰猝灭,且其猝灭程度与DNA的浓度成正比,据此拟定了测定DNA的分析方法。实验了最佳条件,干扰实验,确定了反应机理。该方法简便、快速、灵敏度高。     

基于双重猝灭原理的分子信标定量检测凝血酶

利用G碱基和有机猝灭基团对荧光基团的双重猝灭作用构建了分子信标,建立了一种基于双重猝灭原理的检测凝血酶的简单方法.此分子信标中荧光基团设计为羧基荧光素(FAM),有机猝灭基团设计为Black Hole Quencher 1(BHQ-1),BHQ-1连接3个含有G碱基的核苷酸,分子信标的环设计为凝血酶的核酸适配体.体系中没有凝血酶时,分子信标呈茎环结构,荧光基团FAM与有机猝灭基团BHQ-1及G碱基相互靠近,FAM的荧光在BHQ-1及G碱基的双重猝灭下,其荧光信号很弱;当体系中有凝血酶存在时,分子信标与凝血酶特异性结合,形成G-四联体结构,茎-环结构被破坏,FAM远离猝灭基团BHQ-1及G碱基,其荧光得到恢复.在最适条件下,体系的荧光强度(△I)与凝血酶的浓度(C)在0.4~40 nmol/L范围内具有良好的线性关系,线性回归方程为△I=24.63C(nmol/L)+13.06(R2=0.9972),检出限为0.18 nmol/L(3σ,n=9).实际血样加标回收率为96.3%~98.7%.     

老鼠Tet1蛋白能氧化单链脱氧核糖核酸上的5-甲基胞嘧啶到5-羟甲基胞嘧啶和5-羧基胞嘧啶(英文)

5-甲基胞嘧啶在哺乳动物细胞中具有广泛的作用.而它被双脱氧家族Tet蛋白氧化所得的产物5-羟甲基胞嘧啶、5-醛基胞嘧啶和5-羧基胞嘧啶也被证明在细胞发育和5-甲基胞嘧啶动态平衡调控中具有关键的作用.已有的研究结果表明,Tet蛋白能够识别双链DNA上的5-甲基胞嘧啶,并将其氧化成5-羟甲基胞嘧啶、5-醛基胞嘧啶和5-羧基胞嘧啶.我们通过质谱仪检测发现,老鼠Tet1蛋白的DNA结合结构域还能识别和氧化单链DNA上的5-甲基胞嘧啶.这一发现暗示我们,Tet蛋白家族不但具有已经发现的氧化双链DNA上5-甲基胞嘧啶的功能,还有可能作用于DNA的复制及转录,甚至具有氧化单链RNA上对应的甲基修饰碱基的能力.     

1O-苯基-3-磺酸基-吖啶酮测定DNA的荧光分析新体系研究

10-苯基-3-磺酸基-吖啶酮（PSACR）在pH6．0的六次甲基四胺-HCl缓冲介质中。在372nm的紫外光激发下,于435nm处有很强的荧光发射。DNA的加入,可以使体系荧光在峰位基本不变的情况下,发生猝灭。其猝灭比值与小牛胸腺DNA的质量浓度在0．1—3．0mg／L的范围内呈良好的线性关系,检出限可达0．040mg／L。并用光谱法探讨了PSACR与DNA之间的作用机理,推测二者之间通过嵌插作用结合。     

1,4-二甲基-6,8-二甲氧基-9,10-蒽醌的合成及其与牛血清白蛋白和DNA的相互作用

合成了大黄素类蒽醌衍生物1,4-二甲基-6,8-二甲氧基-9,10-蒽醌(1)并应用紫外光谱、荧光光谱、圆二色谱等方法研究了其与牛血清白蛋白(BSA)和小牛胸腺DNA(ct-DNA)的相互作用.荧光光谱结果表明,化合物1与BSA的相互作用主要以静态猝灭方式使BSA的内源性荧光发生猝灭;圆二色谱表明,化合物1通过疏水作用及形成氢键破坏了α-螺旋结构,导致BSA分子中的α-螺旋含量下降.在pH 7.4时固定DNA的浓度,加入化合物1后,紫外光谱的最大吸收峰发生红移且吸光度加大.荧光光谱表明,化合物1与DNA-4S green NC的结合为竞争性抑制,并可使溶液体系荧光猝灭;圆二色谱表明,随着化合物1的加入,DNA碱基间作用能迅速减弱,表明化合物1与DNA之间为嵌插作用.此外,MTT方法的结果表明,化合物1对结肠癌细胞株HCT116增殖有明显的抑制作用.     

