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

AbstractThe tetradeoxyribonucleotide pAGCG in 1 M NaCl forms duplexes with terminal non-canonical pA·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·A pair in pG-A-/-G-A tandem of the duplex (pGAGCGA)2