A retroviral RNA kissing complex containing only two G⋅C base pairs

A retroviral RNA kissing complex containing only two G⋅C base pairs

Chul-Hyun Kim and
Ignacio Tinoco, Jr.*

Department of Chemistry, University of California, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-1460

Contributed by Ignacio Tinoco, Jr.

Abstract

The dimerization of viral RNA through noncovalent interactions at their 5′ ends is a key step in the life cycle of retroviruses. In Moloney murine leukemia virus, three stem-loops are important in this process. One is a self-complementary tetraloop (H1), but the other two stem-loops (H2, H3) contain highly conserved GACG tetraloops that are not self-complementary sequences. Using two-dimensional NMR, we determined the structure of the H3 stem-loop. Surprisingly, it forms a stable, homodimeric kissing complex through only two intermolecular G⋅C base pairs. Cross-strand interactions of the adenines adjacent to the intermolecular G⋅C base pairs, plus unusual strong electrostatic interactions around the base pairs, contribute to the unexpected stability. This structure shows how even stem-loops without self-complementary sequences can facilitate the intermolecular recognition between two identical RNAs, and thus initiate dimerization and encapsidation of retroviral RNAs.

Footnotes

↵ * To whom reprint requests should be addressed. E-mail: INTinoco{at}lbl.gov.
Data deposition: The atomic coordinates of the H3–18 kissing complex have been deposited in the Protein Data Bank, www.rcsb.org (PDB ID code 1F5U).
Article published online before print: Proc. Natl. Acad. Sci. USA, 10.1073/pnas.170283697.
Article and publication date are at www.pnas.org/cgi/doi/10.1073/pnas.170283697
Abbreviations:

NOE,

nuclear Overhauser effect;

NOESY,

NOE spectroscopy;

HMQC,

heteronuclear multiple quantum correlation;

HSQC,

heteronuclear single quantum coherence;

1D,

one-dimensional;

2D,

two-dimensional;

COSY,

correlation spectroscopy;

DQF,

double quantum filtered;

rMD,

restrained molecular dynamics;

Tm,

melting temperature