A new series of oxyâpeptide nucleic acids (pyrrolidineâbased oxyâpeptide nucleic acids = POPNAs) of four different stereoisomeric forms (cisâL, cisâD, transâL, transâD) 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(A9)s] and dT9 or rU9 were investigated from ultraviolet (UV) melting curves and circular dichroism (CD) spectra. The cisâLâpo(A9) formed the most stable hybrid with dT9, because of the smallest entropy loss, despite the smallest enthalpy gain. In contrast, transâLâpo(A9) formed the most stable hybrid with rU9, because of the largest enthalpy gain, despite the largest entropy loss. The hybrid stability of transâLâpo(A9) with rU9 was significantly improved as compared with a previous version of oxyâpeptide nucleic acid (OPNA) that lacks the pyrrolidine ring. Š 2005 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 84: 267â273, 2006
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