Blunt-end

In molecular biology, 'blunt-end' refers to a DNA or RNA molecule's double-stranded end that lacks single-stranded overhangs. These ends terminate with base pairs that are fully aligned, resulting in a flush, or flat, end. This contrasts with 'sticky ends' (also called 'cohesive ends') which possess single-stranded overhangs that can base-pair with complementary sequences. Blunt ends are often produced by restriction enzymes that cut both strands of DNA at the same location or through mechanical shearing of the DNA molecule. Because of their flat surface, blunt ends are relatively stable but can be less efficient for certain molecular biology techniques compared to sticky ends, as they require specific enzymes (like T4 DNA ligase) and higher concentrations of ATP for ligation (joining) reactions.

Blunt-end meaning with examples

• During DNA cloning, a researcher used a restriction enzyme that produced blunt-end fragments. Ligation of these fragments required T4 DNA ligase and a high concentration of ATP to efficiently join the fragments together. The absence of any single-stranded overhangs increased the challenge of creating a stable junction between the insert and vector DNA.
• After sonication, the DNA was visualized on a gel, and found that many of the fragments had blunt ends. These were used for a sequencing library preparation, which was designed to make the blunt ends compatible with the sequencing platform. This allowed direct sequencing, rather than needing adapters, which often involve blunt ends as well.
• In polymerase chain reaction (PCR), blunt-end fragments can be amplified, and may require specialized polymerases or modifications. The blunt-end PCR product was then ligated into a blunt-end vector using a ligase enzyme designed for this type of ligation. The efficiency depends on the enzyme and reaction conditions.
• Genome editing techniques can involve the creation of blunt ends during DNA breaks using CRISPR-Cas9. After the break is made, the cell's repair mechanisms may then attempt to join the blunt ends, sometimes introducing small insertions or deletions at the break site through the process called non-homologous end joining.