Sequence Dependence of Fluorescent Quenching of Chromophores Covalently Bonded to Oligo-DNAs before and after Duplex Formation

The labeling of oligo- and polynucleotides with fluorescent probes is an important technique for the analysis of DNAs and RNAs. The effect of duplex formation with complementary oligo-DNA on the quenching behavior of two fluorescent chromophores (eosin, Eo and tetramethylrhodamine, TMR) attached to the 5′-terminal of various 10mer oligo-DNAs was investigated and the dependence of the quenching on DNA base sequence is discussed. We found that guanine residues played a major role in the quenching of the fluorescence of the chromophores. Guanine residues on the complementary DNA near the chromophores, in particular, had a significant influence on the quenching.     

Signal modelization for improved precision of assessment of minimum and mean telomere lengths

Telomere length is an important measure of cell and tissue regenerative capacities. The mean telomere length is classically used as global indicator of a tissue telomere length. In skeletal muscle, which is made of postmitotic myonuclei and satellite cells (muscle stem cells), minimum telomere length is also used to assess the telomere length of satellite cells and newly incorporated myonuclei. At present, the estimation of the method reproducibility during the assessment of mean and minimum telomere length using Southern blot analysis has never been documented. The aim of this report is to describe a signal modelization for improved precision of assessment of minimum and mean telomere lengths and to document the method reproducibility. Telomeres are assessed using a Southern technique where the gel is directly hybridized with the specific probe without the membrane-transferring step in order to prevent telomeric low signal loss. We found that the improved signal analysis for determination of telomere length is associated with coefficients of variation ranging from 1.37 to 4.29% for the mean telomeric restriction fragment (TRF) length and from 2.04 to 4.95% for the minimum TRF length. Improved method reproducibility would allow saving time and biological material as duplicate and triplicate measurement of the same sample is no longer required.     

高选择性端粒G-四链体稳定性配体:9-O-多胺取代小檗碱衍生物的合成及活性评价

设计合成了3个多胺取代的小檗碱衍生物5a~5c, 并利用圆二色(CD)光谱、 荧光共振能量转移(FRET)熔点实验、 荧光光谱和聚合酶链反应(PCR)终止实验等手段研究了小檗碱衍生物5a~5c与端粒DNA的相互作用. 结果表明, 小檗碱衍生物5a~5c可以诱导端粒DNA序列形成反平行结构G-四链体, 显著地提高了端粒G-四链体的稳定性, 有效地抑制了端粒的扩增; 而与双链DNA的相互作用则很小, 是高选择性的端粒G-四链体配体.     

Biological effects induced by swift heavy ions of lithium on aqueous solution of plasmid pMTa4

Biological samples exposed to swift heavy ions sustain damage on different components. Damage to DNA, a critical component of a living system, has considerable biological implications. In this study aqueous solution of plasmid pMTa4 was exposed to varying fluence of swift ⁷Li ions and its different topological forms were analysed by agarose gel electrophoresis to study the induced damage. To monitor radiation labile nucleotide sequence the ⁷Li ions exposed plasmid was degraded by three different restriction endonucleases and also analysed by agarose gel electrophoresis. The results show that ⁷Li ions predominantly induced double strand breaks in the plasmid DNA in a dose-dependent manner and affected preferentially the GC-rich motifs of the DNA. The results suggest that ⁷Li ions induce premutagenic lesions at an enhanced frequency in segments of the DNA which are rich in CG content as compared to GC-poor segments.     

NDI-induced Topological Conversion of Human Telomeric G-Quadruplexes from Hybrid-2 to Parallel Form

G-Quadruplexes(GQs), which are formed by G-rich DNA sequences in human telomeres, have become an attractive target for cancer treatment. The ligands to stabilize the conformation of human telomeric GQs in vivo are particularly important for structure-based ligand design and drug development targeting the noncanonical DNA structure. Here we report the conformational conversion of Tel26 induced by a naphthalene diimide(NDI) ligand in K⁺ buffer, even at cellular physiological temperature(37℃) and under mimetic cellular crowding conditions created by Ficoll 70. We provide an insight into the dynamic conversion from initial hybrid-2 GQ topology to final parallel GQ topology. These results are helpful for the design of ligands with GQ conformation regulation.     

