Protein-induced DNA bending: the role of phosphate neutralisation

An important component of protein–nucleic acid interactions is the formation of salt bridges between cationic amino acid side chains and the anionic phosphate groups of the nucleic acid. We have used molecular mechanics to study the energetic and conformational impact of such interactions. Firstly, crystallographic protein–nucleic acid complexes from the Protein Data Bank were analysed in terms of DNA curvature and the presence of salt bridges. For complexes where the DNA is significantly bent, the contribution of salt bridges to this curvature was modelled by studying the effect of neutralising the appropriate phosphate groups. The number and the distribution of salt bridges vary widely for different DNA binding motifs and appear to have very different effects on DNA. In the case of homeodomain, bZIP and helix–loop–helix proteins, salt bridges induce DNA bending, whereas for prokaryotic helix–turn–helix proteins the number of salt bridges is much smaller and little bending is found. By analysing the components of the DNA deformation energy involved in protein binding we show that salt bridges consistently increase the flexibility of the DNA backbone. Received: 1 September 2000 / Accepted: 5 January 2001 / Published online: 3 May 2001     

Influence of magnesium ions on spontaneous opening of DNA base pairs

A large amount of experimental evidence is available for the effects of magnesium ions on the structure and the stability of the DNA double helix. Less is known, however, on how these ions affect the dynamics of the molecule and the stability of each individual base pair. The present work addresses these questions by a study of the DNA duplex [dCGCAGATCTGCG]2, and its interactions with magnesium ions using nuclear magnetic resonance (NMR) spectroscopy and proton exchange. Two-dimensional NMR experiments indicate that binding of magnesium to this DNA duplex does not affect its structure. However, even in the absence of structural changes, magnesium ions specifically affect the exchange properties of imino protons in the four GC/CG base pairs that are located in the interior of the double helix. These specific changes do not result from alterations in the rates of spontaneous opening of these base pairs. Instead, the changes most likely reflect an enhancement in the energetic propensity for spontaneous opening of the GC/CG base pairs that is induced by the binding of magnesium ions.     

Insight into the sequence-specific elements leading to increased DNA bending and ligase-mediated circularization propensity by antitumor trabectedin

Journal of Computer-Aided Molecular Design - DNA curvature is the result of a combination of both intrinsic features of the double helix and external distortions introduced by the environment and...     

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.     

Comparison of magnetic properties of DNA-cetyltrimethyl ammonium complex with those of natural DNA

We prepared the DNA-cetyltrimethyl ammonium complex, as well as the same complex intercalated with stable organic free radicals, and studied their magnetic properties by electron magnetic resonance (EMR) spectroscopy and by measuring the magnetization on a superconducting quantum interference device (SQUID). The UV-vis and CD spectra of DNA-quaternary alkyl ammonium complex (DNA--Q+) in organic solvent clearly demonstrated that it retained the double helical B-form conformation. The interhelical spacing of double strand DNA (dsDNA) increased when the counter ions (Na+) of phosphate groups of the natural DNA were replaced with the long alkyl quaternary ammonium groups. The inter-helical distance of DNA-cetyltrimethyl ammonium (CTMA) was 39.1  as confirmed by X-ray diffractometry. In general, the magnetization of the DNA-CTMA complex solid was found to be significantly lower than that of natural DNA. Moreover, intercalation of the complex with stable organic free radicals did not improve magnetization, which again was in marked contrast to natural DNA. EMR spectroscopic behavior of the complex in the solid state also was quite different from that of natural DNA: The unique broad EMR signal of natural DNA in the low field region with g-value greater than 10 disappeared in the DNA-CTMA complex.     

The crystal structure of the CeNA:RNA hybrid ce(GCGTAGCG):r(CGCUACGC)

