溴化乙锭对B-DNA碱基对特异性识别的分子模拟研究

溴化乙锭是一种常用的DNA荧光探针, 其作用机制是通过插入作用与DNA分子形成稳定的复合物. 分子模拟显示, 溴化乙锭插入碱基对过程中有大小沟选择性, 对结合能的统计分析发现, 溴化乙锭分子更倾向从小沟方向插入到DNA分子中. 由溴化乙锭从小沟方向插入不同碱基对的结合能考察发现, 溴化乙锭对DNA碱基对有特异性识别, 并且与CA碱基对结合能最强. 对溴化乙锭插入DNA分子的驱动力和序列特异性识别的作用力分析, 揭示溴化乙锭插入DNA分子的驱动力和碱基对的特异性识别均以静电作用为主.     

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.     

Natural product DNA major groove binders

Covering: 1980 to 2011. Major groove recognition of DNA by proteins utilizes the variation in hydrogen bond donor/acceptor content that makes DNA base-pairs distinguishable from one another. Specific ligand-DNA interactions in the major groove are necessary to develop approaches for inhibition of DNA-protein interactions. As opposed to minor groove binders, little research has been achieved in recognition of the DNA major groove. This review summarizes the progress in identification of natural products that bind to the major groove of DNA. We first review the natural products, pluramycins, aflatoxins, azinomycins, leinamycin, neocarzinostatin, and ditercalinium, that are known to possess major groove interacting elements. These compounds, however, interact primarily with DNA by intercalation between base-pair steps. Some of these compounds utilize non-covalent interactions in order to position themselves to alkylate DNA at the nucleophilic N7 positions on nearby purine bases. Finally, recent reports of non-covalent major groove binding with carbohydrates, aminoglycosides in particular, have revealed them as promising leads for DNA major groove binding probes or drugs.     

On the molecular mechanism of drug intercalation into DNA: a simulation study of the intercalation pathway, free energy, and DNA structural changes

Intercalation into DNA (insertion between a pair of base pairs) is a critical step in the function of many anticancer drugs. Despite its importance, a detailed mechanistic understanding of this process at the molecular level is lacking. We have constructed, using extensive atomistic computer simulations and umbrella sampling techniques, a free energy landscape for the intercalation of the anticancer drug daunomycin into a twelve base pair B-DNA. A similar free energy landscape has been constructed for a probable intermediate DNA minor groove-bound state. These allow a molecular level understanding of aspects of the thermodynamics, DNA structural changes, and kinetic pathways of the intercalation process. Key DNA structural changes involve opening the future intercalation site base pairs toward the minor groove (positive roll), followed by an increase in the rise, accompanied by hydrogen bonding changes of the minor groove waters. The calculated intercalation free energy change is -12.3 kcal/mol, in reasonable agreement with the experimental estimate -9.4 kcal/mol. The results point to a mechanism in which the drug first binds to the minor groove and then intercalates into the DNA in an activated process, which is found to be in general agreement with experimental kinetic results.     

米托蒽醌与B-DNA相互作用的分子模拟

针对嵌插型抗癌药物米托蒽醌(mitoxantrone,MTX)同B-DNA间作用模式的争议,采用分子模拟方法研究了米托蒽醌分子与B-DNA分子的相互作用.结果表明:米托蒽醌分子插入到B-DNA中有大小沟选择性及碱基对特异性,更倾向从小沟方向插入到DNA分子中;对5'-CG碱基对有特异性识别.通过详细能量项的分析,揭示了米托蒽醌插入DNA分子的驱动力及对碱基的特异性识别作用主要是空间相互作用特别是静电相互作用.在最佳作用位点复合物的构象分析则表明蒽醌环只有一部分插入碱基对中,侧链在小沟中延磷酸基骨架以3'-5'方向伸展,并通过静电作用进一步增强米托蒽醌与B-DNA的结合.     

