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 ...

Aptamers are nucleic acid molecules selected in vitro to bind small molecules, peptides, proteins or even other nucleic acids with high affinity and specificity. They offer a unique opportunity to extend our knowledge on the basic principles of nucleic acid architecture and ligand recognition. Despite their probable absence in organisms, RNA aptamers are likely to play an important role in mole...

We analytically and numerically study the probabilistic properties of inverted and mirror repeats in model sequences of nucleic acids. We consider both perfect and nonperfect repeats, i.e., repeats with mismatches and gaps. The considered sequence models are independent identically distributed (i.i.d.) sequences, Markov processes and long-range sequences. We show that the number of repeats in c...

The monitoring of DNA and RNA biomarkers freely circulating in the blood constitutes the basis of innovative cancer detection methods based on liquid biopsy. Such methods are expected to provide new opportunities for a better understanding of cancer disease at the molecular level, thus contributing to improved patient outcomes. Advanced biosensors can advance possibilities for cancer-related nu...

Noncoding RNAs form an indispensible component of the cellular information processing networks, a role that crucially depends on the specificity of their interactions among each other as well as with DNA and protein. Patterns of intramolecular and intermolecular base pairs govern most RNA interactions. Specific base pairs dominate the structure formation of nucleic acids. Only little details di...

Guanosine forms hydrogen-bonded dimers in DMSO. The equilibrium constant for dimer formation is 0.18 l./mol at 32”, and there is no evidence of higher order aggregates. The structure of the dimer is probably similar to the hydrogen bonding thought to occur in guanylic acid gels but it is not possible from our results to assign a unique hydrogen-bonding scheme. Cytidine and 1-methylguanosine sho...

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...

Structural biology experiments and structure prediction tools have provided many high-resolution three-dimensional structures of nucleic acids. Also, molecular dynamics force field parameters have been adapted to simulating charged and flexible nucleic acid structures on microsecond time scales. Therefore, we can generate the dynamics of DNA or RNA molecules, but we still lack adequate tools fo...

The stability of all single-base mismatched pairs between a peptide nucleic acid 11-mer and its complementary DNA has been quantified in terms of their melting temperature and compared with the limited amount of data published to date. The strength of the interaction was determined by an automated affinity-electrophoretic approach permitting the visualization, in real time, of hybridization bet...