Abstract
A decadeoxyribonucleotide, d(C-C-A-A-G-A-T-T-G-G) (I), forms a duplex in solution. The base pairing pattern in this duplex was studied by proton nuclear magnetic resonance spectroscopy. Five NH...N hydrogen-bonded proton resonances were observed, and they were assigned by nuclear Overhauser enhancement experiments as well as by comparison to five previously assigned NH...N hydrogen-bonded proton resonances in a self-complementary duplex of similar sequence, d(C-C-A-A-G-C-T-T-G-G) (II). The results suggest that the central -G-A- residues of I form G X A base pairs in the helical state. The fact that the H2 proton of A at the sixth position from the 5' end of I showed nuclear Overhauser enhancement when the NH...N hydrogen-bonded proton resonance of G X A was irradiated suggests that the bases of the G X A base pair are oriented in an anti-anti conformation. Comparison of the linewidths at the half height of the NH...N hydrogen-bonded proton resonances of I at 1 degree C suggest that the G X A base pairs are less stable than adjacent A X T base pairs.
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- HOLLEY R. W., APGAR J., EVERETT G. A., MADISON J. T., MARQUISEE M., MERRILL S. H., PENSWICK J. R., ZAMIR A. STRUCTURE OF A RIBONUCLEIC ACID. Science. 1965 Mar 19;147(3664):1462–1465. doi: 10.1126/science.147.3664.1462. [DOI] [PubMed] [Google Scholar]
- Hare D. R., Reid B. R. Direct assignment of the dihydrouridine-helix imino proton resonances in transfer ribonucleic acid nuclear magnetic resonance spectra by means of the nuclear Overhauser effect. Biochemistry. 1982 Apr 13;21(8):1835–1842. doi: 10.1021/bi00537a020. [DOI] [PubMed] [Google Scholar]
- Hare D. R., Reid B. R. Nuclear Overhauser assignment of the imino protons of the acceptor helix and the ribothymidine helix in the nuclear magnetic resonance spectrum of Escherichia coli isoleucine transfer ribonucleic acid: evidence for costacked helices in solution. Biochemistry. 1982 Oct 12;21(21):5129–5135. doi: 10.1021/bi00264a004. [DOI] [PubMed] [Google Scholar]
- Johnston P. D., Redfield A. G. Nuclear magnetic resonance and nuclear Overhauser effect study of yeast phenylalanine transfer ribonucleic acid imino protons. Biochemistry. 1981 Mar 3;20(5):1147–1156. doi: 10.1021/bi00508a016. [DOI] [PubMed] [Google Scholar]
- Kan L. S., Cheng D. M., Jayaraman K., Leutzinger E. E., Miller P. S., Ts'o P. O. Proton nuclear magnetic resonance study of a self-complementary decadeoxyribonucleotide, C-C-A-A-G-C-T-T-G-G. Biochemistry. 1982 Dec 21;21(26):6723–6732. doi: 10.1021/bi00269a017. [DOI] [PubMed] [Google Scholar]
- Lomant A. J., Fresco J. R. Structural and energetic consequences of noncomplementary base oppositions in nucleic acid helices. Prog Nucleic Acid Res Mol Biol. 1975;15(0):185–218. doi: 10.1016/s0079-6603(08)60120-8. [DOI] [PubMed] [Google Scholar]
- Miller P. S., Chandrasegaran S., Dow D. L., Pulford S. M., Kan L. S. Synthesis and template properties of an ethyl phosphotriester modified decadeoxyribonucleotide. Biochemistry. 1982 Oct 26;21(22):5468–5474. doi: 10.1021/bi00265a014. [DOI] [PubMed] [Google Scholar]
- Patel D. J., Kozlowski S. A., Marky L. A., Rice J. A., Broka C., Dallas J., Itakura K., Breslauer K. J. Structure, dynamics, and energetics of deoxyguanosine . thymidine wobble base pair formation in the self-complementary d(CGTGAATTCGCG) duplex in solution. Biochemistry. 1982 Feb 2;21(3):437–444. doi: 10.1021/bi00532a003. [DOI] [PubMed] [Google Scholar]
- Roy S., Redfield A. G. Nuclear Overhauser effect study and assignment of D stem and reverse-Hoogsteen base pair proton resonances in yeast tRNAAsp. Nucleic Acids Res. 1981 Dec 21;9(24):7073–7083. doi: 10.1093/nar/9.24.7073. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Topal M. D., Fresco J. R. Base pairing and fidelity in codon-anticodon interaction. Nature. 1976 Sep 23;263(5575):289–293. doi: 10.1038/263289a0. [DOI] [PubMed] [Google Scholar]
- Topal M. D., Fresco J. R. Complementary base pairing and the origin of substitution mutations. Nature. 1976 Sep 23;263(5575):285–289. doi: 10.1038/263285a0. [DOI] [PubMed] [Google Scholar]
- Traub W., Sussman J. L. Adenine-guanine base pairing ribosomal RNA. Nucleic Acids Res. 1982 Apr 24;10(8):2701–2708. doi: 10.1093/nar/10.8.2701. [DOI] [PMC free article] [PubMed] [Google Scholar]