Escherichia coli bacteria in the logarithmic growth phase have been investigated by UV resonance Raman spectroscopy. Bacterial whole-cell Raman spectra excited at 251 nm reflect nearly exclusively the nucleic acid composition even though a very large fraction of the bacterial mass is composed of protein. It has been demonstrated that if bacteria are grown under controlled (logarithmic growth) c...

In order to scan nucleic acid databases for potentially relevant but as yet unknown signals, we have developed an improved statistical model for pattern analysis of nucleic acid sequences by modifying previous methods based on Markov chains. We demonstrate the importance of selecting the appropriate parameters in order for the method to function at all. The model allows the simultaneous analysi...

We present an all atom potential energy function for the simulation of proteins and nucleic acids. This work is an extension of the CH united atom function recently presented by S. J. Weiner et al. (J . Amer. Chem. SOC., 106,765 (1984). The parameters of our function are based on calculations on ethane, propane, n-butane, dimethyl ether, methyl ethyl ether, tetrahydrofuran, imidazole, indole, d...

Several peptide nucleic acid based artificial nucleases (PNAzymes) are designed to create a bulge in the target RNA, which is a short model of the leukemia related bcr/abl mRNA. The target RNA is cleaved by the PNAzymes with a half-life of down to 11 h (using a 1 : 1 ratio of PNA-conjugate to target) and only upon base-pairing with the substrate. The PNA based systems are also shown to act in a...

Certain intercalating aromatic cations, such as the fluorochrome acridine orange or the antitumor drug Mitoxantrone, induce condensation of nucleic acids in solutions. The appearance of the condensed form during titration of nucleic acids with these intercalating ligands can be quantitatively monitored by light scatter measurements. The resulting highly reproducible light scatter transition cur...

DNA nanoswitches can be designed to detect unlabelled nucleic acid targets and have been shown to discriminate between targets which differ in the identity of only one base. This paper demonstrates that the fluorescent base analogue 2-aminopurine (AP) can be used to discriminate between nanoswitches with and without targets and to discriminate between matched and mismatched targets. In particul...

Multiple lines of evidence support the hypothesis that the early evolution of life was dominated by RNA, which can both transfer information from generation to generation through replication directed by base-pairing, and carry out biochemical activities by folding into functional structures. To understand how life emerged from prebiotic chemistry we must therefore explain the steps that led to ...

Detection of dye-labeled nucleic acids via fluorescence reporting has become a routine technique in molecular biology laboratories. Given this, it is important to note that the quantum yield of fluorophores attached to nucleic acids is dependent upon a number of factors. One of these is the choice of the base that lies adjacent to the fluorescent molecule. Fluorescence quenching by an adjacent ...

Conformational flexibility in nucleic acids provides a basis for complex structures, binding, and signaling. One-base bulges directly neighboring single-base mismatches in nucleic acids can be present in a minimum of two distinct conformations, complicating the examination of the thermodynamics by calorimetry or UV-monitored melting techniques. To provide additional information about such struc...