Watson-Crick Base Pairs with Protecting Groups: The 2-Amino Groups of Purine- and 7-Deazapurine-2,6-Diamine as Target Sites for DNA Functionalization by Selective Nucleobase Acylation

Abstract

The recognition of Watson-Crick base pairs carryingnucleobaseprotecting groups is reported as a new approach for DNA functionalization.The 2-amino groups of purine- and 7-deazapurine-2,6-diamine 2 & PRIME;-deoxyribonucleosidesserved as molecular targets for this functionalization. The 2-aminogroup withstands oligonucleotide deprotection with ammonia, whereasall other protecting groups are released after chemical DNA synthesis.On this basis, a method was developed for the selective functionalizationof oligonucleotides at the 2-position of purines and 7-deazapurines.Melting experiments and T (m) values obtainedfrom hybridization studies revealed that duplexes with protected (2-amino-dA)and (2-amino-7-deaza-dA)-dT base pairs are as stable as their nonprotectedcounterparts. Mismatch discrimination of protected purine- and 7-deazapurine-2,6-diamineDNA was superior to that of nonprotected DNA. Click functionalizationin the minor groove of the DNA double helix became accessible viaintroduction of heptynoyl protecting groups bearing a terminal triplebond. Click reactions with pyrene azide validated the usability. DNAconjugates with bulky pyrene residues at the 2-position (minor groove)developed the same high stability as those functionalized at the 7-position(major groove). This demonstrates the potential of our new methodusing protected base pairs for DNA functionalization and paves theway for new DNA labeling strategies.