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=                             Base pair                              =
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                            Introduction
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A base pair (bp) is a unit consisting of two nucleobases bound to each
other by hydrogen bonds.  They form the building blocks of the DNA
double helix and contribute to the folded structure of both DNA and
RNA. Dictated by specific hydrogen bonding patterns, Watson-Crick base
pairs (guanine-cytosine and adenine-thymine) allow the DNA helix to
maintain a regular helical structure that is subtly dependent on its
nucleotide sequence. The complementary nature of this based-paired
structure provides a redundant copy of the genetic information encoded
within each strand of DNA. The regular structure and data redundancy
provided by the DNA double helix make DNA well suited to the storage
of genetic information, while base-pairing between DNA and incoming
nucleotides provides the mechanism through which DNA polymerase
replicates DNA and RNA polymerase transcribes DNA into RNA. Many
DNA-binding proteins can recognize specific base-pairing patterns that
identify particular regulatory regions of genes.

Intramolecular base pairs can occur within single-stranded nucleic
acids. This is particularly important in RNA molecules (e.g., transfer
RNA), where Watson-Crick base pairs (guanine-cytosine and
adenine-uracil) permit the formation of short double-stranded helices,
and a wide variety of non-Watson-Crick interactions (e.g., G-U or A-A)
allow RNAs to fold into a vast range of specific three-dimensional
structures. In addition, base-pairing between transfer RNA (tRNA) and
messenger RNA (mRNA) forms the basis for the molecular recognition
events that result in the nucleotide sequence of mRNA becoming
translated into the amino acid sequence of proteins via the genetic
code.

The size of an individual gene or an organism's entire genome is often
measured in base pairs because DNA is usually double-stranded. Hence,
the number of total base pairs is equal to the number of nucleotides
in one of the strands (with the exception of non-coding
single-stranded regions of telomeres). The haploid human genome (23
chromosomes) is estimated to be about 3.2 billion bases long and to
contain 20,000-25,000 distinct protein-coding genes. A kilobase (kb)
is a unit of measurement in molecular biology equal to 1000 base pairs
of DNA or RNA. The total amount of related DNA base pairs on Earth is
estimated at 5.0 and weighs 50 billion tonnes. In comparison, the
total mass of the biosphere has been estimated to be as much as 4 TtC
(trillion tons of carbon).


                   Hydrogen bonding and stability
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|282px
|282px
Top, a G.C base pair with three hydrogen bonds. Bottom, an A.T base
pair with two hydrogen bonds. Non-covalent hydrogen bonds between the
bases are shown as dashed lines. The wiggly lines stand for the
connection to the pentose sugar and point in the direction of the
minor groove.

Hydrogen bonding is the chemical interaction that underlies the
base-pairing rules described above. Appropriate geometrical
correspondence of hydrogen bond donors and acceptors allows only the
"right" pairs to form stably. DNA with high GC-content is more stable
than DNA with low GC-content. But, contrary to popular belief, the
hydrogen bonds do not stabilize the DNA significantly; stabilization
is mainly due to stacking interactions.

The smaller nucleobases, adenine and guanine, are members of a class
of double-ringed chemical structures called purines; the smaller
nucleobases, cytosine and thymine (and uracil), are members of a class
of single-ringed chemical structures called pyrimidines. Purines are
complementary only with pyrimidines: pyrimidine-pyrimidine pairings
are energetically unfavorable because the molecules are too far apart
for hydrogen bonding to be established; purine-purine pairings are
energetically unfavorable because the molecules are too close, leading
to overlap repulsion. Purine-pyrimidine base-pairing of AT or GC or UA
(in RNA) results in proper duplex structure. The only other
purine-pyrimidine pairings would be AC and GT and UG (in RNA); these
pairings are mismatches because the patterns of hydrogen donors and
acceptors do not correspond. The GU pairing, with two hydrogen bonds,
does occur fairly often in RNA (see wobble base pair).

Paired DNA and RNA molecules are comparatively stable at room
temperature, but the two nucleotide strands will separate above a
melting point that is determined by the length of the molecules, the
extent of mispairing (if any), and the GC content. Higher GC content
results in higher melting temperatures; it is, therefore, unsurprising
that the genomes of extremophile organisms such as 'Thermus
thermophilus' are particularly GC-rich. On the converse, regions of a
genome that need to separate frequently � for example, the promoter
regions for often-transcribed genes � are comparatively GC-poor (for
example, see TATA box). GC content and melting temperature must also
be taken into account when designing  primers for PCR reactions.


Examples
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The following DNA sequences illustrate pair double-stranded patterns.
By convention, the top strand is written from the 5' end to the 3'
end; thus, the bottom strand is written 3' to 5'.

:A base-paired DNA sequence:
::
::

:The corresponding RNA sequence, in which uracil is substituted for
thymine in the RNA strand:
::
::


                   Base analogs and intercalators
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Chemical analogs of nucleotides can take the place of proper
nucleotides and establish non-canonical base-pairing, leading to
errors (mostly point mutations) in DNA replication and DNA
transcription. This is due to their isosteric chemistry. One common
mutagenic base analog is 5-bromouracil, which resembles thymine but
can base-pair to guanine in its enol form.

Other chemicals, known as DNA intercalators, fit into the gap between
adjacent bases on a single strand and induce frameshift mutations by
"masquerading" as a base, causing the DNA replication machinery to
skip or insert additional nucleotides at the intercalated site. Most
intercalators are large polyaromatic compounds and are known or
suspected carcinogens. Examples include ethidium bromide and acridine.


