- Single-stranded DNA (ssDNA) is a DNA molecule that consists of only one of the two complementary strands that form the typical double helix structure of DNA.
- Unlike double-stranded DNA (dsDNA), which exists in the familiar B-form double helix with base pairing between adenine and thymine, and between cytosine and guanine, ssDNA contains unpaired nucleotide bases and lacks this stable, helical form. This structural difference gives ssDNA distinct biochemical and physical properties, such as increased flexibility and susceptibility to nucleases, especially exonucleases that degrade single-stranded molecules.
- In living systems, ssDNA plays a crucial role in various biological processes. During DNA replication, for example, the double helix is unwound to produce ssDNA templates for the synthesis of new strands. This exposure of single strands is stabilized by proteins such as single-strand binding proteins (SSBs), which prevent premature reannealing and protect the ssDNA from enzymatic degradation. ssDNA intermediates are also central to homologous recombination and DNA repair mechanisms, where they help align homologous regions and facilitate strand exchange. Additionally, some viruses, such as parvoviruses and bacteriophage φX174, have genomes composed entirely of ssDNA, highlighting its viability as a stable genetic material under certain conditions.
- In biotechnology and molecular biology, ssDNA is widely used for a variety of applications. It serves as a primer in polymerase chain reaction (PCR) and DNA sequencing, as probes in hybridization-based assays, and as templates for techniques such as site-directed mutagenesis. ssDNA oligonucleotides are also critical components of antisense therapies, aptamer design, and CRISPR-based genome editing tools. Furthermore, synthetic ssDNA constructs are central to nanotechnology approaches, including DNA origami, where the predictable base pairing of nucleotides is exploited to fold DNA into intricate three-dimensional structures.
- Despite its utility, ssDNA is inherently less stable than dsDNA due to the lack of complementary base pairing, which contributes to a higher tendency for secondary structure formation, such as hairpins or loops, through intramolecular interactions. These structures can interfere with enzymatic processes like replication and transcription. However, this very property is sometimes harnessed to design functional nucleic acid structures with specific shapes and activities.