Cyclohexenyl nucleic acids (CeNA) are characterised by the carbon–carbon double bond replacing the O4′‐oxygen atom of the natural D ‐2′‐deoxyribose sugar ring in DNA. CeNAs exhibit a high conformational flexibility, are stable against nuclease activity and their hybridisation is RNA selective. Additionally, CeNA has been shown to induce an enhanced biological activity when incorporated in siRNA. This makes CeNA a good candidate for siRNA and synthetic aptamer applications. The crystal structure of the synthetic CeNA:RNA hybrid ce(GCGTAGCG):r(CGCUACGC) has been solved with a resolution of 2.50 Å. The CeNA:RNA duplex adopts an anti‐parallel, right‐handed double helix with standard Watson–Crick base pairing. Analyses of the helical parameters revealed the octamer to form an A‐like double helix. The cyclohexenyl rings mainly adopt the ³H₂ conformation, which resembles the C3′‐endo conformation of RNA ribose ring. This C3′‐endo ring puckering was found in most of the RNA residues and is typical for A‐family helices. The crystal structure is stabilised by the presence of hexahydrated magnesium ions. The fact that the CeNA:RNA hybrid adopts an A‐type double helical conformation confirms the high potential of CeNAs for the construction of efficient siRNAs which can be used for therapeutical applications.     

DNA attraction in monovalent and divalent electrolytes

The dependence of the effective force on the distance between two DNA molecules was directly computed from a set of extensive all-atom molecular dynamics simulations. The simulations revealed that in a monovalent electrolyte the effective force is repulsive at short and long distances but can be attractive in the intermediate range. This attractive force is, however, too weak (approximately 5 pN per turn of a DNA helix) to induce DNA condensation in the presence of thermal fluctuations. In divalent electrolytes, DNA molecules were observed to form a bound state, where Mg(2+) ions bridged minor groves of DNA. The effective force in divalent electrolytes was predominantly attractive, reaching a maximum of 42 pN per one turn of a DNA helix.     

Design of a triple-helix-specific cleaving reagent

BACKGROUND: Double-helical DNA can be recognized sequence specifically by oligonucleotides that bind in the major groove, forming a local triple helix. Triplex-forming oligonucleotides are new tools in molecular and cellular biology and their development as gene-targeting drugs is under intensive study. Intramolecular triple-helical structures (H-DNA) are expected to play an important role in the control of gene expression. There are currently no good probes available for investigating triple-helical structures. We previously reported that a pentacyclic benzoquinoquinoxaline derivative (BQQ) can strongly stabilize triple helices. RESULTS: We have designed and synthesized the first triple-helix-specific DNA cleaving reagent by covalently attaching BQQ to ethylenediaminetetraacetic acid (EDTA). The intercalative binding of BQQ should position EDTA in the minor groove of the triple helix. In the presence of Fe(2+) and a reducing agent, the BQQ-EDTA conjugate can selectively cleave an 80 base pair (bp) DNA fragment at the site where an oligonucleotide binds to form a local triple helix. The selectivity of the BQQ-EDTA conjugate for a triplex structure was sufficiently high to induce oligonucleotide-directed DNA cleavage at a single site on a 2718 bp plasmid DNA. CONCLUSIONS: This new class of structure-directed DNA cleaving reagents could be useful for cleaving DNA at specific sequences in the presence of a site-specific, triple-helix-forming oligonucleotide and also for investigating triple-helical structures, such as H-DNA, which could play an important role in the control of gene expression in vivo.     

基于G-四链体结构多态性的核酸纳米技术

G-四链体是由富G核酸形成的独特四链螺旋结构,区别于遵循A-T、G-C碱基互补配对原则形成的传统Watson-Crick双链结构.基于G-四链体的特异分子识别特性,能够引导纳米粒子的有序组装、赋予纳米器件以刺激一响应功能,使得核酸纳米技术领域的内容更丰富多样.本文介绍了G-四链体的结构多态性,从纳米材料组装和纳米器件设...     

Electronic structures and long‐range electron transfer through DNA molecules

Quantum chemical calculation on an entire molecule of segments of native DNA was performed in an ab initio scheme with a simulated aqueous solution environment by overlapping dimer approximation and negative factor counting method. The hopping conductivity was worked out by random walk theory and compared with recent experiment. We conclude that electronic transport in native DNA molecules should be caused by hopping among different bases as well as phosphates and sugar rings. Bloch type transport through the delocalized molecular orbitals on the whole molecular system also takes part in the electronic transport, but should be much weaker than hopping. The complementary strand of the double helix could raise the hopping conductivity for more than 2 orders of magnitudes, while the phosphate and sugar ring backbone could increase the hopping conductivity through the base stacks for about 1 order of magnitude. DNA could transport electrons easily through the base stacks of its double helix but not its single strand. Therefore, the dominate factor that influences the electronic transfer through DNA molecules is the π stack itself instead of the backbone. The final conclusion is that DNA can function as a molecular wire in its double helix form with the conditions that it should be doped, the transfer should be a multistep hopping process, and the time period of the transfer should be comparable with that of an elementary chemical reaction. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 112–130, 2000     

