Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference.
Through binding and fluorescence studies of oligonucleotides covalently attached to a pyrene group via one carbon linker at the sugar residue, we previously found that pyrene-modified RNA oligonucleotides do not emit well in the single-stranded form, yet the attached pyrene emits with a significantly high quantum yield upon binding to a complementary RNA strand. In sharp contrast, similarly modified pyrene-DNA probes exhibit very weak fluorescence both in the double-stranded and single-stranded forms. The pyrene-modified RNA oligonucleotides therefore provide a useful tool for monitoring RNA hybridization. The purpose of this paper is to present the structural basis for the different fluorescence properties of pyrene-modified RNA/RNA and pyrene-modified DNA/DNA duplexes. The results of absorption, fluorescence anisotropy and circular dichroism studies all consistently indicated that the pyrene attached to the RNA duplex is located outside of the duplex, whereas the pyrene incorporated into the DNA duplex intercalates into the double helix. (1)H NMR measurements unambiguously confirmed that the pyrene attached to the DNA duplex indeed intercalates between the base pairs of the duplex. Molecular dynamics simulations support these differences in the local structural elements around the pyrene between the pyrene-RNA/RNA and the pyrene-DNA/DNA duplexes.
Nakamura
Mitsunobu
M
Department of Materials Science and Chemistry, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2201, Japan.
Fukunaga
Yudai
Y
Sasa
Kazuhiro
K
Ohtoshi
Yukinori
Y
Kanaori
Kenji
K
Hayashi
Haruhisa
H
Nakano
Hidehiko
H
Yamana
Kazushige
K
D002942:Circular Dichroism; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D005454:Fluorescence Polarization; D005456:Fluorescent Dyes / Q000737:chemistry*; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D015345:Oligonucleotide Probes / Q000737:chemistry*; D011721:Pyrenes / Q000737:chemistry*; D012330:RNA, Double-Stranded / Q000737:chemistry*
D005456:Fluorescent Dyes; D015345:Oligonucleotide Probes; D011721:Pyrenes; D012330:RNA, Double-Stranded; D004247:DNA; C030984:pyrene