[Show abstract][Hide abstract] ABSTRACT: Microarrays have become an increasingly important tool for biotechnology and molecular diagnostics. Despite many advantages, their sensitivity is still insufficient for such tasks as the analysis of small sample quantities and for the detection of alterations in gene expression of low-abundance genes. Accordingly, amplification strategies are necessary. Approaches to amplify the signal intensity include the increase of the number of dye molecules per target through either particle labels or rolling circle amplification, as used for this study.
Annals of the New York Academy of Sciences 02/2008; 1130(1):287-92. DOI:10.1196/annals.1430.022 · 4.31 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: DNA duplexes were functionalized covalently by clusters of five adjacent chromophores consisting of 5-(pyren-1-yl)-2′-deoxyuridine (Py-U) and 5-(10-methyl-phenothiazin-3-yl)-2′-deoxyuridine (Pz-U). The chromophores form a regular helical π-array along the major groove of duplex DNA when the 5-fold chromophore-modified oligonucleotides are hybridized with an unmodified counter strand. As a result, these chromophores interact significantly and their fluorescence and absorption properties can be modulated by the sequence within the π-array. The 5-fold Py-U stack shows a strongly enhanced emission. The presence of intervening Pz-U groups quenches the fluorescence of the Py-U chromophores. Such modulation of the optical properties within a chromophore stack is potentially useful for optical nanodevices and as nucleic acid sensors for molecular diagnostics. The duplex architecture of DNA is suitable to provide the supramolecular structural scaffold for a directed arrangement of chromophores.
[Show abstract][Hide abstract] ABSTRACT: 8-(Pyren-1-yl)-2'-deoxyguanosine (Py-G) was incorporated synthetically as an optical probe into oligonucleotides. The Py-G group in DNA does not discriminate between any of the four natural nucleosides as a counterbase and exhibits altered optical properties in single strands versus double strands. Thus, the duplex hybridization of Py-G-modified DNA can be observed by both fluorescence and absorption spectroscopy. Moreover, Py-G in DNA can be applied as photoinducable donor for charge transfer processes with small peptides.
[Show abstract][Hide abstract] ABSTRACT: (Figure Presented) Five times is more than fivefold: The helical π-stacked array of pyrene-modified uridine shows a strong fluorescence enhancement that is structure sensitive to base mismatches. As the fluorescence is highly sequence dependent, it can serve as a structure-sensitive probe for DNA.
[Show abstract][Hide abstract] ABSTRACT: Charge transfer through DNA plays an important role in various biological processes as gene damage, damage recognition and repair by proteins. The present thesis investigates the principles of reductive and oxidative charge transfer through DNA and between peptides and oligonucleotides using chemically modified oligonucleotides and peptides. For this purpose various photoexcitable model nucleosides are synthesised, incorporated in DNA and after that their charge transfer behaviour under the influence of DNA binding peptides was spectroscopically and chemically characterised. New fluorescent DNA-labels are also results of this work as important insights in charge transfer processes between peptides and DNA.
[Show abstract][Hide abstract] ABSTRACT: A DNA system consisting of pyrene-modified oligonucleotides and nitrobenzoate (Nb)-modified DNA-binding tripeptides has been applied to study electron-transfer processes through the DNA-peptide interface. 5-(Pyren-1-yl)-2'-deoxyuridine (Py-dU) has been used as the photoinducible charge generator. Upon excitation at 350 nm, a pyrene-like excited state (Py-dU) is formed which undergoes an electron transfer yielding the charge-separated state which is the contact ion pair Py(*)(+)-dU(*)(-). The subsequent electron shift from dU(*)(-) into the base stack competes with charge recombination and can be probed chemically by trapping the electron at the 5-bromo-2'-deoxyuridine (Br-dU) group leading to strand cleavage which can be quantified by HPLC analysis. Several Nb-modified DNA-binding tripeptides influence these DNA-mediated electron-transfer processes as shown by fluorescence spectroscopy experiments. Fluorescence quenching can occur primarily through a reductive electron-transfer process in which the Nb group traps the electron thermodynamically from the contact ion pair Py(*)(+)-dU(*)(-). Moreover, our results indicate that, once the negative charge has been trapped on the peptide, oxidative processes from Py(*)(+) take place resulting in an enhanced and nonspecific strand degradation of the Py-dU-modified duplexes. The latter type of strand cleavage can be inhibited by the presence of tryptophane or tyrosine as part of the peptides. Most remarkably, DNA-binding tripeptides, which bear both the Nb and the tryptophan/tyrosine moiety, are able to trap both the negative and the positive charge from the contact ion pair Py(*)(+)-dU(*)(-).
[Show abstract][Hide abstract] ABSTRACT: 1-ethynylpyrene shows remarkable absorption changes upon DNA hybridization when it is covalently attached to the 8-position of guanine. An absorption band at approximately 420 nm is only present in the duplex, exhibits thermal melting behaviour and provides the basis for a molecular beacon together with 1-ethynylpyrene-modified cytosine.
[Show abstract][Hide abstract] ABSTRACT: (Chemical Equation Presented) Highly acceptable: DNA is a flexible medium with a range of conformational states. Thus, in investigations of the DNA-mediated reductive electron transfer using a modified DNA duplex containing 5-bromo-2′-deoxyuridine (red in picture) as the electron acceptor and pyren-1-yl-2′-deoxyuridine (blue) as the electron donor, a distribution of electron-transfer rates has been observed.