Blunt ends

DNA ends refer to the properties of the end of DNA molecules, which may be sticky ends (cohesive ends), blunt ends or in other forms. The concept is used in molecular biology, especially in cloning or when subcloning inserts DNA into vector DNA. Such ends may be generated by restriction enzymes that cut the DNA – a staggered cut generates two sticky ends, while a straight cut generate blunt ends.

A sticky or cohesive end has protruding single-stranded strands with unpaired nucleotides called overhangs, each overhang can anneal with another complementary one to form base pairs. The two complementary cohesive ends of DNA can anneal together via hydrogen bonding, the stability of these paired ends depends on the melting temperature of the paired overhangs. DNA ligase can join two adjacent strands of DNA by forming a covalent bond between the sugar-phosphate moieties of adjacent nucleotides to join the two together via a phosphodiester bond in a process called ligation. The blunt ends however do not have such protruding strands, and therefore cannot anneal together, and consequently ligation between blunt ends is less efficient.

A single-stranded non-circular DNA molecule has two non-identical ends, the 3' end and the 5' end (usually pronounced "three prime end" and "five prime end"). The numbers refer to the numbering of carbon atoms in the deoxyribose, which is a sugar forming an important part of the backbone of the DNA molecule. In the backbone of DNA the 5' carbon of one deoxyribose is linked to the 3' carbon of another by a phosphate group. The 5' carbon of this deoxyribose is again linked to the 3' carbon of the next, and so forth.

When a molecule of DNA is double stranded, as DNA usually is, the two strands run in opposite directions. Therefore, one end of the molecule will have the 3' end of strand 1 and the 5' end of strand 2, and vice versa in the other end. However, the fact that the molecule is two stranded allows numerous different variations.

The simplest DNA end of a double stranded molecule is called a blunt end. In a blunt-ended molecule both strands terminate in a base pair. Blunt ends are not always desired in biotechnology since when using a DNA ligase to join two molecules into one, the yield is significantly lower with blunt ends. When performing subcloning, it also has the disadvantage of potentially inserting the insert DNA in the opposite orientation desired. On the other hand, blunt ends are always compatible with each other. Here is an example of a small piece of blunt-ended DNA:

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