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′<i>S</i>,5′<i>R</i>)‐2′‐deoxy‐3′,5′‐ ethano‐β ‐<scp>D</scp>‐ribofuranosyl]adenine and ‐thymine

Abstract

Abstract The synthesis of a new type of oligonucleotide (‘bicyclooligodeoxynucleotide’ = bcd(X n )) displaying less conformational flexibility in its sugar‐phosphate backbone is described, and a characterization of the pairing properties and energetics of the decamers bcd(T 10 ) and bcd (A 10 ) 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(T 10 ) pairs less strongly to complementary RNA and DNA, whereas bcd(A 10 ) forms stronger duplexes relative to the natural system. ( ii ) bcd(A 10 ) discriminates between a complementary oligodeoxynucleotide with a mismatch in the center in the same way as d(A 10 ), indicating equal base‐pairing selectivity. ( iii ) bcd(A 10 ) forms more stable triplexes with d(T 10 ) of the pyrimidine‐purine‐pyrimidine (py · pu · py) motif than d(A 10 ). ( iv ) The stability of duplexes containing a bicyclic strand is more sensitive towards salt concentration. The higher sensitivity in bcd(A 10 ) containing duplexes is due to a higher differential cation uptake. ( v ) Differential scanning calorimetric (DSC) analysis of duplex‐formation enthalpies shows Δ H vH in all duplexes containing bicyclooligonucleotides to be more negative than Δ H cal , 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(A 10 )/d(T 10 ), bcd(A 10 )/d(T 10 ), d(A 10 )/bcd(T 10 ), bcd(A 10 )/bcd(T 10 ). ( 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.