Structural analysis of r(GGA)4 found in RNA aptamer for bovine prion protein.
RNA aptamers for bovine prion protein (bPrP) were obtained by in vitro selection. It was found that the r(GGA) triplet repeat was frequently present in these aptamers. We already reported that both DNA and RNA containing the GGA repeat form unique quadruplex structures. The unique structures may be utilized for the recognition of bPrP by these aptamers. One of these aptamers contains four continuous repeat of r(GGA), r(GGA)(4). Here, we analyzed the structure of r(GGA)(4) under physiological ionic conditions by NMR. It was revealed on the basis of characteristic NOEs that an r(GGA)(4) strand forms the quadruplex composed of one G:G:G:G tetrad plane and one G(:A):G:G(:A):G hexad plane. Furthermore, two monomers form a dimeric structure in a tail-to-tail manner. The dimeric quadruplex structure of r(GGA)(4) is similar to that of d(GGA)(4), but the difference between two structures was also noticed.
Matsugami
Akimasa
A
Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
Mashima
Tsukasa
T
Nishikawa
Fumiko
F
Murakami
Kazuyoshi
K
Nishikawa
Satoshi
S
Noda
Ken
K
Yokoyama
Takashi
T
Katahira
Masato
M
D000818:Animals; D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000378:metabolism; D002417:Cattle; D019281:Dimerization; D054856:G-Quadruplexes; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011328:Prions / Q000378:metabolism*
D052157:Aptamers, Nucleotide; D011328:Prions