Stabilization of hairpins and bulged secondary structures of nucleic acids by single incorporation of α,β-D-CNA featuring a gauche(+) alpha torsional angle

Abstract

A constrained dinucleotide unit featuring a gauche(+) alpha torsional angle configuration was used to stabilize DNA hairpin or bulged structures. Large five nucleotides having looped hairpin structures can be stabilized up to +5 degrees C. Depending on the nature of the closing base pair, the increased hairpin stability can be reached through loop moiety preorganization or stem rearrangement induced on the first two base pairs. With an alpha gauche(+) constraint either within or opposite to the bulge, the larger bulged structures had better stabilization

Convertible and conformationally constrained nucleic acids (C2NAs)

“…In that context, unlike its behaviour into T4-hairpin, the (SC5', SP) -C2NA modification was not well tolerated and did not behave as its -CNA analogue that improved, in the same conditions, the bulge thermal stabilities. 13 In the other bulge construction, where the (SC5', SP) -C2NA faced the growing loop (Table 6), it appeared that this modification conferred to the structures roughly the same thermal stability around 40 ±2°C regardless to the loop size. While for the one to three nucleotides loop the gauche(+) constraint was unfavourable or neutral (…”

“…These differences could induce a dramatic change of conformational behaviour. Therefore, the analysis of the conformation of this new family of constrained nucleotides was carried out using 1 H, 13 C, 31 P and 2D NMR techniques, in order to determine the sugar puckering preference of each deoxyribose and the geometry of the oxaza-phosphorinane ring.…”

“…26 Eventually, bulges have been constructed with the gauche(+) constraint within the loop or opposite to the loop using the -C2NA TT modified sequence ODN 13 5'-GATTTGCATATTCATGAG. 13 Restricting the complementary strand generated a constrained loop on the modified strand (Table 5, bulges made with ODN 13 and ODN 15 to 20) whereas expanding the complementary strand with unpaired moiety from one to six nucleotides led to bulged structures facing the constraint (Table 6, bulges made with ODN 13 and ODN 21 to 26). Phosphoramidites 7 and 15 were incorporated with similar yields than those obtained for unmodified nucleotide phosphoramidite with no change either in concentration nor in synthetic cycle time during automated oligonucleotide synthesis.…”

“…11 When featuring the canonical set of values gauche(-)/trans, -D-CNA are perfect B-DNA nucleotide mimics and induce a strong stabilization of duplex structure 12 whereas stability of hairpin or bulge structures can be modulated by using -D-CNA featuring a gauche(+) conformation of the  angle, located in the unpaired moiety of the secondary nucleic acid structure. 13 Since we wanted to keep the D-CNA's general scaffold for their interesting stabilization effects for the newly designed C2NA and because the C5'-carbon was no longer available for further functionalization, we chose to investigate the replacement of one oxygen atom within the dioxa-phosphorinane ring by a nitrogen atom properly alkylated by a propargyl function in order to bring the convertible ability. It was also of importance to keep the natural C5'-O5'-P-O3' bonds unchanged to prevent any change into the internucleotidic length and local geometry.…”

Thio‐ and Seleno‐Dioxaphosphorinane‐Constrained Dinucleotides (D‐CNA): Synthesis and Conformational Study

“…We recently showed that restricting the rotational freedom of the sugar phosphate backbone by means of dioxaphosphorinane rings can favour not only the stabilization of the duplex, but also the preorganization of loops and bulges when those structural elements feature unusual torsion angle value sets. This can result in the stabilization of secondary structures (Figure ) …”