米托蒽醌与生物大分子DNA结合平衡的研究

米托蒽醌(MX)是一个广谱高效的葸醌类抗癌新药(下式),核酸是该类药物的主要细胞作用靶位,它通过与DNA结合,影响DNA的转译和复制,从而起到抗癌作用。研究这类药物与核酸的作用对于阐明抗癌机理具有重要意义,为此,广泛地开展了这方面的研究。     

DNA-ligand binding mode discrimination by characterizing fluorescence resonance energy transfer through lifetime measurements with picosecond resolution

We describe a method for distinguishing between minor groove binders and base intercalators that is based on measurements of the fluorescence lifetime of a donor (D) in the presence of an acceptor (A). The D-A pair is separated by a short double helix DNA with which the ligands interact. By plotting the D fluorescence lifetime as a function of the ligand-to-base pair concentration ratio we find a clear signature that distinguishes between the two binding mechanisms: minor groove binding induces an asymptotic decrease of the D fluorescence lifetime, while intercalation gives a monotonically increasing lifetime and the appearance of an additional short lifetime. We assayed Quinacrine, Hoechst and 4'-6'diamidine-2-phenyl indole, which in control experiments performed on oligodeoxyribonucleotides (oligos) lacking the A are demonstrated not to interfere with the D fluorescence. The changes in fluorescence lifetimes measured in the case of dual-labeled oligos are thus caused by structural changes in the DNA that modify the D-A distance. The appearance of the short-lived transient in the fluorescence decay of Ds attached to dual-labeled oligos upon binding of an intercalator can be interpreted as denaturation.     

Molecular modeling on the recognition of DNA sequence and conformational repair of sheared DNA by novel chiral metal complex D, L-[Co(phen)_2hpip]~(3 )

Recent studies revealed that DNA, once considered as a very stable macromolecular, is rather unstable. Familiar factors, like heavy metal, microbe, high fre-quency electromagnetic radiation and so on, could easily damage the structure of DNA in different …     

Molecular modeling on the recognition of DNA sequence and conformational repair of sheared DNA by novel chiral metal complex D,L-[Co(phen)2hpip]3+

A study on the recognition of DNA sequence and conformational repair of sheared DNA by Novel Chiral Metal complex D,L-[Co(phen)₂hpip]³⁺ (phen=1,10 phenanthroline, hpip=2-[2-hydroxyphenyl] imidazole [4,5-f][1,10] phenanthroline) is carried out with molecular simulations. The results reveal that two isomers of the complex could both recognize the normal DNA in the minor groove orientation, while recognize the sheared DNA in the major groove orientation and both isomers could convert the conformation of mismatched bases from sheared form to parallel form. Further analysis shows that the steric details of complex’s intercalation to base stack determine the results of recognition, which is induced by the steric collision among ancillary ligand phen, bases and DNA backbone, and by the steric crowding occurring in the process of structural expansion of bases and DNA backbone. Detailed analysis reveals that the conformational repair of mismatched bases relates not only to the steric interactions, but also the π-π stack among normal bases, mismatched bases and hpip ligand.     

A comparative DFT study of some N-based aromatic ligand metal complexes as anticancer agents and analysis of their mode of interaction with DNA base pair

Metal complexed anticancer agents interact with DNA nucleobase pairs (AT and GC) through different types of binding mode such as intercalation, groove binding, covalent binding, etc. Minor and major groove binding mechanism of DNA base pair is the key factor for all kinds of anticancer agent; as metal complexes have a great affinity to bind with DNA nucleobase either through minor or major groove. Ligands in metal complexes also play a vital role during the interaction with DNA base pairs; these ligands directly interact with DNA through different interacting modes. Generally, anticancer agents with less sterically hindered N-based aromatic and planar ligands are the key component for DNA binding; as the structure of such ligands are quite compatible for following intercalation and groove binding mechanism. Since, the experimental investigation for drug-DNA nucleobase complexes are extremely complicated, therefore; quantum mechanical calculations might be very helpful for computing the actual interactions in drug-DNA complexes. Quantum mechanical approaches such as density functional theory (DFT) might be a very important and useful tool to investigate the actual mode of interaction of metal complexed antitumor agents with DNA nucleobase. Herein, we have taken some metal complexes with N-based aromatic ligands as antitumor agents to investigate the proper mode of interaction between drug-DNA complexes.     

