Base sequence dependence of the structure and dynamics, and thermodynamic properties of oligonucleotides

From the analyses of^&lt；31&gt；P NMR spectral line shapes of oriented DNA fibers we have previously shown that the backbone conformation of B-DNA is nonuniform which seemed base sequence dependent。Along this finding we proceeded this project to prove the base sequence effects in many other systems and extend it to other properties of DNA.1。^&lt；31&gt；P NMR studies of oriented DNA fibers led the following conclusions：i)homo poly(DA).poly(DT)had unusual structure which could be interpreted as if the helix axis bended to form supercoiled form，ii)RNA-DNA hybrid，poly(RA).poly(DT)exhibited(RA)_n chain as being A form and(DT)_n as being B form，iii)B-DNA in the fibers at high ative humidities underwent three modes of molecular motions i.e，tarotion out the rauidis the rawent three modes of molecular motions i。And iv)the base planes of A-DNA tiled by 20°from the plane perpendicular to the helix axis，while that of B-DNA is nearly perpendicular to the h…More elix axis.2。Thermodynamic properties of conformational transition of DNA。The study of ethanol-induced A-B transition of DNA demonstrated that apparent free energy change for this transition in aqueous solution was 21.2kcal/mol，and that DNA-solvent interaction was unfavorable in ethanol solution so that A form was stabilized。Using a mismatched oligonucleotide，d(CGCGAATTACGCG)，it was shown that activation energy and entropyfor the hairpin loop formation from the double stranded oligomer was56kcal/mol and 137cal/mol/K，respectivley，and therefore concluded that this hairpin formation directly occurred with separation of the complementarychains but not through an intermediate such as cruciform.3..Structure and dynamics of synthetic oligonucleotides in solution.Total assignments of^1H proton spectra of 12kinds of decanuleotides were made and the chemical shift values of aromativ protons were discussed in terms of base seqeunce effects.Thus，a given proton chemical shift was found to be determined within 0.04ppm by nearest neighbor residues，especially by the one at 5‘-side.Theoretically calculated chemical shifts were in good agreement with the observed values for adenosine H2 protons but not for cytidine H5and H6protons.The relaxationtimes T_1and T_2 of aromatic trotons were measured at various frequencies and interpreted in terms of molecular motions including internal motion。Thus，it was found that correlation time for the overall motion was 3.5 ns and that for internal motion was 0.1 ns with and order parameter s=0.9。Less：Less

From the analyses of ^<31>P NMR spectral line shapes of oriented DNA fibers we have previously shown that the backbone conformation of B-DNA is nonuniform which seemed base sequence dependent. Along this finding we proceeded this project to prove the base sequence effects in many other systems and extend it to other properties of DNA.1. ^<31>P NMR studies of oriented DNA fibers led the following conclusions: i) homo poly(dA).poly(dT) had unusual structure which could be interpreted as if the helix axis bended to form supercoiled form, ii) RNA-DNA hybrid, poly(rA).poly(dT) exhibited (rA)_n chain as being A form and (dT)_n as being B form, iii) B-DNA in the fibers at high relative humidities underwent three modes of molecular motions i.e., rotaion about the helix axis, rapid fluctuation of atomic groups and reorientation about the tilted axis, and iv) the base planes of A-DNA tiled by 20゜ from the plane perpendicular to the helix axis, while that of B-DNA is nearly perpendicular to the h … More elix axis.2. Thermodynamic properties of conformational transition of DNA. The study of ethanol-induced A-B transition of DNA demonstrated that apparent free energy change for this transition in aqueous solution was 21.2 kcal/mol, and that DNA-solvent interaction was unfavorable in ethanol solution so that A form was stabilized. Using a mismatched oligonucleotide, d(CGCGAATTACGCG), it was shown that activation energy and entropyfor the hairpin loop formation from the double stranded oligomer was 56 kcal/mol and 137 cal/mol/K, respectivley, and therefore concluded that this hairpin formation directly occurred with separation of the complementarychains but not through an intermediate such as cruciform.3. Structure and dynamics of synthetic oligonucleotides in solution. Total assignments of ^1H proton spectra of 12 kinds of decanuleotides were made and the chemical shift values of aromativ protons were discussed in terms of base seqeunce effects. Thus, a given proton chemical shift was found to be determined within 0.04 ppm by nearest neighbor residues, especially by the one at 5'-side. Theoretically calculated chemical shifts were in good agreement with the observed values for adenosine H2 protons but not for cytidine H5 and H6 protons. The relaxationtimes T_1 and T_2 of aromatic trotons were measured at various frequencies and interpreted in terms of molecular motions including internal motion. Thus, it was found that correlation time for the overall motion was 3.5 ns and that for internal motion was 0.1 ns with and order parameter s=0.9. Less