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Nucleic acids

A nucleic acid is a macromolecule composed of chains of monomeric nucleotides. In biochemistry these


molecules carry genetic information or form structures within cells. The most common nucleic acids are
deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are universal in living things, as they
are found in all cells and viruses. Nucleic acids were first discovered by Friedrich Miescher.

Artificial nucleic acids include peptide nucleic acid (PNA), Morpholino and locked nucleic acid (LNA),
as well as glycol nucleic acid (GNA) and threose nucleic acid (TNA). Each of these is distinguished from
naturally-occurring DNA or RNA by changes to the backbone of the molecule

The term "nucleic acid" is the generic name for a family of biopolymers, named for their role in the cell
nucleus. The monomers from which nucleic acids are constructed are called nucleotides.

Each nucleotide consists of three components: a nitrogenous heterocyclic base, which is either a purine or a
pyrimidine; a pentose sugar; and a phosphate group. Nucleic acid types differ in the structure of the sugar in their
nucleotides - DNA contains 2-deoxyriboses while RNA contains ribose (where the only difference is the presence
of a hydroxyl group). Also, the nitrogenous bases found in the two nucleic acid types are different: adenine,
cytosine, and guanine are found in both RNA and DNA, while thymine only occurs in DNA and uracil only occurs
in RNA. Other rare nucleic acid bases can occur, for example inosine in strands of mature transfer RNA.

Nucleic acids are usually either single-stranded or double-stranded, though structures with three or more
strands can form. A double-stranded nucleic acid consists of two single-stranded nucleic acids held together by
hydrogen bonds, such as in the DNA double helix. In contrast, RNA is usually single-stranded, but any given strand
may fold back upon itself to form secondary structure as in tRNA and rRNA. Within cells, DNA is usually double-
stranded, though some viruses have single-stranded DNA as their genome. Retroviruses have single-stranded RNA
as their genome.

The sugars and phosphates in nucleic acids are connected to each other in an alternating chain, linked by
shared oxygens, forming a phosphodiester bond. In conventional nomenclature, the carbons to which the phosphate
groups attach are the 3' end and the 5' end carbons of the sugar. This gives nucleic acids polarity. The bases extend
from a glycosidic linkage to the 1' carbon of the pentose sugar ring. Bases are joined through N-1 of pyrimidines
and N-9 of purines to 1' carbon of ribose through N-β glycosyl bond.

Nucleosides are glycosylamines consisting of a nucleobase (often referred to simply base) bound to a
ribose or deoxyribose sugar. Examples of these include cytidine, uridine, adenosine, guanosine, thymidine and
inosine.

Nucleosides can be phosphorylated by specific kinases in the cell on the sugar's primary alcohol group (-CH2−OH),
producing nucleotides, which are the molecular building blocks of DNA and RNA.

Nucleosides can be produced by de novo synthesis pathways, particularly in the liver; but they are more abundantly
supplied via ingestion and digestion of nucleic acids in the diet, whereby nucleotidases break down nucleotides
(such as the thymine nucleotide) into nucleosides (such as thymidine) and phosphate. The nucleosides, in turn, are
subsequently broken down:

• in the lumen of the digestive system by nucleosidases into nucleobases and ribose deoxyribose)
• inside the cell by nucleoside phosphorylases into nitrogenous bases, and ribose-1-phosphate or
deoxyribose-1-phosphate.

In medicine several nucleoside analogues are used as antiviral or anticancer agents. The viral polymerase
incorporates these compounds with non-canon bases. These compounds are activated in the cells by being
converted into nucleotides, they are administered as nuclosides since charged nucleotides cannot easily cross cell
membranes.
In molecular biology several analogues of the sugar back bone exist. Due to the low stability of RNA, which is
prone to hydrolysis, several more stable alternative nucleoside/nucleotide analogues are used which correctly bind
to RNA. This is achieved by using a different backbone sugar. These analogues include LNA, morpholino, PNA.

In sequencing dideoxynucleotides are used. These nucleotides possess a non-canon sugar, dideoxyribose which
lacks 3' hydroxyl group (which accepts the phosphate) and therefore cannot bond with the next base, terminating
the chain as DNA polymerases mistake it for a regular deoxyribonucleotide.

Nucleotides are organic compounds that consist of three joined structures: a nitrogenous base, a sugar, and
a phosphate group. The most common nucleotides can be divided into two groups (purines and pyrimidines) based
on the structure of the nitrogenous base. The joined sugar is either ribose or deoxyribose.

