TY - JOUR
T1 - An in vitro-selected RNA receptor for the GAAC loop
T2 - Modular receptor for non-GNRA-type tetraloop
AU - Ishikawa, Junya
AU - Furuta, Hiroyuki
AU - Ikawa, Yoshiya
N1 - Funding Information:
Grants-in-Aid for Scientific Research (B) [23310161 to Y.I.]; JSPS Fellows [11J00683 to J.I.]; and on Innovative Areas ‘Emergence in Chemistry’ [23111717 to Y.I.] Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan. Funding for open access charge: Grant-in-Aid for Scientific Research (B) [23310161] from the MEXT, Japan.
PY - 2013/4
Y1 - 2013/4
N2 - Although artificial RNA motifs that can functionally replace the GNRA/receptor interaction, a class of RNA-RNA interacting motifs, were isolated from RNA libraries and used to generate designer RNA structures, receptors for non-GNRA tetraloops have not been found in nature or selected from RNA libraries. In this study, we report successful isolation of a receptor motif interacting with GAAC, a non-GNRA tetraloop, from randomized sequences embedded in a catalytic RNA. Biochemical characterization of the GAAC/receptor interacting motif within three structural contexts showed its binding affinity, selectivity and structural autonomy. The motif has binding affinity comparable with that of a GNRA/receptor, selectivity orthogonal to GNRA/receptors and structural autonomy even in a large RNA context. These features would be advantageous for usage of the motif as a building block for designer RNAs. The isolated motif can also be used as a query sequence to search for unidentified naturally occurring GANC receptor motifs.
AB - Although artificial RNA motifs that can functionally replace the GNRA/receptor interaction, a class of RNA-RNA interacting motifs, were isolated from RNA libraries and used to generate designer RNA structures, receptors for non-GNRA tetraloops have not been found in nature or selected from RNA libraries. In this study, we report successful isolation of a receptor motif interacting with GAAC, a non-GNRA tetraloop, from randomized sequences embedded in a catalytic RNA. Biochemical characterization of the GAAC/receptor interacting motif within three structural contexts showed its binding affinity, selectivity and structural autonomy. The motif has binding affinity comparable with that of a GNRA/receptor, selectivity orthogonal to GNRA/receptors and structural autonomy even in a large RNA context. These features would be advantageous for usage of the motif as a building block for designer RNAs. The isolated motif can also be used as a query sequence to search for unidentified naturally occurring GANC receptor motifs.
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U2 - 10.1093/nar/gkt040
DO - 10.1093/nar/gkt040
M3 - Article
C2 - 23382175
AN - SCOPUS:84876066418
VL - 41
SP - 3748
EP - 3759
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 6
ER -