52basepair

52basepair is a term used to describe a double-stranded DNA fragment consisting of 52 base pairs. In B-form DNA, a fragment of this length spans roughly 17.7 nanometers along the helical axis and has a molecular mass of about 34 kilodaltons. The physical properties of a 52 base pair fragment, including melting temperature and stability, depend on its sequence and GC content.

Synthesis and handling are straightforward for this length. Such fragments are typically generated as synthetic oligonucleotides by solid-phase phosphoramidite chemistry and then converted into double-stranded DNA by annealing with a complementary strand. Purification commonly employs methods like polyacrylamide gel electrophoresis or high-performance liquid chromatography to remove truncated products. They are usually stored at low temperature to maintain integrity.

Applications for a 52 base pair fragment include serving as calibration or reference standards in gel electrophoresis, sequencing, and quantitative assays. They can act as model sequences for studying hybridization behavior, design of short primers or probes, and inclusion as small inserts or barcodes in cloning or sequencing workflows. In DNA nanotechnology, short fragments of this length may function as components in simple assemblies or as testing units for binding interactions.

Limitations include sequence dependence of stability, potential formation of secondary structures, and reduced usefulness for applications requiring longer DNA scaffolds. The term 52basepair is a descriptive label rather than a formal standard, and its practical meaning centers on a 52-base-pair double-stranded DNA fragment.

See also: base pair, DNA duplex, oligonucleotide, primer, sequencing.