Silver‐Mediated Homochiral and Heterochiral α‐dC/β‐dC Base Pairs: Synthesis of α‐dC through Glycosylation and Impact of Consecutive, Isolated, and Multiple Metal Ion Pairs on DNA Stability

Abstract

Isolated and consecutive heterochiral a-dC-base pairs have been incorporated into 12-mer oligonucleotide duplexes at various positions, thereby replacing Watson-Crick pairs. To this end, an ew synthesis of the a-d anomer of dC has been developed, and oligonucleotides containing a-dC residues have been synthesized.S ilver-mediated base pairs were formed upon the addition of silver ions. Furthermore, we have established that heterochiral a-dC-dCb ase pairs can approach the stability of aW atson-Crickp air, whereas homochiral dC-dC pairs are significantly less stable.Ap ositional change of the silver-mediated base pairs affects the duplex stability and reveals the nearest-neighbor influence.W hen the number of silver ions was equivalentt ot he number of duplex base pairs (12), non-meltings ilver-rich complexes were formed. Structuralc hanges have been supportedb yc irculard ichroism (CD) spectra,w hich showed that the B-DNA structure was maintained whilst the silver ion concentration was low.A th igh silver ion concentration, silver-rich complexesd isplaying different CD spectra were formed.

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

“…This wire consists of silver‐mediated homo pairs of dT ⋅ dT, dG ⋅ dG, and dC ⋅ dC instead of Watson–Crick base pairs. Other complex structures exist that rely on the sequence and amount of silver ions added to the DNA duplexes [30, 34b, 39–41] . Argentophilic interactions have also to be considered [42] …”

“…[33] Recently,w e showedt hat the anomeric heterochiral a-dC•b-dC pairi sm ore stable than the homochiral b-dC•b-dC and a-dC•a-dC pairs. [23,34] The number of bound silver ions per base pair was determined by spectrophotometric titration:O ne or two silver ions were found to be present in the metal-mediated base pairs. Furthermore, it was observedt hat not only dC•dC mismatchesf orm silver-mediated base pairs, because stable duplexesw ere also generated after the addition of silver ions to mismatches of dC with dT, [34,35] dA, [34] or 7-deaza-dA.…”

Consecutive Silver(I) Ion Incorporation into Oligonucleotides containing Cytosine‐Cytosine Mispairs

“…[18,23,27] No T m upon addition of excess Ag I indicates that the duplex was saturated with Ag I ions by forming Ag-mediated base pairs and the electrostatic bonds between Ag I ions and the sugarphosphate of the DNA backbone. [24,[25][26]33,37] The conformational change of the dsDNA II + III in solution was further studied by CD before and after Ag I incorporation from one to twenty equivalents per duplex, and corresponding CD spectra are shown in Figure 1B. The positive and negative peaks centred at around 280 nm and 240 nm were observed for the dsDNA till the addition of three Ag I , respectively, which is Bform like conformations.…”

“…[31,32] The impact of consecutive and multiple Ag I ion incorporation was also studied for this base pair, found the formation of non-melting silver-rich complexes in the presence of a higher number of Ag I ion. [33] Most of these studies replaced the canonical Watson-Crick pairs of the DNA duplexes, followed by metal ion mediation. Therefore, more studies of multiple DNA mismatches of the canonical Watson-Crick pairs are needed to observe their structural diversity and stability to better understand the change in properties and the bulk effect of Ag I incorporation.…”

“…UV absorbance gradually decreased with the increase of Ag I ions, resulted to non-sigmoidal melting profile of the duplexes in the presence of high concentration of Ag I ( Figure S3), indicating that a high Ag I -rich dsDNA does not melt. [33] However, the corresponding values of T m of the Ag I -mediated dsDNA were estimated by normalizing those T m profiles and are given in Table S1 for low incorporated Ag I ions. It is expected that Ag I binding to the mispair will increase the T m significantly.…”