Abstract
A new series of oxy‐peptide nucleic acids (pyrrolidine‐based oxy‐peptide nucleic acids = POPNAs) of four different stereoisomeric forms (cis‐L, cis‐D, trans‐L, trans‐D) have been synthesized. To find a favorable stereoisomer of POPNA for hybridization with DNA or RNA, thermodynamic parameters and conformations of the hybrids between the four stereoisomers with 9 adenine bases [po(A~9~)s] and dT~9~ or rU~9~ were investigated from ultraviolet (UV) melting curves and circular dichroism (CD) spectra. The cis‐L‐po(A~9~) formed the most stable hybrid with dT~9~, because of the smallest entropy loss, despite the smallest enthalpy gain. In contrast, trans‐L‐po(A~9~) formed the most stable hybrid with rU~9~, because of the largest enthalpy gain, despite the largest entropy loss. The hybrid stability of trans‐L‐po(A~9~) with rU~9~ was significantly improved as compared with a previous version of oxy‐peptide nucleic acid (OPNA) that lacks the pyrrolidine ring. © 2005 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 84: 267–273, 2006
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