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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 aDNA 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:

verhangs and sticky ends[edit]

Non-blunt ends are created by various overhangs. An overhang is a stretch of unpaired nucleotides in the end of a DNA molecule. These unpaired nucleotides can be in either strand, creating either 3' or 5' overhangs. These overhangs are in most cases palindromic.

The simplest case of an overhang is a single nucleotide. This is most often adenosine and is created as a 3' overhang by some DNA polymerases. Most commonly this is used in cloning PCR products created by such an enzyme. The product is joined with a linear DNA molecule with 3' thymine overhangs. Since adenine and thymine form a base pair, this facilitates the joining of the two molecules by a ligase, yielding a circular molecule.

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Blunt ends may result from the breaking of double-stranded DNA; however, there are no overhangs or unpaired bases.

Longer overhangs are called cohesive ends or sticky ends. They are most often created by restriction endonucleases when they cut DNA. Very often they cut the two DNA strands four base pairs from each other, creating a four-base 5' overhang in one molecule and a complementary 5' overhang in the other. These ends are called cohesive since they are easily joined back together by a ligase.

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Blunt Ends : A straight cut, down through the DNA that results in a flat pair of bases on the ends of the DNA.

 Sticky Ends : Staggered ends on a DNA molecule with short, single-stranded overhangs.

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Blunt and sticky ends areresult of restriction endonuclease action on double stranded DNA.Sticky Ends – are staggered ends on a DNA molecule with short, single-stranded overhangs. Blunt Ends  are a straight cut, down through the DNA that results in a flat pair of bases on the ends of the DNA.