Incorporating 2‑Thiouracil into Short Double-Stranded
RNA-Binding Peptide Nucleic Acids for Enhanced Recognition of A‑U
Pairs and for Targeting a MicroRNA Hairpin Precursor
Posted on 2019-07-26 - 21:14
Chemically modified
short peptide nucleic acids (PNAs) recognize
RNA duplexes under near physiological conditions by major-groove PNA·RNA–RNA
triplex formation and show great promise for the development of RNA-targeting
probes and therapeutics. Thymine (T) and uracil (U) are often incorporated
into PNAs to recognize A-U pairs through major-groove T·A-U and
U·A-U base triple formation. Incorporation of a modified nucleobase,
2-thiouracil (s2U), into triplex-forming oligonucleotides
stabilizes both DNA and RNA triplexes. Thiolation of uracil causes
a decrease in the dehydration energy penalty for triplex formation
as well as a decrease in the pKa of the
N3 atom, which may result in improved hydrogen bonding in addition
to enhanced base stacking interactions, similar to the previously
reported thiolation effect of pseudoisocytosine (J to L substitution).
Here, we incorporated s2U into short PNAs, followed by
binding studies of a series of s2U-modified PNAs. We demonstrated
by nondenaturing polyacrylamide gel electrophoresis and thermal melting
experiments that s2U and L incorporated into dsRNA-binding
PNAs (dbPNAs) enhance the recognition of A-U and G-C pairs, respectively,
in RNA duplexes in a position-independent manner, with no appreciable
binding to the DNA duplex. Combining s2U and L modifications
in dbPNAs facilitates enhanced recognition of dsRNAs and maintains
selective binding to dsRNAs over ssRNAs. We further demonstrated through
a cell-free assay the application of the s2U- and L-modified
dbPNAs (8-mer, with a molecular mass of ∼2.3 kDa) in the inhibition
of the pre-microRNA-198 maturation in a substrate-specific manner.
Thus, s2U-modified dbPNAs may be generally useful for the
enhanced and selective recognition of RNA duplexes and for the regulation
of RNA functions.
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Ong, Alan Ann
Lerk; Toh, Desiree-Faye Kaixin; Krishna, Manchugondanahalli S.; Patil, Kiran M.; Okamura, Katsutomo; Chen, Gang (2019). Incorporating 2‑Thiouracil into Short Double-Stranded
RNA-Binding Peptide Nucleic Acids for Enhanced Recognition of A‑U
Pairs and for Targeting a MicroRNA Hairpin Precursor. ACS Publications. Collection. https://doi.org/10.1021/acs.biochem.9b00521
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AUTHORS (6)
AO
Alan Ann
Lerk Ong
DT
Desiree-Faye Kaixin Toh
MK
Manchugondanahalli S. Krishna
KP
Kiran M. Patil
KO
Katsutomo Okamura
GC
Gang Chen