homoduplexes

Homoduplexes are DNA or RNA molecules consisting of two identical strands that have annealed to each other. In DNA, this would involve a double helix formed by two complementary strands that happen to have the exact same sequence. Similarly, in RNA, a homoduplex refers to a double-stranded RNA molecule where both strands have identical sequences. This is in contrast to the typical heteroduplex formation in nucleic acids, where two complementary but not necessarily identical strands hybridize.

The formation of homoduplexes is generally thermodynamically unfavorable under standard conditions because it requires the disruption of base pairing rules. However, under specific experimental conditions, such as high salt concentrations or elevated temperatures followed by slow cooling, or when the sequence is highly repetitive, homoduplex formation can occur. In some biological contexts, homoduplex formation can be a transient intermediate or a product of specific enzymatic activities, though it is less common than heteroduplex formation. For example, certain DNA repair mechanisms or DNA replication processes might involve transient homoduplex structures. In molecular biology research, homoduplex formation can sometimes be an artifact of experimental procedures, particularly when working with single-stranded DNA or RNA under annealing conditions. Careful control of experimental parameters is crucial to avoid or mitigate unwanted homoduplex formation.