Nucleic Acids Research Advance Access originally published online on March 26, 2009
Nucleic Acids Research 2009 37(10):3342-3353; doi:10.1093/nar/gkp187
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Nucleic Acids Research, 2009, Vol. 37, No. 10 3342-3353
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs
1Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, 2Department Plant Pathology, North Carolina State University, Raleigh, NC 27695-7616, USA, 3Institute of Organic Chemistry, Technical University, 
odz 90-924, Poland and 4Department of Organic Chemistry, Faculty of Chemistry, University of Barcelona, Barcelona 08028, Spain
*To whom correspondence should be addressed. Tel: +1 919 515 6188; Fax: +1 919 515 2047; Email: paul_agris{at}ncsu.edu
Received December 10, 2008. Revised March 5, 2009. Accepted March 6, 2009.
Replication of human immunodeficiency virus (HIV) requires base pairing of the reverse transcriptase primer, human tRNALys3, to the viral RNA. Although the major complementary base pairing occurs between the HIV primer binding sequence (PBS) and the tRNA's 3'-terminus, an important discriminatory, secondary contact occurs between the viral A-rich Loop I, 5'-adjacent to the PBS, and the modified, U-rich anticodon domain of tRNALys3. 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, s2U34, and pseudouridine, 
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, U162•39 and G163•A38, that maintained a reasonable A-form helix diameter. The tRNA's s2U34 stabilized the interaction between the A-rich HIV Loop I sequence and the U-rich anticodon, whereas the tRNA's 39 stabilized the adjacent mismatched pairs.