This article may require cleanup to meet Wikipedia's quality standards. Please discuss this issue on the talk page or replace this tag with a more specific message. This article has been tagged since January 2007.

DNA end refers to the properties of the end of a molecule of DNA. The concept is important in molecular biology, especially in cloning. All the terms can also be used in reference to RNA. Image File history File links Broom_icon. ... In science, a molecule is a group of atoms in a definite arrangement held together by chemical bonds. ... The structure of part of a DNA double helix Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. ... Molecular biology is the study of biology at a molecular level. ... Molecular cloning refers to the procedure of isolating a defined DNA sequence and obtaining multiple copies of it in vivo. ... This article or section does not adequately cite its references or sources. ...

Single-stranded DNA molecules

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. Deoxyribose Deoxyribose, also known as D-Deoxyribose and 2-deoxyribose, is an aldopentose — a monosaccharide containing five carbon atoms, and including an aldehyde functional group. ... Above is a ball-and-stick model of the inorganic hydrogenphosphate anion (HPO42−). Colour coding: P (orange); O (red); H (white). ...

Variations in double-stranded molecules

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.

Blunt ends

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. On the other hand, blunt ends are always compatible with each other. Here is an example of a small piece of blunt-ended DNA: Base pairs, of a DNA molecule. ... It has been suggested that sticky end/blunt end be merged into this article or section. ...

 5'-CTGATCTGACTGATGCGTATGCTAGT-3' 3'-GACTAGACTGACTACGCATACGATCA-5' 

Overhangs and sticky ends

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. A nucleotide is a chemical compound that consists of a heterocyclic base, a sugar, and one or more phosphate groups. ...

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 products is joined with a linear DNA molecule with 5' 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. Here is an example of a A-overhang: The chemical structure of adenosine Adenosine is a nucleoside comprised of adenine attached to a ribose (ribofuranose) moiety via a β-N9-glycosidic bond. ... 3D structure of the DNA-binding helix-hairpin-helix motifs in human DNA polymerase beta A DNA polymerase is an enzyme that assists in DNA replication. ... Wikipedia does not yet have an article with this exact name. ... For the similarly-spelled vitamin compound, see Thiamine Thymine, also known as 5-methyluracil, is a pyrimidine nucleobase. ... Base pairs, of a DNA molecule. ...

 5'-ATCTGACTA-3' 3'-TAGACTGA-5' 

Longer overhangs are called cohessive 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 3' overhang in the other molecule and a complementary 5' overhang in the other. These ends are called cohessive since they are easily joined back together by a ligase. Also, since different restriction endonucleases usually create different overhangs, it is possible cut a piece of DNA with two different enzymes and the join it with another DNA molecule with ends created by the same enzymes. Since the overhangs have to be complementary in order for the ligase to work, the two molecules can only join in one orientation. This is often highly desirable in molecular biology. A restriction enzyme (or restriction endonuclease) is an enzyme that cuts double-stranded DNA. The enzyme makes two incisions, one through each of the phosphate backbones of the double helix without damaging the bases. ... Molecular biology is the study of biology at a molecular level. ...

For example, these two "sticky" ends are compatible:

 5'-ATCTGACT + GATGCGTATGCT-3' 3'-TAGACTGACTACG CATACGA-5'  

They can form complementary base pairs in the overhang region:

  GATGCGTATGCT-3' 5'-ATCTGACT CATACGA-5' 3'-TAGACTGACTACG 

References