Effect of C5-amino substituent on 2'-deoxyuridine base pairing with 2'-deoxyadenosine: investigation by ¹H and ¹³C NMR spectroscopy

Abstract

Substituents at 5-position of a pyrimidine base are known to affect its base pairing properties with complementary purines, either by altering the imino N3-H acidity or by modifying the acceptor strength of C2 and C4 carbonyls. This paper reports comparative base pair property of 5-methyl-2'-deoxyuridine (dT) and 5-amino-2'-deoxyuridine (dUNH₂) with 2'-deoxyadenosine (dA) as their 3',5'-di-t-butyldimethylsilyl derivatives in chloroform-d. Using ¹H and ¹³C NMR, it is demonstrated that the 5-NH₂ substituent in 2'-deoxyuridine results in (i) decreased association (lower K_a) with 2'-deoxyadenosine compared to dA:dT complexation and (ii) increased receptor strength of C2 carbonyl compared to C4 carbonyl and (iii) lower temperature for separation of 6-amino protons of dA due to its complexation with dUNH₂ compared to that with dT.