二氢杨梅素-锌配合物的合成及其与DNA相互作用研究

合成了二氢杨梅素-锌配合物(DMY-Zn),采用紫外可见光谱、红外光谱、元素分析及热重分析(TG-DTA)法对其结构进行了表征,结果表明二氢杨梅素与Zn2+离子形成了配合物,其组成为[C15H10O8Zn].2H2O。采用EB为荧光探针利用荧光滴定法和粘度法进一步研究了二氢杨梅素-锌配合物与DNA的相互作用,发现二氢杨梅素-锌配合物与DNA有较强的相互作用,能和EB竞争与DNA结合,插入到ctDNA相邻的碱基对中,其作用方式为插入作用,Stern-Volmer线性猝灭常数Ksq为1.01。     

7,8-二氢-8-氧鸟嘌呤碱基对的量子化学研究

遗传信息的完整性不断受氧化基因的威胁,7,8-二氢-8-氧鸟嘌呤（8-oxo-G）是氧化DNA损伤最常见的产物. 氧化碱基会引起基因突变、癌变及衰老等. 应用量子化学方法分析得出：鸟嘌呤（G）被氧化为8-oxo-G后,其电荷分布、氢键的供体和受体位点的数目和位置随之改变,N7和O6原子所带的电荷变得更负,使得它们作为氢键供体的能力增强. 从而G被误认为其他碱基,与正常碱基形成多种氢键复合物. 可将8-oxo-G划分为3个作用位点与正常碱基相互作用. 与正常的单体相比,碱基对中形成氢键的受体原子上所带电荷平均变负0.05e,占原电荷的8%; 供体H原子所带电荷平均变正0.02e,占原电荷的4%. 1位点与正常碱基作用形成的氢键复合物更稳定,2位点和3位点性质相似,水溶剂使碱基对的结合能力减弱,其中与C作用形成氢键复合物的结合能减弱程度最大,且使碱基对结合能力的次序改变. 在8-oxo-G导致的GC→TA突变中,亲核反应位点从G所在链转到A（C）所在链,影响酶对碱基的识别,从而产生基因突变.     

木犀草素-7-O-葡萄糖苷与双链DNA的相互作用研究

采用电喷雾质谱(ESI-MS)、紫外吸收光谱(UV)以及荧光光谱结合溴化乙锭荧光探针研究黄酮类化合物木犀草 素-7-O-葡萄糖苷与双链DNA的相互作用. 质谱研究结果表明木犀草素-7-O-葡萄糖苷可与双链DNA形成复合物, 且Lug与DNA之间存在氢键作用, 通过串联质谱数据推断出其结合模式为插入型. 紫外吸收光谱研究结果表明DNA的加入使木犀草素-7-O-葡萄糖苷产生明显的减色红移效应, 说明该化合物可能插入DNA双螺旋碱基对间. 荧光光谱研究结果表明木犀草素-7-O-葡萄糖苷能引起溴化乙锭-DNA体系荧光强度明显减弱和波长轻微蓝移, 主要是单一的静态猝灭, 猝灭常数K_q=8.61×10¹¹ L·mol^-1·s^-1, 进一步说明Lug与DNA的主要作用方式为插入型.     

