DNA Base Pair Polarities of Pyrimidine(s)-Purine(s) (Pyu) dsDNA induce stronger Hybridization and unique DNA Conformation compared to Purine(s)-Pyrimidine(s) (Puy) dsDNA

Abstract

The present study introduces a concept of DNA base pair polarity in double-stranded DNA (dsDNA), which has led the serial investigation of hydrogen bonding magnetic resonance-based gene regulation. DNA base pair polarity is characterized by hydrogen bonding between electrostatically positive purine and negative pyrimidine, exerting the stabilization and organization of dsDNA. Comparison of DNA hybridization potential between Pyu (pyrimidine(s)-purine(s)) and Puy (purine(s)-pyrimidine(s)) oligo-dsDNAs in EtBr intercalated electrophoresis showed that Pyu ds(nTnA) (n=3, 4,5,6,7,8,10,12) and ds(nCnA) (n=7,8,10,12) exhibit stronger hybridization than Puy ds(nAnT) and ds(nAnC), respectively. In the HPLC for DNA conformation change in 0.1M NaCl solution, Pyu oligo-dsDNA tended to have a larger peak area than Puy oligo-dsDNA, indicating that the former had a more extended and organized DNA conformation than the latter. FT-IR results showed that Pyu ds3T3A, ds3C3G, dsCTCGAG, and dsTCTAGA showed higher IR absorbance at 3400-3200 cm-1 than Puy ds3A3T, ds3G3C, dsGAGCTC, and dsAGATCT, respectively, indicating Pyu oligo-dsDNAs have increased N-H stretching in hybridization than Puy oligo-dsDNAs. In vitro RNA transcription from template plasmid DNAs inserted with six segments of Pyu ds6(TCTGA) and positive ds14(GA) produced more RNA than those with seven segments of palindromic Pyu ds(CATG) and negative ds14(CT), respectively, indicating the former plays a stimulating role for RNA transcription while the latter plays an inhibitory role. When comparing PCR primers between Pyu ds12/n(nCnA) and Puy ds12/n(nAnC) (n=1,2,3,4,6,12), Pyu primers can easily hybridize on template DNA and subsequently produce abundant DNA compared to Puy primers. The data suggest that Pyu oligo-dsDNAs hybridize strongly and form distinctive conformation, thereby stimulating RNA transcription more than Puy oligo-dsDNAs. Since Pyu oligo-dsDNA appears to preserve DNA signal and conformation relevant to DNA function more efficiently than Puy dsDNA, it is proposed that the entire DNA code can be divided into Pyu dsDNAs with unique DNA base pair polarities.