Nucleotides are the structural units of RNA and DNA. They also serve as important cofactors in cellular signaling
and metabolism. These cofactors include CoA, flavin adenine dinucleotide, flavin mononucleotide, adenosine
triphosphate and nicotinamide adenine dinucleotide phosphate.

Ribonucleic acid (RNA) is a nucleic acid and consists of a long chain of nucleotide units. Each nucleotide
consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA is very similar to DNA, but differs in a few
important structural details: in the cell, RNA is usually single-stranded, while DNA is usually double-stranded;
RNA nucleotides contain ribose while DNA contains deoxyribose (a type of ribose that lacks one oxygen atom);
and RNA has the base uracil rather than thymine that is present in DNA.

RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other
enzymes. RNA is central to the synthesis of proteins. Here, a type of RNA called messenger RNA carries
information from DNA to structures called ribosomes. These ribosomes are made from proteins and ribosomal
RNAs, which come together to form a molecular machine that can read messenger RNAs and translate the
information they carry into proteins. There are RNAs with other roles – in particular regulating which genes are
expressed, but also as the genome of most viruses.

Structure

Watson-Crick base pairs in a siRNA (hydrogen atoms are not shown)

Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1'
position, generally adenine (A), cytosine (C), guanine (G) or uracil (U). Adenine and guanine are purines, cytosine
and uracil are pyrimidines. A phosphate group is attached to the 3' position of one ribose and the 5' position of the
next. The phosphate groups have a negative charge each at physiological pH, making RNA a charged molecule
(polyanion). The bases may form hydrogen bonds between cytosine and guanine, between adenine and uracil and
between guanine and uracil. However other interactions are possible, such as a group of adenine bases binding to
each other in a bulge, or the GNRA tetraloop that has a guanine–adenine base-pair.
Chemical structure of RNA

An important structural feature of RNA that distinguishes it from DNA is the presence of a hydroxyl group at the 2'
position of the ribose sugar. The presence of this functional group causes the helix to adopt the A-form geometry
rather than the B-form most commonly observed in DNA. This results in a very deep and narrow major groove and
a shallow and wide minor groove. A second consequence of the presence of the 2'-hydroxyl group is that in
conformationally flexible regions of an RNA molecule (that is, not involved in formation of a double helix), it can
chemically attack the adjacent phosphodiester bond to cleave the backbone.

RNA is transcribed with only four bases (adenine, cytosine, guanine and uracil), but there are numerous modified
bases and sugars in mature RNAs. Pseudouridine (Ψ), in which the linkage between uracil and ribose is changed
from a C–N bond to a C–C bond, and ribothymidine (T), are found in various places (most notably in the TΨC loop
of tRNA). Another notable modified base is hypoxanthine, a deaminated adenine base whose nucleoside is called
inosine. Inosine plays a key role in the wobble hypothesis of the genetic code. There are nearly 100 other naturally
occurring modified nucleosides, of which pseudouridine and nucleosides with 2'-O-methylribose are the most
common. The specific roles of many of these modifications in RNA are not fully understood. However, it is notable
that in ribosomal RNA, many of the post-transcriptional modifications occur in highly functional regions, such as
the peptidyl transferase center and the subunit interface, implying that they are important for normal function.

The functional form of single stranded RNA molecules, just like proteins, frequently requires a specific tertiary
structure. The scaffold for this structure is provided by secondary structural elements which are hydrogen bonds
within the molecule. This leads to several recognizable "domains" of secondary structure like hairpin loops, bulges
and internal loops. Since RNA is charged, metal ions such as Mg2+ are needed to stabilise many secondary
structures.

Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in the
development and functioning of all known living organisms and some viruses. The main role of DNA molecules is
the long-term storage of information. DNA is often compared to a set of blueprints or a recipe, or a code, since it
contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The
DNA segments that carry this genetic information are called genes, but other DNA sequences have structural
purposes, or are involved in regulating the use of this genetic information.

Chemically, DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars
and phosphate groups joined by ester bonds. These two strands run in opposite directions to each other and are
therefore anti-parallel. Attached to each sugar is one of four types of molecules called bases. It is the sequence of
these four bases along the backbone that encodes information. This information is read using the genetic code,
which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into
the related nucleic acid RNA, in a process called transcription.Within cells, DNA is organized into structures called
chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication.
Eukaryotic organisms (animals, plants, fungi, and protists) store their DNA inside the cell nucleus, while in
prokaryotes (bacteria and archae) it is found in the cell's cytoplasm. Within the chromosomes, chromatin proteins
such as histones compact and organize DNA. These compact structures guide the interactions between DNA and
other proteins, helping control which parts of the DNA are transcribed.