The specific interaction between metal cation and mismatch base pair in duplex RNA

Abstract

We have already found that mercury (II) cation specifically binds to T:T mismatch base pair in heteroduplex DNA, which increases the melting temperature of heteroduplex DNA involving T:T mismatch base pair by about 4 degrees C. We have also found that silver (I) cation specifically binds to C:C mismatch base pair in heteroduplex DNA, which increases the melting temperature of heteroduplex DNA involving C:C mismatch base pair by about 4 degrees C. In the present study, to examine whether the specific interaction between metal cation and mismatch base pair can be also formed in duplex RNA, we investigated the effect of the metal cation on the thermal stability of homoduplex and heteroduplex RNA. Addition of mercury (II) cation increased the melting temperature of heteroduplex RNA containing U:U mismatch base pair by about 6 degrees C. The thermal stability of homoduplex RNA containing U:A or A:U perfectly matched base pair and heteroduplex RNA containing A:A mismatch base pair was not significantly changed by the addition of mercury (II) cation. On the other hand, addition of silver (I) cation increased the melting temperature of heteroduplex RNA containing C:C mismatch base pair by about 4 degrees C. The thermal stability of homoduplex RNA containing C:G or G:C perfectly matched base pair and heteroduplex RNA containing G:G mismatch base pair was not significantly changed by the addition of silver (I) cation. We conclude that the specific interaction between metal cation and mismatch base pair can be formed in duplex RNA as in the case of duplex DNA.