In molecular biology, a reading frame is a way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets. Where these triplets equate to amino acids or stop signals during translation, they are called codons.
A single strand of a nucleic acid molecule has a phosphoryl end, (called the 5′-end) and a hydroxyl, or (3′-end). These then define the 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, 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.
In transcription, a template DNA strand is transcribed in the 3'→5' direction, beginning at the promoter region, by an RNA polymerase, which separates the strands of double-stranded DNA. RNA polymerase attaches nucleotides and builds the primary RNA transcript in the 5'→3' direction, antiparallel to the template DNA strand.
In translation, a mature mRNA strand is translated in the 5'→3' direction by a ribosome to produce a polypeptide chain. Reading frames in the 3'→5' direction on the mRNA strand may be disregarded during translation. There are therefore three possible reading frames for an mRNA strand that can be used during translation, although usually only one reading frame is used. Each reading frame corresponds to a different starting nucleotide.
Multiple reading frames
The usage of multiple reading frames leads to the possibility of overlapping genes; there may be many of these in virus, prokaryote, and mitochondrial genomes. Some viruses, e.g. Hepatitis B virus and BYDV, use several overlapping genes in different reading frames.
In rare cases, a translating ribosome may shift from one frame to another, a translational frameshift. 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.
Open reading frame
An open reading frame (ORF) is a continuous sequence of DNA that contains a start codon, a subsequent region which usually has a length which is a multiple of 3 nucleotides, and a stop codon in the same reading frame.
- Rainey S, Repka J. "Quantitative sequence and open reading frame analysis based on codon bias". Systemics, Cybernetics and Informatics 4 (1): 65–72.
- Badger JH, Olsen GJ (April 1999). "CRITICA: Coding Region Identification Tool Invoking Comparative Analysis". Mol Biol Evol 16 (4): 512–24. doi:10.1093/oxfordjournals.molbev.a026133. PMID 10331277.
- Lander, Eric. "MITx 7.00x Biology".
- Lodish (2007). Molecular Cell Biology (6th ed.). W. H. Freeman. p. 121. ISBN 1429203145.
- Johnson Z, Chisholm S (2004). "Properties of overlapping genes are conserved across microbial genomes". Genome Res 14 (11): 2268–72. doi:10.1101/gr.2433104. PMC 525685. PMID 15520290.
- Benjamin C. Pierce (2012). Genetics: a conceptual approach. W. H. Freeman. ISBN 9781429232500.