                     Unnatural base pair (UBP)
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An unnatural base pair (UBP) is a designed subunit (or nucleobase) of
DNA which is created in a laboratory and does not occur in nature.
DNA sequences have been described which use newly created nucleobases
to form a third base pair, in addition to the two base pairs found in
nature, A-T (adenine - thymine) and G-C (guanine - cytosine).  A few
research groups have been searching for a third base pair for DNA,
including teams led by Steven A. Benner, Philippe Marliere, Floyd
Romesberg and Ichiro Hirao. Some new base pairs have been reported.

In 1989 Steven Benner (then working at the Swiss Federal Institute of
Technology in Zurich) and his team led with modified forms of cytosine
and guanine into DNA molecules 'in vitro'. The nucleotides, which
encoded RNA and proteins, were successfully replicated 'in vitro'.
Since then, Benner's team has been trying to engineer cells that can
make foreign bases from scratch, obviating the need for a feedstock.

In 2002, Ichiro Hirao's group in Japan developed an unnatural base
pair between 2-amino-8-(2-thienyl)purine (s) and pyridine-2-one (y)
that functions in transcription and translation, for the site-specific
incorporation of non-standard amino acids into proteins. In 2006, they
created 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and
pyrrole-2-carbaldehyde (Pa) as a third base pair for replication and
transcription. Afterward, Ds and
4-[3-(6-aminohexanamido)-1-propynyl]-2-nitropyrrole (Px) was
discovered as a high fidelity pair in PCR amplification. In 2013, they
applied the Ds-Px pair to DNA aptamer generation by 'in vitro'
selection (SELEX) and demonstrated the genetic alphabet expansion
significantly augment DNA aptamer affinities to target proteins.

In 2012, a group of American scientists led by Floyd Romesberg, a
chemical biologist at the Scripps Research Institute in San Diego,
California, published that his team designed an unnatural base pair
(UBP).  The two new artificial nucleotides or 'Unnatural Base Pair'
(UBP) were named d5SICS and dNaM. More technically, these artificial
nucleotides bearing hydrophobic nucleobases, feature two fused
aromatic rings that form a (d5SICS-dNaM) complex or base pair in DNA.
His team designed a variety of 'in vitro' or "test tube" templates
containing the unnatural base pair and they confirmed that it was
efficiently replicated with high fidelity in virtually all sequence
contexts using the modern standard 'in vitro' techniques, namely PCR
amplification of DNA and PCR-based applications. Their results show
that for PCR and PCR-based applications, the d5SICS-dNaM unnatural
base pair is functionally equivalent to a natural base pair, and when
combined with the other two natural base pairs used by all organisms,
A-T and G-C, they provide a fully functional and expanded six-letter
"genetic alphabet".

In 2014 the same team from the Scripps Research Institute reported
that they synthesized a stretch of circular DNA known as a plasmid
containing natural T-A and C-G base pairs along with the
best-performing UBP Romesberg's laboratory had designed and inserted
it into cells of the common bacterium 'E. coli' that successfully
replicated the unnatural base pairs through multiple generations. The
transfection did not hamper the growth of the 'E. coli' cells and
showed no sign of losing its unnatural base pairs to its natural DNA
repair mechanisms. This is the first known example of a living
organism passing along an expanded genetic code to subsequent
generations. Romesberg said he and his colleagues created 300 variants
to refine the design of nucleotides that would be stable enough and
would be replicated as easily as the natural ones when the cells
divide.  This was in part achieved by the addition of a supportive
algal gene that expresses a nucleotide triphosphate transporter which
efficiently imports the triphosphates of both d5SICSTP and dNaMTP into
'E. coli' bacteria. Then, the natural bacterial replication pathways
use them to accurately replicate a plasmid containing d5SICS-dNaM.
Other researchers were surprised that the bacteria replicated these
human-made DNA subunits.

The successful incorporation of a third base pair is a significant
breakthrough toward the goal of greatly expanding the number of amino
acids which can be encoded by DNA, from the existing 20 amino acids to
a theoretically possible 172, thereby expanding the potential for
living organisms to produce novel proteins. The artificial strings of
DNA do not encode for anything yet, but scientists speculate they
could be designed to manufacture new proteins which could have
industrial or pharmaceutical uses. Experts said the synthetic DNA
incorporating the unnatural base pair raises the possibility of life
forms based on a different DNA code.


                        Length measurements
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The following abbreviations are commonly used to describe the length
of a D/RNA molecule:
* bp  = base pair(s)�one bp corresponds to approximately 3.4 �
(340
pm)  of length along the strand, and to roughly 618 or 643 daltons for
DNA and RNA respectively.
* kb (= kbp) = kilo base pairs = 1,000 bp
* Mb (= Mbp) = mega base pairs = 1,000,000 bp
* Gb = giga base pairs = 1,000,000,000 bp.

For single-stranded DNA/RNA, units of nucleotides are used�abbreviated
nt (or knt, Mnt, Gnt)�as they are not paired.
To distinguish between units of computer storage and bases, kbp, Mbp,
Gbp, etc. may be used for base pairs.

The centimorgan is also often used to imply distance along a
chromosome, but the number of base pairs it corresponds to varies
widely. In the Human genome, the centimorgan is about 1 million base
pairs.


                              See also
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* List of Y-DNA single-nucleotide polymorphisms
* Non-canonical base pairing


                          Further reading
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*  (See esp. ch. 6 and 9)
*
*
*


                           External links
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*
[https://web.archive.org/web/20060624093746/http://bioweb.pasteur.fr/seqanal/int
erfaces/dan.html
DAN]�webserver version of the EMBOSS tool for calculating melting
temperatures


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