Skip to main content
U.S. flag

An official website of the United States government

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

Dissecting Structural Transitions in the HIV-1 Dimerization Initiation Site RNA using 2-aminopurine fluorescence



Hui-wen Lee, Katharine T. Briggs, John Marino


A highly conserved 35 nucleotide RNA stem-loop, the dimerization initiation site (DIS), in the 5 untranslated region (UTR) of the human immunodeficiency virus type I (HIV-1) genome has been identified as the sequence primarily responsible for initiation of viral genome dimerization. The DIS initiates viral genome dimerization through a loop-loop kissing interaction and is converted from an intermediate kissing to a more thermodynamically stable extended duplex dimer in a conformational rearrangement that is chaperoned by the HIV-1 nucleocapsid protein (NCp7). Here we describe fluorescence methods designed to probe local RNA dynamics and structural transitions associated with the DIS dimer formation and its NCp7 chaperoned structural conversion. These methods take advantage of the exquisite sensitivity of the quantum yield of the fluorescent nucleotide base analog, 2-aminopurine (2-AP), to its immediate structural and dynamic environment. The 2-AP fluorescence methods described allow a detailed kinetic and thermodynamic examination of this type of RNA-RNA interaction, as well as an analysis of the molecular mechanism of NCp7 chaperone activity.


HIV-1, dimerization initiation site (DIS), viral genome dimerization, RNA-RNA kissing interaction, folding kinetics, 2-aminopurine fluorescence.


Lee, H. , Briggs, K. and Marino, J. (2009), Dissecting Structural Transitions in the HIV-1 Dimerization Initiation Site RNA using 2-aminopurine fluorescence, Methods, [online], (Accessed June 14, 2024)


If you have any questions about this publication or are having problems accessing it, please contact

Created September 30, 2009, Updated October 12, 2021