A novel stable RNA pentaloop that interacts specifically with a motif peptide of lambda-N protein.
To achieve a novel specific peptide-nucleic acid binding model, we designed an in vitro selection procedure to decrease the energetic contribution of the electrostatic interaction in the total binding energy and to increase the contribution of hydrogen bonding and pi-pi stacking. After the selection of hairpin-loop RNAs that specifically bound to a model peptide of lambda N protein (N peptide), a new thermostable pentaloop RNA motif (N binding thermostable RNA hairpin: NTS RNA) was revealed. The obtained NTS RNA was able to bind to the N peptide with superior specificity to the boxB RNA, which is the naturally occurring partner of the lambda N protein.
Kawakami
Junji
J
Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Higashinada-ku, Kobe, Japan. kawakami@konan-u.ac.jp
Sugimoto
Naoki
N
Tokitoh
Hisanori
H
Tanabe
Yoshiatsu
Y
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001483:Base Sequence; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism*; D013379:Substrate Specificity; D054334:Viral Regulatory and Accessory Proteins / Q000737:chemistry* / Q000378:metabolism*
C059417:N protein, Bacteriophage lambda; D054334:Viral Regulatory and Accessory Proteins; D012313:RNA