Ru(Ⅲ)、Rh(Ⅲ)、Pd(Ⅱ)离子与ct-DNA的相互作用研究

本文以中药小檗碱作为分子探针，在0.01mol·L^-1醋酸-醋酸钠缓冲体系中，用紫外-可见吸收及荧光光谱法研究了Ru(Ⅲ)、Rh(Ⅲ)、Pd(Ⅱ)三种贵金属离子与DNA的键合相互作用。实验发现Ru(Ⅲ)离子对小檗碱-DNA二元体系的荧光有较强的猝灭作用;而Rh(Ⅲ)、Pd(Ⅱ)两种离子则对该二元体系产生显著的荧光敏化作用。考察了EDTA对贵金属离子、小檗碱及DNA三元混合体系的荧光光谱的影响，初步探讨了贵金属离子与DNA可能的键合机理。     

Mode of binding of camptothecins to double helix oligonucleotides

We report an NMR study on the interaction of topotecan (Tpt) and other camptothecins (Cpts) with several double helix and single strand oligonucleotides. The results obtained by (31)P NMR spectroscopy, nuclear Overhauser experiments (NOE) and molecular dynamics (MD) simulations show that Cpt drugs do not intercalate into the double helix, as suggested by many authors. Phosphorus NMR spectra indicated that no deformation occurs at any level of the phosphodiester backbone, while 2D NOESY experiments allowed the detection of several contacts between the aromatic protons of Cpts and those of the double helix. Models of the drug/oligonucleotide complexes, built on the basis of NOE data, show that the drug is located at the end of the double helix, by stacking the A and B rings with the guanine or cytidine of the terminal CG base pairs, with a preference for the 3[prime or minute]-terminal end sites. Cpts interact with double strand, as well as with single strand oligomers, as can be seen from the NMR shift variation observed on the drug protons; but this shielding effect cannot be an evidence of intercalation, as it is largely due to external non-specific interactions of the positively charged drug with the negatively charged ionic surface of the oligonucleotide. The molecular weight of one of the complexes was obtained from the correlation time value. The conformational behaviour of the DNA fragment d(CGTACG)(2) was studied by MD simulations on a ns time scale in the presence of water molecules and Na(+) ions. Different models were examined and the deformations induced on the phosphodiester backbone by molecules that are known to intercalate, were monitored by MD simulations.     

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.     

Chiral Carbon Dots Mimicking Topoisomerase I To Mediate the Topological Rearrangement of Supercoiled DNA Enantioselectively

Nanomaterials with enzyme-mimetic activities are possible alternatives to natural enzymes. Mimicking enzymatic enantioselectivity remains a great challenge. Herein, we report that cysteine-derived chiral carbon dots (CDs) can mimic topoisomerase I to mediate topological rearrangement of supercoiled DNA enantioselectively. d -CDs can more effectively catalyze the topological transition of plasmid DNA from supercoiled to nicked open-circular configuration than l -CDs. Experiments suggest the underlying mechanism: d -CDs intercalatively bind with DNA double helix more strongly than l -CDs; the intercalative CDs can catalyze the production of hydroxyl radicals to cleave phosphate backbone in one strand of the double helix, leading to topological rearrangement of supercoiled DNA. Molecular dynamics (MD) simulation show that the stronger affinity for hydrogen-bond formation and hydrophobic interaction between d -cysteine and DNA than that of l -cysteine is the origin of enantioselectivity.     

Water clustering and percolation in low hydration DNA shells

The hydrogen-bonded networks of water at the surface of a model DNA molecule are analyzed. At low hydrations, only small water clusters are attached to the DNA surface, whereas, at high hydrations, it is homogeneously covered by a spanning water network. The spanning water network is formed via a percolation transition at an intermediate hydration number of about 15 water molecules per nucleotide, which is very close to the midpoint of polymorphic transitions between A- and B-forms of the double helix. The percolation transition can occur in both A- and B-DNA hydration shells with nearly identical percolation thresholds. However, the mechanism of the percolation transition in A- and B-DNA is qualitatively different in regard to the roles played by the two opposite grooves of the double helix. Free ions can shift the percolation threshold by preventing some water molecules from hydrogen bond networking. The results corroborate the suggested relationship between water percolation and the low hydration polymorphism in DNA.     