Molecular modeling on the recognition of DNA sequence and conformational repair of sheared DNA by novel chiral metal complex D,L-[Co(phen)2hpip]3+

A study on the recognition of DNA sequence and conformational repair of sheared DNA by Novel Chiral Metal complex D,L-[Co(phen)₂hpip]³⁺ (phen=1,10 phenanthroline, hpip=2-[2-hydroxyphenyl] imidazole [4,5-f][1,10] phenanthroline) is carried out with molecular simulations. The results reveal that two isomers of the complex could both recognize the normal DNA in the minor groove orientation, while recognize the sheared DNA in the major groove orientation and both isomers could convert the conformation of mismatched bases from sheared form to parallel form. Further analysis shows that the steric details of complex’s intercalation to base stack determine the results of recognition, which is induced by the steric collision among ancillary ligand phen, bases and DNA backbone, and by the steric crowding occurring in the process of structural expansion of bases and DNA backbone. Detailed analysis reveals that the conformational repair of mismatched bases relates not only to the steric interactions, but also the π-π stack among normal bases, mismatched bases and hpip ligand.     

From IHF protein to design and synthesis of a sequence-specific DNA bending peptide

The design and synthesis of a small peptide that mimics the integration host factor (IHF), a major nucleoid-associated protein, is reported. IHF induces DNA compaction by sequence-specific binding that leads to significant bending of the DNA double strand. In a modular approach a small L-lysine dendrimer responsible for nonspecific charge-charge interactions was linked to a cyclopeptide. The latter was designed for specific DNA recognition in the minor groove followed by bending of the double strand.     

Major versus minor groove DNA binding of a bisarginylporphyrin hybrid molecule: A molecular mechanics investigation

On the basis of theoretical computations, we have recently synthesised [Perrée-Fauvet, M. and Gresh, N., Tetrahedron Lett., 36 (1995) 4227] a bisarginyl conjugate of a tricationic porphyrin (BAP), designed to target, in the major groove of DNA, the d(GGC GCC)2 sequence which is part of the primary binding site of the HIV-1 retrovirus site [Wain-Hobson, S. et al., Cell, 40 (1985) 9]. In the theoretical model, the chromophore intercalates at the central d(CpG)2 step and each of the arginyl arms targets O6/N7belonging to guanine bases flanking the intercalation site. Recent IR and UV-visible spectroscopic studies have confirmed the essential features of these theoretical predictions [Mohammadi, S. et al., Biochemistry, 37 (1998) 6165]. In the present study, we compare the energies of competing intercalation modes of BAP to several double-stranded oligonucleotides, according to whether one, two or three N- methylpyridinium rings project into the major groove. Correspondingly, three minor groove binding modes were considered, the arginyl arms now targeting N3, O2 sites belonging to the purine or pyrimidine bases flanking the intercalation site. This investigation has shown that: (i) in both the major and minor grooves, the best-bound complexes have the three N-methylpyridinium rings in the groove opposite to that of the phenyl group bearing the arginyl arms; (ii) major groove binding is preferred over minor groove binding by a significant energy (29 kcal/mol); and (iii) the best-bound sequence in the major groove is d(GGC GCC)2 with two successive guanines upstream from the intercalation. On the other hand, due to the flexibility of the arginyl arms, other GC-rich sequences have close binding energies, two of them being less stable than it by less than 8 kcal/mol. These results serve as the basis for the design of derivatives of BAP with enhanced sequence selectivities in the major groove.     

DNA double helices recognize mutual sequence homology in a protein free environment

The structure and biological function of the DNA double helix are based on interactions recognizing sequence complementarity between two single strands of DNA. A single DNA strand can also recognize the double helix sequence by binding in its groove and forming a triplex. We now find that sequence recognition occurs between intact DNA duplexes without any single-stranded elements as well. We have imaged a mixture of two fluorescently tagged, double helical DNA molecules that have identical nucleotide composition and length (50% GC; 294 base pairs) but different sequences. In electrolytic solution at minor osmotic stress, these DNAs form discrete liquid-crystalline aggregates (spherulites). We have observed spontaneous segregation of the two kinds of DNA within each spherulite, which reveals that nucleotide sequence recognition occurs between double helices separated by water in the absence of proteins, consistent with our earlier theoretical hypothesis. We thus report experimental evidence and discuss possible mechanisms for the recognition of homologous DNAs from a distance.     

