Nucleic‐Acid Analogues with Restricted Conformational Flexibility in the Sugar‐Phosphate Backbone (‘bicyclo‐DNA’). Part 3. Synthesis, pairing properties, and calorimetric determination of duplex and triplex stability of decanucleotides from [(3′S,5′R)‐2′‐deoxy‐3′,5′‐ ethano‐β ‐D‐ribofuranosyl]adenine and ‐thymine

Abstract

AbstractThe synthesis of a new type of oligonucleotide (‘bicyclooligodeoxynucleotide’ = bcd(Xn)) displaying less conformational flexibility in its sugar‐phosphate backbone is described, and a characterization of the pairing properties and energetics of the decamers bcd(T10) and bcd (A10) with each other and with complementary RNA and DNA sequences by UV‐spectroscopic and calorimetric techniques is given. The results can be summarized as follows: (i) bcd(T10) pairs less strongly to complementary RNA and DNA, whereas bcd(A10) forms stronger duplexes relative to the natural system. (ii) bcd(A10) discriminates between a complementary oligodeoxynucleotide with a mismatch in the center in the same way as d(A10), indicating equal base‐pairing selectivity. (iii) bcd(A10) forms more stable triplexes with d(T10) of the pyrimidine‐purine‐pyrimidine (py · pu · py) motif than d(A10). (iv) The stability of duplexes containing a bicyclic strand is more sensitive towards salt concentration. The higher sensitivity in bcd(A10) containing duplexes is due to a higher differential cation uptake. (v) Differential scanning calorimetric (DSC) analysis of duplex‐formation enthalpies shows ΔHvH in all duplexes containing bicyclooligonucleotides to be more negative than ΔHcal, which is compatible with the formation of catenated structures. (vi) Isothermal titration calorimetry (ITC) provides a complete set of thermodynamic data including duplex and triplex association constants for the systems d(A10)/d(T10), bcd(A10)/d(T10), d(A10)/bcd(T10), bcd(A10)/bcd(T10). (vii) All duplexes containing bicyclic strands show a (numerically) reduced pairing entropy term with respect to that of the natural system. (viii) Enthalpies from DSC and ITC are similar, suggesting that the enthalpic contribution from ordered single strands to the overall duplex‐formation enthalpy plays a minor role in the duplexes investigated.