10-苯基-吖啶酮测定核酸的荧光分析新体系研究

10-苯基-吖啶酮（PACR）是吖啶类强荧光物质,在pH6．5的Tds-HCl的缓冲介质中,在258nm的紫外光激发下,于420nm处有很强的荧光发射。核酸的加入,可以使得体系荧光在峰位基本不变的情况下,发生荧光猝灭。其荧光猝灭程度与小牛胸腺DNA在0．1～3．0mg／L范围内呈良好的线性关系,检出限可达0．044mg／L。本文还用光谱法探讨了10-苯基-吖啶酮与DNA之间的作用机理,认为二者之间可能存在嵌插作用。     

Label-free fluorescent molecular beacon based on a small fluorescent molecule non-covalently bound to the intentional gap site in the stem moiety

A label-free fluorescent molecular beacon (MB) based on a fluorescent molecule, 5,6,7-trimethyl-1,8-naphthyridin-2-ylamine (ATMND) which is non-covalently bound to the intentional gap site in the stem moiety of the label-free MB, was developed. In the absence of a cDNA, ATMND fluorescence is significantly quenched because it binds to the unpaired cytosine at the gap site by hydrogen bonding. As a result, the label-free MB shows almost no fluorescence. Upon hybridization with cDNA, the label-free MB undergoes a conformational change to destroy the gap site. This results in an effective fluorescent enhancement because of the release of the ATMND from the gap site to the solution. Fluorescence titration shows that ATMND strongly binds to the cytosine at the gap site (K₁₁ > 10⁶). Circular-dichroism spectroscopy indicates that the binding of ATMND at the gap site of the stem moiety does not induce a significant conformational change to the hairpin DNA. Under optimal conditions, the fluorescent intensity of the label-free MB increases with an increase in cDNA concentration from 50 nM to 1.5 μM. A detection limit of 20 nM cDNA was achieved. A single mismatched target ss-DNA can be effectively discriminated from cDNA. The advantage of the label-free MB is that both its ends can be left free to introduce other useful functionalities. In addition, the label-free MB synthesis introduced in this paper is relatively simple and inexpensive because no label is required.     

Affinity labeling of a single guanine bulge

We have developed a conceptually new method for the selective labeling of duplex DNA containing a guanine bulge with a masked form of fluorescent 2-amino-1,8-naphthyridine. A naphthyridine derivative 2 tethering DNA-alkylating epoxide was synthesized from (S)-epichlorohydrin and naphthyridine derivative 1, which selectively binds to the guanine bulge duplex. HPLC analysis of the labeling reaction of bulge duplex d(GTT GTGTTG GA)/d(CAA CA A ACC T) (TGT/A_A) with 2 showed a formation of 2-TGT adduct for the guanine bulge. The reaction proceeded for the guanine bulge and a reduced efficiency for the cytosine bulge, but not at all for adenine and thymine bulges. The site of covalent bond formation in 2-TGT was unambiguously identified at the guanine two bases away from the bulge by the use of MALDI-TOF MS analysis of the oligomer fragments produced by strand scission. The labeling reaction was also observed for the guanine bulge flanking two G-C base pairs (CGC/G_G), producing a 2:1 adduct (2.2-CGC). Upon hydrolysis of 2-TGT and 2.2-CGC with concentrated hydrogen chloride, a release of fluorescent 2-aminonaphthyridine from the adduct was clearly detected, verifying a concept of an affinity labeling of the guanine bulge with a masked fluorescent chromophore. The affinity labeling targeting of the guanine bulge is a conceptually novel method for the postsynthetic labeling of DNA. Hybridization, to the target sequence, of a probe DNA possessing one extra guanine especially between two cytosines provides a unique site for the labeling by masked fluorophore 2. The technique may have broad application in genetic typing without using a conventional synthesis of fluorescent-labeled DNA oligomers.     

