Thermodynamic and spectral properties of DNA miniduplexes with the terminal G·A mispairs and 3′ or 5′ dangling bases

The tetradeoxyribonucleotide pAGCG in 1 M NaCl forms duplexes with terminal non-canonical pA x G pairs with stability significantly exceeding that for the duplex (pAGCT)2 and lower than that for the duplex (pCGCG)2. The deoxyriboduplex (pAGCG)2 is considerably stabilized by 3'-Y and slightly by 5'-X dangling bases. Therefore, the stability of duplexes with 3' dangling bases decreases in the order (pAGCGY)2 > (pCGCGA)2 > (pAGCTA)2. The sum of the independent stabilizing effect of the of 5'-pG and 3'-A dangling bases on the (pAGCG)2 core duplex is higher than that of the additional terminal pG x A pair in pG-A-/-G-A tandem of the duplex (pGAGCGA)2.