Editing Nucleic acid sequence (section)

== Nucleotides ==
[[File:RNA chemical structure.GIF|thumb|Chemical structure of RNA]]
[[Image:RNA-codons.svg|thumb|A series of codons in part of a [[mRNA]] molecule. Each codon consists of three [[nucleotide]]s, usually representing a single [[amino acid]].]]
{{Main|Nucleotide}}

Nucleic acids consist of a chain of linked units called nucleotides. Each nucleotide consists of three subunits: a [[phosphate]] group and a [[sugar]] ([[ribose]] in the case of [[RNA]], [[deoxyribose]] in [[DNA]]) make up the backbone of the nucleic acid strand, and attached to the sugar is one of a set of [[nucleobase]]s. The nucleobases are important in [[base pair]]ing of strands to form higher-level [[Nucleic acid secondary structure|secondary]] and [[Nucleic acid tertiary structure|tertiary structures]] such as the famed [[Nucleic acid double helix|double helix]].

The possible letters are ''A'', ''C'', ''G'', and ''T'', representing the four [[nucleotide]] [[nucleobase|bases]] of a DNA strand – [[adenine]], [[cytosine]], [[guanine]], [[thymine]] – [[covalent]]ly linked to a [[phosphodiester bond|phosphodiester]] backbone. In the typical case, the sequences are printed abutting one another without gaps, as in the sequence AAAGTCTGAC, read left to right in the [[Directionality (molecular biology)|5' to 3']] direction. With regards to [[transcription (biology)|transcription]], a sequence is on the coding strand if it has the same order as the transcribed RNA.

One sequence can be [[Complementarity (molecular biology)|complementary]] to another sequence, meaning that they have the base on each position in the complementary (i.e., A to T, C to G) and in the reverse order. For example, the complementary sequence to TTAC is GTAA. If one strand of the double-stranded DNA is considered the sense strand, then the other strand, considered the antisense strand, will have the complementary sequence to the sense strand.

=== Notation ===
{{Main|Nucleic acid notation}}

While A, T, C, and G represent a particular nucleotide at a position, there are also letters that represent ambiguity which are used when more than one kind of nucleotide could occur at that position. The rules of the International Union of Pure and Applied Chemistry ([[IUPAC]]) are as follows:<ref name=":0">{{Cite journal |date=1986 |title=Nomenclature for incompletely specified bases in nucleic acid sequences. Recommendations 1984. Nomenclature Committee of the International Union of Biochemistry (NC-IUB). |journal=Proceedings of the National Academy of Sciences |language=en |volume=83 |issue=1 |pages=4–8 |doi=10.1073/pnas.83.1.4 |issn=0027-8424 |pmc=322779 |pmid=2417239 |doi-access=free}}</ref>

For example, '''W''' means that either an adenine or a thymine could occur in that position without impairing the sequence's functionality.

{| class="wikitable" style="margin-left:25px; margin-top:0px; text-align:center;"
|+List of symbols
! Symbol<ref name="iupac">{{Cite web |last=Nomenclature Committee of the International Union of Biochemistry (NC-IUB) |year=1984 |title=Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences |url=http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html |access-date=2008-02-04}}</ref> !! Meaning/derivation !!colspan=5| Possible bases|| Complement
|-
| '''A''' ||align=left| [[Adenine|'''A'''denine]] || A || || || ||rowspan=5| 1 || T (or U)
|-
| '''C''' ||align=left| [[Cytosine|'''C'''ytosine]] || || C || || || G
|-
| '''G''' ||align=left| [[Guanine|'''G'''uanine]] || || || G || || C
|-
| '''T''' ||align=left| [[Thymine|'''T'''hymine]] || || || || T  || A
|-
| '''U''' ||align=left| [[Uracil|'''U'''racil]] || || || || U || A
|- bgcolor=#e8e8e8
| '''W''' ||align=left| '''W'''eak || A || || || T ||rowspan=6| 2 || S
|- bgcolor=#e8e8e8
| '''S''' ||align=left| '''S'''trong || || C || G ||  || W
|- bgcolor=#e8e8e8
| '''M''' ||align=left| [[Amine|a'''M'''ino]] || A || C || || || K
|- bgcolor=#e8e8e8
| '''K''' ||align=left| [[Ketone|'''K'''eto]] || || || G || T  || M
|- bgcolor=#e8e8e8
| '''R''' ||align=left| [[Purine|pu'''R'''ine]] || A || || G ||  || Y
|- bgcolor=#e8e8e8
| '''Y''' ||align=left| [[Pyrimidine|p'''Y'''rimidine]] || || C || || T || R
|-
| '''B''' ||align=left|  not A ('''B''' comes after A) || || C || G || T  ||rowspan=4| 3 || V
|-
| '''D''' ||align=left|  not C ('''D''' comes after C) || A || || G || T || H
|-
| '''H''' ||align=left| not G ('''H''' comes after G)|| A || C || || T || D
|-
| '''V''' ||align=left| not T ('''V''' comes after T and U) || A || C || G || || B
|- bgcolor=#e8e8e8
| '''N''' ||align=left|  any '''N'''ucleotide (not a gap) || A || C || G || T || 4 || N
|-
|'''Z''' ||align=left| [[0|'''Z'''ero]] || || || ||  || 0 || Z
|}

These symbols are also valid for RNA, except with U (uracil) replacing T (thymine).<ref name=":0" />

Apart from adenine (A), cytosine (C), guanine (G), thymine (T) and uracil (U), DNA and RNA also contain bases that have been modified after the nucleic acid chain has been formed. In DNA, the most common modified base is [[5-Methylcytidine|5-methylcytidine]] (m5C). In RNA, there are many modified bases, including [[pseudouridine]] (Ψ), [[dihydrouridine]] (D), [[inosine]] (I), [[ribothymidine]] (rT) and [[7-methylguanosine]] (m7G).<ref>{{Cite web |title=BIOL2060: Translation |url=https://www.mun.ca/biology/desmid/brian/BIOL2060/BIOL2060-22/CB22.html |website=mun.ca}}</ref><ref>{{Cite web |title=Research |url=http://www.biogeo.uw.edu.pl/research/grupaC_en.html |website=uw.edu.pl}}</ref> [[Hypoxanthine]] and [[xanthine]] are two of the many bases created through [[mutagen]] presence, both of them through deamination (replacement of the amine-group with a carbonyl-group). Hypoxanthine is produced from [[adenine]], and xanthine is produced from [[guanine]].<ref>{{Cite journal |last=Nguyen |first=T |last2=Brunson |first2=D |last3=Crespi |first3=C L |last4=Penman |first4=B W |last5=Wishnok |first5=J S |last6=Tannenbaum |first6=S R |date=April 1992 |title=DNA damage and mutation in human cells exposed to nitric oxide in vitro |journal=Proc Natl Acad Sci USA |volume=89 |issue=7 |pages=3030–034 |bibcode=1992PNAS...89.3030N |doi=10.1073/pnas.89.7.3030 |pmc=48797 |pmid=1557408 |doi-access=free}}</ref> Similarly, deamination of [[cytosine]] results in [[uracil]].

;Example of comparing and determining the % difference between two nucleotide sequences
* AA'''T'''CC'''GC'''TAG
* AA'''A'''CC'''CT'''TAG

Given the two 10-nucleotide sequences, line them up and compare the differences between them. Calculate the percent difference by taking the number of differences between the DNA bases divided by the total number of nucleotides. In this case there are three differences in the 10 nucleotide sequence. Thus there is a 30% difference.