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2′β‐Fluoro‐Tricyclo Nucleic Acids (2′F‐tc‐ANA): Thermal Duplex Stability, Structural Studies, and RNase H Activation
Author(s) -
Istrate Alena,
Katolik Adam,
Istrate Andrei,
Leumann Christian J.
Publication year - 2017
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.201701476
Subject(s) - nucleic acid , rna , rnase p , oligonucleotide , rnase h , dna , duplex (building) , chemistry , ribonuclease , stereochemistry , nucleic acid thermodynamics , nucleic acid structure , biochemistry , gene
We describe the synthesis, thermal stability, structural and RNase H activation properties of 2′β‐fluoro‐tricyclo nucleic acids (2′F‐tc‐ANA). Three 2′F‐tc‐ANA nucleosides (T, 5Me C and A) were synthesized starting from a previously described fluorinated tricyclo sugar intermediate. NMR analysis and quantum mechanical calculations indicate that 2′F‐tc‐ANA nucleosides prefer sugar conformations in the East and South regions of the pseudorotational cycle. UV‐melting experiments revealed that non‐consecutive insertions of 2′F‐tc‐ANA units in DNA reduce the affinity to DNA and RNA complements. However, an oligonucleotide with five contiguous 2′F‐tc‐ANA‐T insertions exhibits increased affinity to complementary RNA. Moreover, a fully modified 10‐mer 2′F‐tc‐ANA oligonucleotide paired to both DNA (+1.6 °C/mod) and RNA (+2.5 °C/mod) with significantly higher affinity compared to corresponding unmodified DNA, and similar affinity compared to corresponding tc‐DNA. In addition, CD spectroscopy and molecular dynamics simulations indicate that the conformation of the 2′F‐tc‐ANA/RNA duplex is similar to that of a DNA/RNA duplex. Moreover, in some sequence contexts, 2′F‐tc‐ANA promotes RNase H‐mediated cleavage of a complementary RNA strand. Taken together, 2′F‐tc‐ANA represents a nucleic acid analogue that offers the advantage of high RNA affinity while maintaining the ability to activate RNase H, and can be considered a prospective candidate for gene silencing applications.