The Effect of Chemical Structure on the DNA Binding Behavior of Tricyclic Heteroaromatic Ligands

It is well-known that small organic ligands can bind to the double-stranded nucleic acids by three modes, i.e.s grooving binding, intercalation, and electrostatic binding. Usually, intercalation of the ligands into the double helix involves the insertion of a planar atomatic cation into base stack of the helix, while groove binding of small molecules is pertaining to the docking of thin ribbon-like molecules in the minor groove of the helix. In both cases, electrostatic and hydrophobic interactions can afford additional stabilization for the binding.     

Polypyridyl-Based Copper Phenanthrene Complexes: Combining Stability with Enhanced DNA Recognition

We report a series of copper(II) artificial metallo-nucleases (AMNs) and demonstrate their DNA damaging properties and in-vitro cytotoxicity against human-derived pancreatic cancer cells. The compounds combine a tris-chelating polypyridyl ligand, di-(2-pycolyl)amine (DPA), and a DNA intercalating phenanthrene unit. Their general formula is Cu-DPA-N,N' (where N,N'=1,10-phenanthroline (Phen), dipyridoquinoxaline (DPQ) or dipyridophenazine (DPPZ)). Characterisation was achieved by X-ray crystallography and continuous-wave EPR (cw-EPR), hyperfine sublevel correlation (HYSCORE) and Davies electron-nuclear double resonance (ENDOR) spectroscopies. The presence of the DPA ligand enhances solution stability and facilitates enhanced DNA recognition with apparent binding constants (K_app) rising from 10⁵ to 10⁷ m ⁻¹ with increasing extent of planar phenanthrene. Cu-DPA-DPPZ, the complex with greatest DNA binding and intercalation effects, recognises the minor groove of guanine–cytosine (G-C) rich sequences. Oxidative DNA damage also occurs in the minor groove and can be inhibited by superoxide and hydroxyl radical trapping agents. The complexes, particularly Cu-DPA-DPPZ, display promising anticancer activity against human pancreatic tumour cells with in-vitro results surpassing the clinical platinum(II) drug oxaliplatin.     

Noncovalent DNA binding drives DNA alkylation by leinamycin: evidence that the Z,E-5-(thiazol-4-yl)-penta-2,4-dienone moiety of the natural product serves as an atypical DNA intercalator

Molecular recognition and chemical modification of DNA are important in medicinal chemistry, toxicology, and biotechnology. Historically, natural products have revealed many interesting and unexpected mechanisms for noncovalent DNA binding and covalent DNA modification. The studies reported here characterize the molecular mechanisms underlying the efficient alkylation of duplex DNA by the Streptomyces-derived natural product leinamycin. Previous studies suggested that alkylation of duplex DNA by activated leinamycin (2) is driven by noncovalent association of the natural product with the double helix. This is striking because leinamycin does not contain a classical noncovalent DNA-binding motif, such as an intercalating unit, a groove binder, or a polycation. The experiments described here provide evidence that leinamycin is an atypical DNA-intercalating agent. A competition binding assay involving daunomycin-mediated inhibition of DNA alkylation by leinamycin provided evidence that activated leinamycin binds to duplex DNA with an apparent binding constant of approximately 4.3 ± 0.4 × 10(3) M(-1). Activated leinamycin caused duplex unwinding and hydrodynamic changes in DNA-containing solutions that are indicative of DNA intercalation. Characterization of the reaction of activated leinamycin with palindromic duplexes containing 5'-CG and 5'-GC target sites, bulge-containing duplexes, and 5-methylcytosine-containing duplexes provided evidence regarding the orientation of leinamycin with respect to target guanine residues. The data allow construction of a model for the leinamycin-DNA complex suggesting how a modest DNA-binding constant combines with proper positioning of the natural product to drive efficient alkylation of guanine residues in the major groove of duplex DNA.     

