ja6b11825_si_001.pdf (920.3 kB)
Enhanced Binding Affinity for an i‑Motif DNA Substrate Exhibited by a Protein Containing Nucleobase Amino Acids
Version 2 2017-03-22, 20:03
Version 1 2017-03-17, 12:49
journal contribution
posted on 2017-03-06, 00:00 authored by Xiaoguang Bai, Poulami Talukder, Sasha M. Daskalova, Basab Roy, Shengxi Chen, Zhongxian Li, Larisa M. Dedkova, Sidney M. HechtSeveral
variants of a nucleic acid binding motif (RRM1) of putative
transcription factor hnRNP LL containing nucleobase amino acids at
specific positions have been prepared and used to study binding affinity
for the BCL2 i-motif DNA. Molecular modeling suggested
a number of amino acids in RRM1 likely to be involved in interaction
with the i-motif DNA, and His24 and Arg26 were chosen for modification
based on their potential ability to interact with G14 of the i-motif
DNA. Four nucleobase amino acids were introduced into RRM1 at one
or both of positions 24 and 26. The introduction of cytosine nucleobase 2 into position 24 of RRM1 increased the affinity of the modified
protein for the i-motif DNA, consistent with the possible Watson–Crick
interaction of 2 and G14. In comparison, the introduction
of uracil nucleobase 3 had a minimal effect on DNA affinity.
Two structurally simplified nucleobase analogues (1 and 4) lacking both the N-1 and the 2-oxo substituents were also
introduced in lieu of His24. Again, the RRM1 analogue containing 1 exhibited enhanced affinity for the i-motif DNA, while the
protein analogue containing 4 bound less tightly to the
DNA substrate. Finally, the modified protein containing 1 in lieu of Arg26 also bound to the i-motif DNA more strongly than
the wild-type protein, but a protein containing 1 both
at positions 24 and 26 bound to the DNA less strongly than wild type.
The results support the idea of using nucleobase amino acids as protein
constituents for controlling and enhancing DNA–protein interaction.
Finally, modification of the i-motif DNA at G14 diminished RRM1–DNA
interaction, as well as the ability of nucleobase amino acid 1 to stabilize RRM1–DNA interaction.