Editing Reading frame

{{Short description|A specific grouping of the "letters" of a genetic sequence into threes}}<!-- "A" included for clarity: grouping as a result not a process --> 
[[File:Reading Frame.png|thumb|400px|An example of three possible forward reading frames for a strand of DNA.

<div align="center"><span style="color:steelblue;">'''AGG·TGA·CAC·CGC·AAG·CCT·TAT·ATT·AGC'''</span><br />A'''<span style="color:red;">·GGT·GAC·ACC·GCA·AGC·CTT·ATA·TTA</span>'''·GC<br />AG<span style="color:green;">'''·GTG·ACA·CCG·CAA·GCC·TTA·TAT·TAG·'''</span>C</div>]]
In [[molecular biology]], a '''reading frame''' is a specific choice out of the possible ways to read the [[nucleic acid sequence|sequence of nucleotides]] in a [[nucleic acid]] ([[DNA]] or [[RNA]]) molecule as a sequence of triplets. Where these triplets equate to [[amino acid]]s or stop signals during [[Translation (biology)|translation]], they are called [[codon]]s.

A single strand of a [[nucleic acid]] molecule has a [[phosphoryl]] end, called the [[5′-end]], and a [[hydroxyl]] or [[3′-end]]. These define the [[Directionality (molecular biology)|5′→3′ direction]]. There are three reading frames that can be read in this 5′→3′ direction, each beginning from a different nucleotide in a triplet. In a double stranded nucleic acid, an additional three reading frames may be read from the other, [[Complementarity (molecular biology)|complementary]] strand in the 5′→3′ direction along this strand. As the two strands of a double-stranded nucleic acid molecule are antiparallel, the 5′→3′ direction on the second strand corresponds to the 3′→5′ direction along the first strand.<ref>{{cite journal |title=Quantitative sequence and open reading frame analysis based on codon bias |journal=Systemics, Cybernetics and Informatics |volume=4 |issue=1 |pages=65–72 |vauthors=Rainey S, Repka J |url=http://www.iiisci.org/Journal/CV$/sci/pdfs/P842315.pdf }}</ref><ref name=pmid10331277>{{cite journal|title=CRITICA: Coding Region Identification Tool Invoking Comparative Analysis |vauthors=Badger JH, Olsen GJ |journal=Mol Biol Evol |date=April 1999 |volume=16 |issue=4 |pages=512–24 |pmid=10331277 |doi=10.1093/oxfordjournals.molbev.a026133|doi-access=free }}</ref>

In general, at the most, one reading frame in a given section of a nucleic acid, is biologically relevant ([[open reading frame]]). Some viral transcripts can be translated using multiple, overlapping reading frames. There is one known example of overlapping reading frames in mammalian [[mitochondrial DNA]]: coding portions of genes for 2 subunits of ATPase overlap.

[[File:Open reading frame.jpg|thumbnail|right|An example of a section of DNA translated by a computer in all six possible reading frames. The Open Reading Frames (ORFs) for Gene 1 and 2 are highlighted]]

== Genetic code ==
{{Main|Genetic code}}DNA encodes protein sequence by a series of three-nucleotide [[codon]]s. Any given sequence of DNA can therefore be read in six different ways: Three reading frames in one direction (starting at different nucleotides) and three in the opposite direction. During [[Transcription (biology)|transcription]], the RNA polymerase read the template DNA strand in the 3′→5′ direction, but the mRNA is formed in the 5′ to 3′ direction.<ref>{{cite book |title = Molecular Cell Biology |edition = 6th |last = Lodish |year = 2007 |publisher = W. H. Freeman |isbn = 978-1429203142 |page = 121 }}</ref> The mRNA is single-stranded and therefore only contains three possible reading frames, of which only one is [[Translation (biology)|translated]]. The codons of the mRNA reading frame are translated in the 5′→3′ direction into [[amino acids]] by a [[ribosome]] to produce a [[polypeptide|polypeptide chain]].

==Open reading frame==
{{main|Open reading frame}}
An [[open reading frame]] (ORF) is a reading frame that has the potential to be [[Transcription (genetics)|transcribed]] into RNA and [[Translation (biology)|translated]] into protein. It requires a continuous sequence of DNA which may include a [[start codon]], through a subsequent region which has a length that is a multiple of 3 nucleotides, to a [[stop codon]] in the same reading frame.<ref name="pierce2012b12">{{cite book | author = Benjamin C. Pierce |title = Genetics: a conceptual approach | publisher = [[W. H. Freeman]] | year = 2012 | isbn = 9781429232500 | ref = pierce2012}}</ref>

When a putative amino acid sequence resulting from the translation of an ORF remained unknown in mitochondrial and chloroplast genomes, the corresponding open reading frame was called an unidentified reading frame (URF). For example, the [[MT-ATP8]] gene was first described as URF A6L when the complete human [[mitochondrial genome]] was sequenced.<ref name="pmid7219534">{{cite journal |vauthors=Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG | title = Sequence and organization of the human mitochondrial genome | journal = Nature | volume = 290 | issue = 5806 | pages = 457–65 |date=April 1981 | pmid = 7219534 | doi = 10.1038/290457a0| bibcode = 1981Natur.290..457A | s2cid = 4355527 }}</ref>

==Multiple reading frames==
[[File:Homo sapiens-mtDNA~NC 012920-ATP8+ATP6 Overlap.svg|thumb|300px|The two reading frames used by the human mitochondrial genes ''MT-ATP8'' and ''MT-ATP6''.]]

The usage of multiple reading frames leads to the possibility of [[overlapping gene]]s; there may be many of these in viral, prokaryote, and mitochondrial [[genome]]s.<ref name=Johnson_2004>{{cite journal |vauthors=Johnson Z, Chisholm S | title = Properties of overlapping genes are conserved across microbial genomes | journal = Genome Res | volume = 14 | issue = 11 | pages = 2268–72 | year = 2004 | pmid = 15520290 | doi = 10.1101/gr.2433104 | pmc = 525685}}</ref> Some viruses, e.g. [[hepatitis B virus]] and [[BYDV]], use several overlapping genes in different reading frames.

In rare cases, a ribosome may shift from one frame to another during translation of an mRNA ([[translational frameshift]]). This causes the first part of the mRNA to be translated in one reading frame, and the latter part to be translated in a different reading frame. This is distinct from a [[frameshift mutation]], as the nucleotide sequence (DNA or RNA) is not altered—only the frame in which it is read.

==See also==
* [[Genetic code]]
* [[Directionality (molecular biology)]]
* [[Sense (molecular biology)]]

==References==
<references />

{{GeneticTranslation}}

{{DEFAULTSORT:Reading Frame}}
[[Category:Protein biosynthesis]]
[[Category:Genetics]]
[[Category:Molecular biology]]