Targeting abasic sites and single base bulges in DNA with metalloinsertors

The site-specific recognition of abasic sites and single base bulges in duplex DNA by sterically expansive rhodium metalloinsertors has been investigated. Through DNA photocleavage experiments, Rh(bpy)2(chrysi)3+ is shown to bind both abasic sites and single base bulges site-specifically and, upon irradiation, to cleave the backbone of the defect-containing DNA. Photocleavage titrations reveal that the metal complex binds DNA containing an abasic site with high affinity (2.6(5) x 106 M-1), comparably to the metalloinsertor and a CC mismatch. The complex binds single base bulge sites with lower affinity (approximately 105 M-1). Analysis of cleavage products and the correlation of affinities with helix destabilization suggest that Rh(bpy)2(chrysi)3+ binds both lesions via metalloinsertion, as observed for Rh binding at mismatched sites, a binding mode in which the mismatched or unpaired bases are extruded from the helix and replaced in the base stack by the sterically expansive ligand of the metalloinsertor.     

Fluorescent trimethyl-substituted naphthyridine as a ligand for C-C mismatch detection in CCG trinucleotide repeats

We report on the selective binding of 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND) to C-C mismatch present in the hairpin structures of (CCG)(n) trinucleotide repeats that are associated with neurological diseases; this binding is accompanied by significant fluorescence quenching of ATMND.     

Use of abasic site-containing DNA strands for nucleobase recognition in water

Nucleobase recognition in water is successfully achieved by the use of an abasic site (AP site) as the molecular recognition field. We intentionally construct the AP site in DNA duplex so as to orient the AP site toward a target nucleobase and examine the complexation of 2-amino-7-methylnaphthyridine (AMND) with nucleobases at the AP site. AMND is found to selectively bind to cytosine (C) base with a 1:1 binding constant of >106 M-1, accompanied by remarkable quenching of its fluorescence. In addition to hydrogen bonding, a stacking interaction with nucleobases flanking the AP site seems responsible for the binding properties of AMND at the AP site. Possible use of AMND is also presented for selective and visible detection of a single-base alternation related to the cytosine base.     

Simultaneous fluorescence light-up and selective multicolor nucleobase recognition based on sequence-dependent strong binding of berberine to DNA abasic site

Label-free DNA nucleobase recognition by fluorescent small molecules has received much attention due to its simplicity in mutation identification and drug screening. However, sequence-dependent fluorescence light-up nucleobase recognition and multicolor emission with individual emission energy for individual nucleobases have been seldom realized. Herein, an abasic site (AP site) in a DNA duplex was employed as a binding field for berberine, one of isoquinoline alkaloids. Unlike weak binding of berberine to the fully matched DNAs without the AP site, strong binding of berberine to the AP site occurs and the berberine's fluorescence light-up behaviors are highly dependent on the target nucleobases opposite the AP site in which the targets thymine and cytosine produce dual emission bands, while the targets guanine and adenine only give a single emission band. Furthermore, more intense emissions are observed for the target pyrimidines than purines. The flanking bases of the AP site also produce some modifications of the berberine's emission behavior. The binding selectivity of berberine at the AP site is also confirmed by measurements of fluorescence resonance energy transfer, excited-state lifetime, DNA melting and fluorescence quenching by ferrocyanide and sodium chloride. It is expected that the target pyrimidines cause berberine to be stacked well within DNA base pairs near the AP site, which results in a strong resonance coupling of the electronic transitions to the particular vibration mode to produce the dual emissions. The fluorescent signal-on and emission energy-modulated sensing for nucleobases based on this fluorophore is substantially advantageous over the previously used fluorophores. We expect that this approach will be developed as a practical device for differentiating pyrimidines from purines by positioning an AP site toward a target that is available for readout by this alkaloid probe.     

Bulged Guanine is Uniquely Sensitive to Damage Caused by Visible‐Light Irradiation of Ethidium Bound to DNA: A Possible Role in Mutagenesis

The interaction of ethidium bromide (=3,8‐diamino‐5‐ethyl‐6‐phenylphenanthridinium bromide; EB) with a series of duplex DNA oligomers having single‐base bulges and single‐base mis‐pairs was investigated (Fig. 1). Physical and spectroscopic analysis reveals no definitive evidence for selective binding of EB at the bulge or mis‐pair. However, irradiation of the bound EB with VIS light leads to lesions in the DNA selectively in the sequence having a bulged guanine. This reaction is attributed to the formation of an exciplex between the lowest excited singlet state of the EB and the bulged guanine. The exciplex is trapped by H₂O, which initiates a sequence of reactions that lead to piperidine‐requiring strand cleavage at this site. Significantly, the damaged bulged guanine is not recognized by E. coli formamidopyrimidine glycosylase (Fpg), which is part of a base‐excision repair system for oxidative damage to DNA. Thus, DNA containing a bulged guanine and having a bound intercalator may be irreparably damaged by exposure to VIS light, even though normal duplex DNA is relatively inert under these conditions.     

