The structure of the human tRNA[sup]Lys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs

• Published in: Nucleic acids research Vol. 37; no. 10; p. 3342
• Main Authors: Bilbille, Yann, Vendeix, Franck A P, Guenther, Richard, Malkiewicz, Andrzej, Ariza, Xavier, Vilarrasa, Jaume, Agris, Paul F
• Format: Journal Article
• Language: English
• Published: Oxford Oxford Publishing Limited (England) 01.06.2009
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkp187

Replication of human immunodeficiency virus (HIV) requires base pairing of the reverse transcriptase primer, human tRNA[sup]Lys3, to the viral RNA. Although the major complementary base pairing occurs between the HIV primer binding sequence (PBS) and the tRNA's 3[variant prime]-terminus, an important discriminatory, secondary contact occurs between the viral A-rich Loop I, 5[variant prime]-adjacent to the PBS, and the modified, U-rich anticodon domain of tRNA[sup]Lys3. The importance of individual and combined anticodon modifications to the tRNA/HIV-1 Loop I RNA's interaction was determined. The thermal stabilities of variously modified tRNA anticodon region sequences bound to the Loop I of viral sub(sero)types G and B were analyzed and the structure of one duplex containing two modified nucleosides was determined using NMR spectroscopy and restrained molecular dynamics. The modifications 2-thiouridine, s[sup]2U[sub]34, and pseudouridine, Ψ[sub]39, appreciably stabilized the interaction of the anticodon region with the viral subtype G and B RNAs. The structure of the duplex results in two coaxially stacked A-form RNA stems separated by two mismatched base pairs, U[sub]162*Ψ[sub]39 and G[sub]163*A[sub]38, that maintained a reasonable A-form helix diameter. The tRNA's s[sup]2U[sub]34 stabilized the interaction between the A-rich HIV Loop I sequence and the U-rich anticodon, whereas the tRNA's Ψ[sub]39 stabilized the adjacent mismatched pairs.