Reactivity of Bulged Bases in Duplex DNA with Redox-active Nickel and Cobalt Complexes

The square-planar, macrocyclic complex NiCR (CR=(2,12-dimethyl-3,7,11,17-tetraazabicyclo[11.3.1]heptadeca-1(17),2,11,13,15-pentaenato)) as well as CoCl 2 have been investigated as catalysts for the site-specific oxidation of bulged T, C, and A nucleotides in duplex DNA oligomers. Previous studies of NiCR using KHSO 5 as oxidant indicated that this combination of reagents successfully probes the accessibility of N7 of guanine residues in non-canonical DNA and folded RNA structures. In the present study, the order of reactivity of bulged bases in synthetic oligodeoxynucleotides with NiCR/KHSO 5 is shown to be G>C>T～A. Although the nickel complex generates a less-reactive oxidant than does cobalt, its selectivity for bulged bases is much greater, rendering it a useful probe of exposed Cs and Ts in addition to Gs in DNA and RNA structure.     

Fluorescence Energy Transfer Study of Interstrand DNA Cross-linking Caused by Rigid Bisintercalator

The intermolecular cross-linking of DNA with a rigid bisintercalator, 1,4-bis(( N -methylquinolinium-4-yl)vinyl)benzene (pMQVB) has been studied using fluorescence resonance energy transfer (FRET), fluorescence anisotropy measurements, and dynamic fluorescence microscopy. Short DNA duplexes, single-labeled with fluorescein (donor) and x-rhodamine (acceptor), were used as energy transfer partners. Due to the quenching effect of pMQVB on the emission of both fluorescein and x-rhodamine, the energy transfer was monitored using the corrected Stern-Volmer plots. The cross-linking ability of pMQVB depended on the ligand structure; the planar E , E isomer cross-linked DNA contrary to the non-planar E , Z isomer. Dynamic fluorescence microscopy observation also demonstrated the ability of pMQVB to cross-link large T4 DNA molecules.     

The Binding Pocket at the Interface of Multimeric Telomere G-quadruplexes: Myth or Reality?

Human telomeric DNA with hundreds of repeats of the 5’-TTAGGG-3’ motif plays a crucial role in several biological processes. It folds into G-quadruplex (G4) structures and features a pocket at the interface of two contiguous G4 blocks. Up to now no structural NMR and crystallographic data are available for ligands interacting with contiguous G4s. Naphthalene diimide monomers and dyads were investigated as ligands of a dimeric G4 of human telomeric DNA comparing the results with those of the model monomeric G4. Time-resolved fluorescence, circular dichroism, isothermal titration calorimetry and molecular modeling were used to elucidate binding features. Ligand fluorescence lifetime and induced circular dichroism unveiled occupancy of the binding site at the interface. Thermodynamic parameters confirmed the hypothesis as they remarkably change for the dyad complexes of the monomeric and dimeric telomeric G4. The bi-functional ligand structure of the dyads is a fundamental requisite for binding at the G4 interface as only the dyads engage in complexes with 1 : 1 stoichiometry, lodging in the pocket at the interface and establishing multiple interactions with the DNA skeleton. In the absence of NMR and crystallographic data, our study affords important proofs of binding at the interface pocket and clues on the role played by the ligand structure.     

Synthesis of a ruthenium(II) polypyridine complex with 1,10-phenanthrolineselenazole as ligand and investigation of its G-quadruplex DNA-binding properties

A new Ru(II) complex, [Ru(bpy)₂L](ClO₄)₂ (bpy?=?2,2′-bipyridine, L?=?1,10-phenanthrolineselenazole), has been synthesized and structurally characterized by elemental analysis, ESI-MS, and ¹H NMR. The interaction of human telomeric oligomer 5′-AG₃(T₂AG₃)₃-3′ with the Ru(II) complex was explored by competition FRET experiment, ?uorescence titration, circular dichroism spectroscopy, thermal denaturation, polymerase chain reaction stop assay, and TRAP assay. The Ru(II) complex can selectively bind to G-quadruplex DNA. The results indicated that the complex not only induces a remarkable conformational change of human telomeric DNA, but also has the ability to stabilize the G-quadruplex.     

Docking study of cistanoside C to telomeric DNA fragment

Experiments show that the natural products phenyl propanoid glycosides (PPGs) extracted from the plant Pedicularis spicata are capable of repairing DNA damaged by oxygen radicals. Based on kinetic measurements and experiments on tumor cells, a theoretical study of the interaction between PPG molecule Cistanoside C and telomeric DNA fragment has been carried out. The docking calculations performed using JUMNA software showed that the Cistanoside C could be docked into the minor groove of telomeric DNA and form complexes with the geometry suitable for an electron transfer between guanine radical and the ligand. Such complexes can be formed without major distortions of DNA structure and are further stabilized by the interaction with the saccharide side-groups.