Heterochiral DNA with Complementary Strands with α-d and β-d Configurations: Hydrogen-Bonded and Silver-Mediated Base Pairs with Impact of 7-Deazapurines Replacing Purines

Heterochiral DNA with hydrogen-bonded and silver-mediated base pairs have been constructed using complementary strands with nucleosides with α-d or β-d configuration. Anomeric phosphoramidites were employed to assemble the oligonucleotides. According to the T_m values and thermodynamic data, the duplex stability of the heterochiral duplexes was similar to that of homochiral DNA, but mismatch discrimination was better in heterochiral DNA. Replacement of purines by 7-deazapurines resulted in stable parallel duplexes, thereby confirming Watson–Crick-type base pairing. When cytosine was facing cytosine, thymine or adenine residues, duplex DNA formed silver-mediated base pairs in the presence of silver ions. Although the CD spectra of single strands with α-d configuration display mirror-like shapes to those with the β-d configuration, the CD spectra of the hydrogen-bonded duplexes and those with a limited number of silver pairs show a B-type double helix almost indistinguishable from natural DNA. Nonmelting silver ion–DNA complexes with entirely different CD spectra were generated when the number of silver ions was equal to the number of base pairs.     

Structural basis for bifunctional zinc(II) macrocyclic complex recognition of thymine bulges in DNA

The zinc(II) complex of 1-(4-quinoylyl)methyl-1,4,7,10-tetraazacyclododecane (cy4q) binds selectively to thymine bulges in DNA and to a uracil bulge in RNA. Binding constants are in the low-micromolar range for thymine bulges in the stems of hairpins, for a thymine bulge in a DNA duplex, and for a uracil bulge in an RNA hairpin. Binding studies of Zn(cy4q) to a series of hairpins containing thymine bulges with different flanking bases showed that the complex had a moderate selectivity for thymine bulges with neighboring purines. The dissociation constants of the most strongly bound Zn(cy4q)-DNA thymine bulge adducts were 100-fold tighter than similar sequences with fully complementary stems or than bulges containing cytosine, guanine, or adenine. In order to probe the role of the pendent group, three additional zinc(II) complexes containing 1,4,7,10-tetraazacyclododecane (cyclen) with aromatic pendent groups were studied for binding to DNA including 1-(2-quinolyl)methyl-1,4,7,10-tetraazacyclododecane (cy2q), 1-(4-biphenyl)methyl-1,4,7,10-tetraazacyclododecane (cybp), and 5-(1,4,7,10-tetraazacyclododecan-1-ylsulfonyl)-N,N-dimethylnaphthalen-1-amine (dsc). The Zn(cybp) complex binds with moderate affinity but little selectivity to DNA hairpins with thymine bulges and to DNA lacking bulges. Similarly, Zn(dsc) binds weakly both to thymine bulges and hairpins with fully complementary stems. The zinc(II) complex of cy2q has the 2-quinolyl moiety bound to the Zn(II) center, as shown by (1)H NMR spectroscopy and pH-potentiometric titrations. As a consequence, only weak (500 μM) binding is observed to DNA with no appreciable selectivity. An NMR structure of a thymine-bulge-containing hairpin shows that the thymine is extrahelical but rotated toward the major groove. NMR data for Zn(cy4q) bound to DNA containing a thymine bulge is consistent with binding of the zinc(II) complex to the thymine N3(-) and stacking of the quinoline on top of the thymine. The thymine-bulge bound zinc(II) complex is pointed into the major groove, and there are interactions with the guanine positioned 5' to the thymine bulge.