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 carrying nucleobase protecting groups is reported as a new approach for DNA functionalization. The 2-amino groups of purine-and 7-deazapurine-2,6diamine 2′-deoxyribonucleosides served as molecular targets for this functionalization. The 2-amino group withstands oligonucleotide deprotection with ammonia, whereas all other protecting groups are released after chemical DNA synthesis. On this basis, a method was developed for the selective functionalization of oligonucleotides at the 2position of purines and 7-deazapurines. Melting experiments and T m values obtained from hybridization studies revealed that duplexes with protected (2-amino-dA) and (2-amino-7-deaza-dA)-dT base pairs are as stable as their nonprotected counterparts. Mismatch discrimination of protected purine-and 7-deazapurine-2,6-diamine DNA was superior to that of nonprotected DNA. Click functionalization in the minor groove of the DNA double helix became accessible via introduction of heptynoyl protecting groups bearing a terminal triple bond. Click reactions with pyrene azide validated the usability. DNA conjugates 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 method using protected base pairs for DNA functionalization and paves the way for new DNA labeling strategies.

Nucleobase-Functionalized 7-Deazaisoguanine and 7-Deazapurin-2,6-diamine Nucleosides: Halogenation, Cross-Coupling, and Cycloaddition

“…TLC (silica gel, CH 2 Cl 2 /MeOH, 5:1) R f 0.5. Analytical data were identical to those described in the literature …”

“…The 7-alkynylated 7-deazapurin-2,6-diamine ribo- and 2′-deoxyribonucleosides 4h and 5i , k were prepared by Sonogashira cross-coupling reaction from the 7-iodo compounds 4g and 5g according to a reported procedure (Scheme ). ,, Then, in method I, the same protocol was applied for the synthesis of 7-alkynylated 4i , k and 5h . From 4k , the TMS group was removed by K 2 CO 3 in MeOH (→ 4i ).…”

“…. 17 Compound 4h was prepared according to the literature and obtained as a colorless solid. TLC (silica gel, CH 2 Cl 2 /MeOH, 5:1) R f 0.5.…”