ECENT evidence suggests that it is possible to effect transformation of mammalian cells by exogenous nucleic acids.15 Thus the administration of large amounts of nucleic acids to humans as an’ experimental or therapeutic maneuver may be envisaged. Since little is known of the biologic properties of nucleic acids, apart from their pre-eminent role in directing protein synthesis and cell replicat...

SUMMARY JaDis is a Java application for computing evolutionary distances between nucleic acid sequences and G+C base frequencies. It allows specific comparison of coding sequences, of non-coding sequences or of a non-coding sequence with coding sequences. AVAILABILITY http://pbil.univ-lyon1.fr/software/jadis.html

The equilibrium of stacked and unstacked base pairs is of central importance for all nucleic acid structure formation processes. The stacking equilibrium is influenced by intramolecular interactions between nucleosides but also by interactions with the solvent. Realistic simulations on nucleic acid structure formation and flexibility require an accurate description of the stacking geometry and ...

Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy -c ln m for a loop of length m, we study homopolymeric single-stranded nucleic acid chains under external force and varying temperature. In the thermodynamic limit of a lon...

Short single-stranded nucleic acids are ubiquitous in biological processes; understanding their physical properties provides insights to nucleic acid folding and dynamics. We used small-angle x-ray scattering to study 8-100 residue homopolymeric single-stranded DNAs in solution, without external forces or labeling probes. Poly-T's structural ensemble changes with increasing ionic strength in a ...

We demonstrate the first use of smartphone spectrophotometry for readout of fluorescence-based biological assays. We evaluated the smartphone fluorimeter in the context of a fluorescent molecular beacon (MB) assay for detection of specific nucleic acid sequences in a liquid test sample and compared performance against a conventional laboratory fluorimeter. The capability of distinguishing a one...

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...

The nucleocapsid protein (NC) of HIV type 1 is a nucleic acid chaperone that facilitates the rearrangement of nucleic acids into conformations containing the maximum number of complementary base pairs. We use an optical tweezers instrument to stretch single DNA molecules from the helix to coil state at room temperature in the presence of NC and a mutant form (SSHS NC) that lacks the two zinc fi...