Anomeric and Enantiomeric 2’‐Deoxycytidines: Base Pair Stability in the Absence and Presence of Silver Ions

Abstract

Dodecamer duplex DNA containing anomeric (α/ β-d) and enantiomeric (β-l/β-d) 2'-deoxycytidine mismatches was studied with respect to base pair stability in the absence and presence of silver ions. Stable duplexes with silver-mediated cytosine-cytosine pairs were formed by all anomeric and enantiomeric combinations. Stability changes were observed depending on the composition of the mismatches. Most strikingly, the new silver-mediated base pair of anomeric α-d-dC with enantiomeric β-l-dC is superior to the well-noted β-d/β-d-dC pair in terms of stability. CD spectra were used to follow global helical changes of DNA structure.

Anomeric DNA Strand Displacement with α‐D Oligonucleotides as Invaders and Ethidium Bromide as Fluorescence Sensor for Duplexes with α/β‐, β/β‐ and α/α‐D Configuration

“…However, the displacement reaction could be unambiguously confirmed by CD spectra [26] . From previous CD studies on homochiral duplexes with both strands in α‐D configuration, it was known that their CD spectra showed a distinct negative Cotton effect around 270 nm, which is not observed for heterochiral α/β duplexes and duplexes with both strands in β‐D configuration [12d,27] …”

“…Oligonucleotides are shown in Table 1. Some of them were newly prepared using solid‐phase synthesis and employing phosphoramidite chemistry; others were already described in previous papers of our laboratory [12d] . For that, four α‐D and four β‐D phosphoramidites were processed.…”

“…The system was suggested by Séquin [13] and the Imbach group [12a] and others made important contributions to this topic [14] . Also, DNA with both strands in α‐D configuration, the counterpart of canonical DNA, forms double strands [12d,15] . They are more stable than those of canonical DNA [12d,15] .…”

“…Also, DNA with both strands in α‐D configuration, the counterpart of canonical DNA, forms double strands [12d,15] . They are more stable than those of canonical DNA [12d,15] . The strand orientation of heterochiral α/β DNA is parallel, [16] whereas the homochiral α/α DNA displays an antiparallel alignment [12d,15] similar to canonical DNA.…”

“…They are more stable than those of canonical DNA [12d,15] . The strand orientation of heterochiral α/β DNA is parallel, [16] whereas the homochiral α/α DNA displays an antiparallel alignment [12d,15] similar to canonical DNA. Anomeric base recognition follows the principles of Watson‐Crick base pairing with slight modifications.…”