Electrophoretic properties of complexes between DNA and the cationic surfactant cetyltrimethylammonium bromide

We use agarose gel electrophoresis to characterize how the monovalent catioinic surfactant cetyltrimethylammonium bromide (CTAB) compacts double-stranded DNA, which is detected as a reduction in electrophoretic DNA velocity. The velocity reaches a plateau at a ratio R = 1.8 of CTAB to DNA-phosphate charges, i.e., above the neutralization point, and the complexes retain a net negative charge at least up to R = 200. Condensation experiments on a mixture of two DNA sizes show that the complexes formed contain only one condensed DNA molecule each. These CTAB-DNA globules were further characterized by time-resolved measurements of their velocity inside the gel, which showed that CTAB does not dissociate during the migration but possibly upon entry into the gel. Using the Ogston-model for electrophoresis of spherical particles, the measured in-gel velocity of the globule is quantitatively consistent with CTAB having two opposite effects, reduction of both the electrophoretic charge and DNA coil size. In the case of CTAB the two effects nearly cancel, which can explain why opposite velocity shifts (globule faster than uncomplexed DNA) have been observed with some catioinic condensation agents. Dissociation of the complexes by addition of anionic surfactants was also studied. The DNA release from the globule was complete at a mixing ratio between anionic and cationic surfactants equal to 1, in agreement with equilibrium studies. Circular DNA retained its supercoiling, and this demonstrates a lack of DNA nicking in the compaction-release cycle which is important in DNA transfection and purification applications.     

Multiplex amplified product-length polymorphism analysis of 36 mitochondrial single-nucleotide polymorphisms for haplogrouping of East Asian populations

We present a reliable, rapid, and economical multiplex amplified product-length polymorphism (APLP) method for analyzing the haplogroup-diagnostic mitochondrial single-nucleotide polymorphisms (mtSNPs) in East Asian populations. By examining only 36 haplogroup-specific mtSNPs in the coding region by using four 9-multiplex polymerase chain reaction (PCR) and subsequent electrophoresis, we could safely assign 1815 individuals from 8 populations of Japanese, Korean, Chinese, and Germans to 45 relevant haplogroups. This multiplex APLP analysis of coding-region mtSNPs for haplogrouping is especially useful not only for molecular phylogenetic studies but also for large-scale association studies due to its rapid and economical nature. This is the first panel of mtSNPs in the coding region to be used for haplogrouping of East Asian populations.     

Detecting DNA Damage with a Silver Solid Amalgam Electrode

Mercury electrodes modified with supercoiled (sc) DNA have been used as highly sensitive tools for the detection of DNA strand breaks or as sensors for DNA cleaving substances. In this paper we show that silver solid amalgam electrode (AgSAE), in connection with alternating current voltammetry, provides similar information about DNA damage as the hanging mercury drop electrode. The AgSAE can be used for the detection of enzymatic or chemical DNA cleavage in solution or at the electrode surface. AgSAE modified with scDNA can be utilized as a sensor for DNA nicking substances.     

Monte Carlo Simulation of the Assembly of bis‐Biotinylated DNA and Streptavidin

We present Monte Carlo simulations of the self‐assembly of bivalent bis‐biotinylated DNA molecules with the tetravalent biotin‐binding protein streptavidin (STV). By fitting the STV binding probabilities for the four possible valencies, the modelling correctly reproduces the dependencies of various network parameters experimentally observed in an earlier study. The combined results from the experimental and theoretical studies suggest that the binding probability for divalent STV formation is about 50 times larger than for the formation of trivalent and about 200 times larger than for tetravalent STV. In accordance with the experimental results, the modelling also indicates that the mixture of an equimolar ratio of DNA and STV leads to a maximum in size of the oligomeric DNA–STV clusters formed. Furthermore, we found a percolation transition in which the DNA cluster size increases rapidly with increasing DNA concentration resulting in the formation of a single supercluster at elevated concentrations. This behaviour coincides with the occurrence of an immobile band previously observed in electrophoretic experiments, indicating the formation of extremely large DNA–STV aggregate networks.     

