Configurational preference of pyrrolidine-based oxy-peptide nucleic acids as hybridization counterparts with DNA and RNA.
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.
Kitamatsu
Mizuki
M
Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Japan.
Shigeyasu
Masanori
M
Saitoh
Mamoru
M
Sisido
Masahiko
M
D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D020135:Peptide Nucleic Acids / Q000737:chemistry*; D011759:Pyrrolidines / Q000737:chemistry; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D013056:Spectrophotometry, Ultraviolet; D013237:Stereoisomerism; D013696:Temperature; D013816:Thermodynamics
D020135:Peptide Nucleic Acids; D011759:Pyrrolidines; D012313:RNA; D004247:DNA