Nucleic acid hybridization

8.5 Detecting Nucleic Acid Hybridization

The double-helical structure of nucleic acids, in which one strand binds specifically to its exact complement, could not have been designed to be more useful for the study of biology. The ease of designing assays based on this feature is responsible for the incredibly fast pace that has characterized molecular biology research since its inception. With the incorporation of fluorescence technolo...

Nucleic Acid Hybridization – General Aspects

Topological constraints in nucleic acid hybridization kinetics

A theoretical examination of kinetic mechanisms for forming knots and links in nucleic acid structures suggests that molecules involving base pairs between loops are likely to become topologically trapped in persistent frustrated states through the mechanism of 'helix-driven wrapping'. Augmentation of the state space to include both secondary structure and topology in describing the free energy...

Optimizing the specificity of nucleic acid hybridization.

The specific hybridization of complementary sequences is an essential property of nucleic acids, enabling diverse biological and biotechnological reactions and functions. However, the specificity of nucleic acid hybridization is compromised for long strands, except near the melting temperature. Here, we analytically derived the thermodynamic properties of a hybridization probe that would enable...

Fluorescent hybridization probes for nucleic acid detection.

Due to their high sensitivity and selectivity, minimum interference with living biological systems, and ease of design and synthesis, fluorescent hybridization probes have been widely used to detect nucleic acids both in vivo and in vitro. Molecular beacons (MBs) and binary probes (BPs) are two very important hybridization probes that are designed based on well-established photophysical princip...