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.     

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.     

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.     

Theoretical study of fast repair of DNA damage by cistanoside C and analogs: Mechanism and docking

Experiments show that the natural substances phenylpropanoid glycosides (PPGs) extracted from pelicularis 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 molecules and isolated DNA bases, as well as a DNA fragment has been performed. An interaction mechanism reported early has been refined. The docking calculations performed using junction minimization of nucleic acids (JUMNA) software showed that the PPG molecules can be docked into the minor groove of 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 rhamnosyl side-groups.     

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.     

Electrochemical DNA Biosensors Applicable to the Study of Interactions Between DNA and DNA Intercalators

Electrochemical DNA biosensors, based either on carbon paste electrode (CPE) or hanging mercury drop electrode (HMDE) were prepared. These biosensors were used in the study of interaction between double stranded DNA (dsDNA) and single stranded DNA (ssDNA) and acridine orange, a well known DNA intercalator. The different electrochemical behaviors were compared in the article.     

Change Trees and Mutagrams for the Visualization of Local Changes in Sequence Data

The analysis of local changes in sequence data is of interest for various applications such as the segmentation of DNA and other genetic sequences, or financial data sequences. Patterns of change that can be characterized as local jump change or slope change are of special interest. We propose simple graphical tools to visualize such patterns of local change. The concept of mode trees—developed for the visualization of local patterns in densities—is adapted to visualize patterns of local change in dependency on a threshold parameter by means of a change tree . The simultaneous visualization of scale effects, in analogy to SiZer, motivates another graphical device, the mutagram . We illustrate these concepts with several sets of sequence data.     

Synthesis of P-Chiral [ 18 O]-Labeled Isotopomeric Oligo(deoxyribonucleoside Phosphorothioate)s and Phosphates

Diastereomerically pure, isotopically labeled 5'- O -DMT-nucleoside-3'- O -(2-thio-4,4-"spiro"-pentamethylene-1,3,2-[ 18 O]oxathiaphospholane)s and -(2-oxo-4,4-"spiro"-pentamethylene-1,3,2-[ 18 O]oxathiaphospholane)s suitable for stereocontrolled synthesis of P-chiral oligonucleotide [ 18 O]phosphorothioates and [ 18 O]phosphates were synthesized. Obtained in that way "chimeric" oligonucleotide d[A PO A PS-Rp,Sp A PS-Rp , Sp A PS-Rp C PS(18O)-Rp G PS-Rp T PS-Rp T PS-Rp,Sp T PO T] was used for determination of the stereochemistry of hydrolysis by endonuclease from Serratia marcescens .