Specific and predictable hybridization of the polynucleotide sequences to their
complementary counterparts plays a fundamental role in the rational design of new nucleic …

A new 3-Site-Per-Nucleotide coarse-grained model for DNA is presented. The model
includes anisotropic potentials between bases involved in base stacking and base pair …

Although the thermodynamics of DNA hybridization is generally well established, the
kinetics of this classic transition is less well understood. Providing such understanding has …

To simulate long time and length scale processes involving DNA it is necessary to use a
coarse-grained description. Here we provide an overview of different approaches to such …

An ultrasensitive optical biosensor for microRNA-155 (miR-155) was developed to diagnose
breast cancer at early stages. At first, the probe DNA covalently bind to the negatively …

Hybridization‐based electrochemical DNA sensors have become a methodological
mainstay in a wide variety of fields. Among the possible assay formats, sandwich …

A recently published coarse-grained DNA model [DM Hinckley, GS Freeman, JK Whitmer,
and JJ de Pablo, J. Chem. Phys. 139, 144903 (2013)] is used to study the hybridization …

Spherical nucleic acids (SNAs) are a class of structures typically made nanoparticle by
arranging linear nucleic acids at high density around a small-molecule the development …

Signaling properties of a fluorescent hairpin oligonucleotide molecular beacon (MB)
encoded to recognize protein survivin (Sur) mRNA have been investigated. The process of …

This thesis presents a novel coarse-grained model of DNA, in which bases are represented
as rigid nucleotides. The model is shown to quantitatively reproduce many phenomena …