Primer binding site

HIV primer binding site (PBS)
	Predicted secondary structure and sequence conservation of HIV_PBS
Identifiers
Symbol	HIV_PBS
Rfam	RF00375
Other data
RNA type	Cis-reg
Domain(s)	Eukaryota; Viruses
SO	SO:0000233
PDB structures	PDBe

A primer binding site is a region of a nucleotide sequence where an RNA or DNA single-stranded primer binds to start replication. The primer binding site is on one of the two complementary strands of a double-stranded nucleotide polymer, in the strand which is to be copied, or is within a single-stranded nucleotide polymer sequence.[1]

A PCR primer binding site is a site where a polymerase chain reaction (PCR) primer binds, to prime duplication of a complement to an existing DNA or RNA sequence.

The HIV primer binding site is a structured RNA element in the genomes of retroviruses to which tRNA binds to initiate reverse transcription. In HIV, the tRNA is tRNA(3)(Lys)[2] although it can use other tRNAs.[3] It consists of 18 nucleotides and follows the U5 region of the 5'-long terminal repeat (LTR) of the retrovirus.[4]

References

Berg, Jeremy M.; Tymoczko, John L. & Stryer, Lubert. (c. 2002). "DNA Replication of Both Strands Proceeds Rapidly from Specific Start Sites". Biochemistry. New York: W. H. Freeman and Co.
Beerens, N; Groot F; Berkhout B (2001). "Initiation of HIV-1 reverse transcription is regulated by a primer activation signal". J Biol Chem. 276 (33): 31, 247–31, 256. doi:10.1074/jbc.M102441200. PMID 11384976.
Das, AT; Klaver B; Berkhout B (1995). "Reduced replication of human immunodeficiency virus type 1 mutants that use reverse transcription primers other than the natural tRNA(3)(Lys)". J Virol. 69 (5): 3, 090–3, 097. doi:10.1128/JVI.69.5.3090-3097.1995. PMC 189010. PMID 7707537.
Damgaard CK, Andersen ES, Knudsen B, Gorodkin J, Kjems J (2004). "RNA interactions in the 5' region of the HIV-1 genome". J Mol Biol. 336 (2): 369–379. doi:10.1016/j.jmb.2003.12.010. PMID 14757051.

External links

Page for HIV primer binding site (PBS) at Rfam

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[1] Berg, Jeremy M.; Tymoczko, John L. & Stryer, Lubert. (c. 2002). "DNA Replication of Both Strands Proceeds Rapidly from Specific Start Sites". Biochemistry. New York: W. H. Freeman and Co.

[2] Beerens, N; Groot F; Berkhout B (2001). "Initiation of HIV-1 reverse transcription is regulated by a primer activation signal". J Biol Chem. 276 (33): 31, 247–31, 256. doi:10.1074/jbc.M102441200. PMID 11384976.

[3] Das, AT; Klaver B; Berkhout B (1995). "Reduced replication of human immunodeficiency virus type 1 mutants that use reverse transcription primers other than the natural tRNA(3)(Lys)". J Virol. 69 (5): 3, 090–3, 097. doi:10.1128/JVI.69.5.3090-3097.1995. PMC 189010. PMID 7707537.

[pmid14757051-4] Damgaard CK, Andersen ES, Knudsen B, Gorodkin J, Kjems J (2004). "RNA interactions in the 5' region of the HIV-1 genome". J Mol Biol. 336 (2): 369–379. doi:10.1016/j.jmb.2003.12.010. PMID 14757051.