Heterochiral DNA with Complementary Strands with α‐d and β‐d Configurations: Hydrogen‐Bonded and Silver‐Mediated Base Pairs with Impact of 7‐Deazapurines Replacing Purines

Abstract

HeterochiralD NA with hydrogen-bondedand silver-mediated base pairs have been constructed using complementary strandsw ith nucleosides with ad or b-d configuration. Anomeric phosphoramidites were employed to assemble the oligonucleotides. According to the T m values and thermodynamic data, the duplex stabilityo ft he heterochiral duplexes was similart ot hat of homochiral DNA, but mismatch discrimination was better in heterochiral DNA. Replacement of purinesb y7-deazapurines resulted in stable paralleld uplexes, thereby confirming Watson-Crick-type base pairing. When cytosine wasf acing cytosine, thymine or adenine residues, duplex DNA formed silver-mediated base pairs in the presence of silver ions. Although the CD spectra of single strands with ad configuration display mirror-like shapes to those with the b-d configuration, the CD spectra of the hydrogen-bonded duplexes and those with al imited number of silver pairs show aB-type double helix almost indistinguishable from naturalD NA. Nonmelting silver ion-DNA complexesw ith entirely different CD spectra were generatedwhen the number of silver ions was equalt ot he number of base pairs.

The 2‐Amino Group of 8‐Aza‐7‐deaza‐7‐bromopurine‐2,6‐diamine and Purine‐2,6‐diamine as Stabilizer for the Adenine–Thymine Base Pair in Heterochiral DNA with Strands in Anomeric Configuration

“…On the contrary, melting of heterochiral duplexes results in a bathochromic shift (10 nm) of the positive lobe accompanied by a strong reduction of the amplitude. Moreover, the shape of both sets of melting curves (homochiral and heterochiral) are different to those reported recently having dA–dT base pairs instead of 2 –dT pairs [8] . In particular, the hypsochromic (homochiral duplexes) and bathochromic (heterochiral duplexes) shifts are more characteristic for the 2 –dT pair.…”

“…Oligonucleotide M r calcd [a] M r found [b] ODN-1 b-5'-d(TAGGTCAATACT) [20] - [20] -ODN-3 a-5'-d(TCATAACTGGAT) [8] 3644. 2 corresponds to 8-aza-7-deaza-7-bromopurine-2,6-diamine 2'-deoxyribonucleoside.…”

“…Moreover,t he shapeo fb oth sets of meltingc urves (homochiral and heterochiral) are different to those reportedr ecently having dA-dT base pairs instead of 2-dT pairs. [8] In particular,t he hypsochromic (homochiral du-plexes)a nd bathochromic (heterochiral duplexes) shifts are more characteristic for the 2-dT pair.W hen the CD dataa t 220 nm were plotted againstt he ellipticity, T m values wereo btained that are almost identical to those of the UV melting curves.…”

“…Recently, we reported on the structural perturbation of heterochiral DNA (Figure 2 b). Here, heterochiral DNA means that two diastereoisomeric strands with α‐D and β‐D configuration and not enantiomeric oligonucleotides as in d ‐/ l ‐DNA form the double helix (Figure 2 b, motif VI) [8] . The heterochiral DNA forms parallel chains, [9] displays a global helical B‐type structure similar to canonical DNA, and represents an autonomous recognition system beneficial to various fields in nucleic acid chemistry, biology, and for the construction of nanodevices.…”

“…Here, heterochiral DNA meanst hat two diastereoisomeric strandsw ith a-D and b-D configuration and not enantiomeric oligonucleotides as in d-/l-DNA form the double helix (Figure 2b,m otif VI). [8] The heterochiralD NA forms parallel chains, [9] displays aglobal helical B-type structure similar to canonical DNA, and represents an autonomous recognition system beneficial to variousf ields in nucleic acid chemistry,b iology,a nd fort he construction of nanodevices. Early attempts to stabilizeh eterochiral DNA used the aanomer of 5-propynyl-2'-deoxycytidine, [10] the a-D anomer of 1, [11] and aL NA derivative.…”