Enantioselective Assembly of a Ruthenium(II) Polypyridyl Complex into a Double Helix

Evolution can increase the complexity of matter by self‐organization into helical architectures, the best example being the DNA double helix. One common aspect, apparently shared by most of these architectures, is the presence of covalent bonds within the helix backbone. Here, we report the unprecedented crystal structures of a metal complex that self‐organizes into a continuous double helical structure, assembled by non‐covalent building blocks. Built up solely by weak stacking interactions, this alternating tread stairs‐like double helical assembly mimics the DNA double helix structure. Starting from a racemic mixture in aqueous solution, the ruthenium(II) polypyridyl complex forms two polymorphic structures of a left‐handed double helical assembly of only the Λ‐enantiomer. The stacking of the helices is different in both polymorphs: a crossed woodpile structure versus a parallel columnar stacking.     

Chiral Carbon Dots Mimicking Topoisomerase I To Mediate the Topological Rearrangement of Supercoiled DNA Enantioselectively

Nanomaterials with enzyme‐mimetic activities are possible alternatives to natural enzymes. Mimicking enzymatic enantioselectivity remains a great challenge. Herein, we report that cysteine‐derived chiral carbon dots (CDs) can mimic topoisomerase I to mediate topological rearrangement of supercoiled DNA enantioselectively. d ‐CDs can more effectively catalyze the topological transition of plasmid DNA from supercoiled to nicked open‐circular configuration than l ‐CDs. Experiments suggest the underlying mechanism: d ‐CDs intercalatively bind with DNA double helix more strongly than l ‐CDs; the intercalative CDs can catalyze the production of hydroxyl radicals to cleave phosphate backbone in one strand of the double helix, leading to topological rearrangement of supercoiled DNA. Molecular dynamics (MD) simulation show that the stronger affinity for hydrogen‐bond formation and hydrophobic interaction between d ‐cysteine and DNA than that of l ‐cysteine is the origin of enantioselectivity.     

Label-free detection of DNA molecules on the dendron based self-assembled monolayer by electrochemical impedance spectroscopy

We report preparation of a novel platform for effective DNA hybridization and its application to the detection of single mismatched DNA. Cone-shaped dendrimer molecules have been immobilized on the gold surface at equidistance, 3.1 nm, from each other with a probe DNA molecule attached to the top of each dendrimer so that enough space would be secured for effective hybridization. This arrangement allows each probe DNA molecule to form a natural DNA double helix upon hybridization with a target DNA molecule. The single nucleotide polymorphism at either the central or end position of the 25-mer target DNA has been shown to be effectively discriminated against on this platform from each other as well as from a complementary DNA by electrochemical impedance measurements. We also report adverse effects exerted by probe ions, Fe(CN)₆^3−/4−, on DNA hybridization reactions. The significance of the results for the use in DNA analysis is discussed.     

Ultrafast exciton transfers in DNA and its nonlinear optical spectroscopy

We have calculated the nonlinear response function of a DNA duplex helix including the contributions from the exciton population and coherence transfers by developing an appropriate exciton theory as well as by utilizing a projector operator technique. As a representative example of DNA double helices, the B-form (dA)10-(dT)10 is considered in detail. The Green functions of the exciton population and coherence transfer processes were obtained by developing the DNA exciton Hamiltonian. This enables us to study the dynamic properties of the solvent relaxation and exciton transfers. The spectral density describing the DNA base-solvent interactions was obtained by adjusting the solvent reorganization energy to reproduce the absorption and steady-state fluorescence spectra. The time-dependent fluorescence shift of the model DNA system is found to be ultrafast and it is largely determined by the exciton population transfer processes. It is further shown that the nonlinear optical spectroscopic techniques such as photon echo peak shift and two-dimensional photon echo can provide important information on the exciton dynamics of the DNA double helix. We have found that the exciton-exciton coherence transfer plays critical roles in the peculiar energy transfer and ultrafast memory loss of the initially created excitonic state in the DNA duplex helix.