Initial DNA Interactions of the Binuclear Threading Intercalator Λ,Λ‐[μ‐bidppz(bipy)4Ru2]4+: An NMR Study with [d(CGCGAATTCGCG)]2

Binuclear polypyridine ruthenium compounds have been shown to slowly intercalate into DNA, following a fast initial binding on the DNA surface. For these compounds, intercalation requires threading of a bulky substituent, containing one Ru^II, through the DNA base‐pair stack, and the accompanying DNA duplex distortions are much more severe than with intercalation of mononuclear compounds. Structural understanding of the process of intercalation may greatly gain from a characterisation of the initial interactions between binuclear Ru^II compounds and DNA. We report a structural NMR study on the binuclear Ru^II intercalator Λ,Λ‐B (Λ,Λ‐[μ‐bidppz(bipy)₄Ru₂]⁴⁺; bidppz=11,11′‐bis(dipyrido[3,2‐a:2′,3′‐c]phenazinyl, bipy = 2,2′‐bipyridine) mixed with the palindromic DNA [d(CGCGAATTCGCG)]₂. Threading of Λ,Λ‐B depends on the presence and length of AT stretches in the DNA. Therefore, the latter was selected to promote initial binding, but due to the short stretch of AT base pairs, final intercalation is prevented. Structural calculations provide a model for the interaction: Λ,Λ‐B is trapped in a well‐defined surface‐bound state consisting of an eccentric minor‐groove binding. Most of the interaction enthalpy originates from electrostatic and van der Waals contacts, whereas intermolecular hydrogen bonds may help to define a unique position of Λ,Λ‐B. Molecular dynamics simulations show that this minor‐groove binding mode is stable on a nanosecond scale. To the best of our knowledge, this is the first structural study by NMR spectroscopy on a binuclear Ru compound bound to DNA. In the calculated structure, one of the positively charged Ru²⁺ moieties is near the central AATT region; this is favourable in view of potential intercalation as observed by optical methods for DNA with longer AT stretches. Circular dichroism (CD) spectroscopy suggests that a similar binding geometry is formed in mixtures of Λ,Λ‐B with natural calf thymus DNA. The present minor‐groove binding mode is proposed to represent the initial surface interactions of binuclear Ru^II compounds prior to intercalation into AT‐rich DNA.     

Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP

Background: Structural studies by nuclear magnetic resonance (NMR) of RNA and DNA aptamer complexes identified through in vitro selection and amplification have provided a wealth of information on RNA and DNA tertiary structure and molecular recognition in solution. The RNA and DNA aptamers that target ATP (and AMP)' with micromolar affinity exhibit distinct binding site sequences and secondary structures. We report below on the tertiary structure of the AMP-DNA aptamer complex in solution and compare it with the previously reported tertiary structure of the AMP-RNA aptamer complex in solution.Results: The solution structure of the AMP-DNA aptamer complex shows, surprisingly, that two AMP molecules are intercalated at adjacent sites within a rectangular widened minor groove. Complex formation involves adaptive binding where the asymmetric internal bubble of the free DNA aptamer zippers up through formation of a continuous six-base mismatch segment which includes a pair of adjacent three-base platforms. The AMP molecules pair through their Watson-Crick edges with the minor groove edges of guanine residues. These recognition G·A mismatches are flanked by sheared G·A and reversed Hoogsteen G·G mismatch pairs.Conclusions: The AMP-DNA aptamer and AMP-RNA aptamer complexes have distinct tertiary structures and binding stoichiometries. Nevertheless, both complexes have similar structural features and recognition alignments in their binding pockets. Specifically, AMP targets both DNA and RNA aptamers by intercalating between purine bases and through identical G·A mismatch formation. The recognition G·A mismatch stacks with a reversed Hoogsteen G·G mismatch in one direction and with an adenine base in the other direction in both complexes. It is striking that DNA and RNA aptamers selected independently from libraries of 10¹⁴ molecules in each case utilize identical mismatch alignments for molecular recognition with micromolar affinity within binding-site pockets containing common structural elements.