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10. Configurational preference of pyrrolidine-based oxy-peptide nucleic acids as hybridization counterparts with DNA and RNA.

Author

Kitamatsu M, Shigeyasu M, Saitoh M, and Sisido M

Subjects
Circular Dichroism, DNA chemistry, Pyrrolidines chemistry, RNA chemistry, Spectrophotometry, Ultraviolet, Stereoisomerism, Temperature, Thermodynamics, DNA metabolism, Nucleic Acid Conformation, Nucleic Acid Hybridization, Peptide Nucleic Acids chemistry, RNA metabolism
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., (Copyright 2006 Wiley Periodicals, Inc.)

Published
2006
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