Molecular modeling of intercalation complexes of antitumor active 9-aminoacridine and a [d,e]-anellated isoquinoline derivative with base paired deoxytetranucleotides

Summary Intercalators are molecules capable of sliding between DNA base pairs without breaking up the hydrogen bonds between the DNA bases. On the basis of molecular mechanics calculations structural, models of B-DNA tetranucleotide intercalation complexes of some cytostatic active 9-aminoacridines and of a [d, e]-anellated isoquinoline derivative are presented. The drug complexes are stabilized by energetically favouredvan der Waals interactions and by selective hydrogen bonds between the side chains of the drugs and the DNA bases. Semiempirical quantum chemistry calculations revealed that the chromophoric system of the intercalators is able to form ,-charge-transfer interactions with the purine bases of the base paired deoxytetranucleotides. The theoretical findings are of interest for a more specific drug design of cytostatically active agents.

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Molecular Modeling von Interkalationskomplexen antitumoraktiver 9-Aminoacridine sowie eines [d, e]-anellierten Isochinolinderivates mit basengepaarten Desoxytetranukleotiden

Zusammenfassung Interkalatoren sind Moleküle, die in der Lage sind, sich zwischen DNA-Basenpaare einzulagern, ohne die Wasserstoffbrücken zwischen den DNA-Basen aufzubrechen. Auf der Basis von molekülmechanischen Rechnungen werden Tetranukleotid-Interkalationskomplexe von verschiedenen zytostatisch aktiven 9-Aminoacridinen und von einem [d, e]-anellierten Isochinolinderivat präsentiert. Die Komplexe werden durch energetisch günstigevan der Waals-Interaktionen sowie durch selektive Wasserstoffbrückenbindungen zwischen den Seitenketten der Wirkstoffe und den DNA-Basen stabilisiert. Semiempirische quantenchemische Rechnungen ergaben, daß der Chromophor der Interkalatoren in der Lage ist, ,-charge-transfer Wechselwirkungen mit den Purinbasen der basengepaarten Desoxytetranukleotide auszubilden. Die theoretischen Ergebnisse sind für ein spezifischeres Wirkstoffdesign zytostatisch aktiver Verbindungen von Interesse.

     

Synthesis of novel analogs of aromatic peptide nucleic acids (APNAs) with modified conformational and electrostatic properties

Aromatic peptide nucleic acid analogs having an N-(2-aminobenzyl)glycine backbone (APNA 1) were previously identified as promising new leads for the design of polyaromatic DNA mimics. Structural modifications of 1, which lock the aromatic backbone into a unique conformation, while maintaining the same space distribution between the nucleobases as in 1, were investigated. The electrostatic potential of the aromatic backbone was also modified in an attempt to improve the solubility of these compounds in aqueous media and to evaluate how the quadrapole of the aromatic backbone may influence the biophysical properties of the APNA oligomers. PNA hexamers containing a single monomer insert of each new APNA monomer were used to explore the hybridization properties of these analogs with poly rA and poly dA. Preliminary results indicated that these modifications do not seriously alter the molecular recognition properties of APNAs towards DNA and RNA.     

Study on the Interaction between Gatifloxacin Mesylate and Salmon Sperm DNA by Fluorescence Method

The interaction between gatifloxacin mesylate (GM) and salmon sperm DNA was studied by fluorescence spectrometry and ultra‐violet (UV) spectrometry. Additions of salmon sperm DNA to GM solution resulted in its strong fluorescence quenching and UV absorbance decrease due to the strong interaction between GM and salmon sperm DNA. Both the maximum fluorescence emission wavelength and the maximum UV absorbance wavelength of GM did not change with the increasing concentration of salmon sperm DNA, indicating no intercalative binding existed between them. The Stern‐Volmer plot indicated that the fluorescence‐quenching constant at different temperatures or different salmon sperm DNA concentration ranges was different. Effects of ionic strength and I^? on the fluorescence quenching of GM by salmon sperm DNA indicated that electrostatic interaction and groove binding coexisted between them.     

白藜芦醇的电化学行为及其与DNA的相互作用

采用电化学方法研究了白藜芦醇在pH=2~13的缓冲溶液中的电化学行为、抗氧化能力及其与DNA的相互作用. 研究结果表明， 在2.011的溶液中, 白藜芦醇产生的P4和P5波分别是其二价和三价阴离子的还原波. 在最佳实验条件下, 微分脉冲极谱图上IP3在8.0×10-8~2.0×10-6 mol/L范围内与白藜芦醇的浓度呈线性关系, 检出限为4×10-8 mol/L. 将该法用于中药虎杖中白藜芦醇含量的测定, 结果与高效液相色谱法一致.