Conformational Study of Two Short Pentadeoxyribonucleotides, d-CpCpApApG and d-CpTpTpGpG, and Their Fragments by Proton Nuclear Magnetic Resonance

D. M. Cheng, L. S. Kan, E. E. Leutzinger, K. Jayaraman, P. S. Miller, P. O.P. Ts'o

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39 Scopus citations


Two pentadeoxyribonucleotides, d-CpCpApApG and d-CpTpTpGpG, and their short fragments, d-CpCpA, d-CpCpApA, d-TpGpG, and d-TpTpGpG, were synthesized by the phosphodiester or phosphotriester method and have been studied thoroughly by 1H NMR spectroscopy. All the non-exchangeable base proton resonances (about 8–10 per each pentamer) of these two series of oligodeoxynucleotides have been assigned by the “incremental method”. The chemical shift and coupling constant values of the nonexchangeable sugar proton resonances (35 per each pentamer) have been determined by spectral simulation method, and the assignments of these 35 resonances were achieved by both the “incremental method” and the “sequential homodecoupling” method. Through the chemical shift vs. temperature profile, the assignments of the proton resonances at one temperature (usually at high temperature, i.e., 75 °C) can be extended to other temperatures. Thus, together with other NMR techniques, the strategy of (i) incremental procedure, (ii) sequential homodecoupling techniques, and (iii) chemical shifts vs. temperature measurement is now shown to be effective for total assignment of all resolvable proton resonances in oligonucleotides. The coupling constants of these known sugar proton resonances provide valuable information about the backbone conformation, particularly with respect to the influence of chain length and base composition of these oligodeoxynucleotides. The sugar conformation was shown to be predominantly in the 2E form (over 65%). The addition of 5′-deoxyadenylic acid and 5′-deoxyguanylic acid to the 3′-OH of a nucleoside is more effective in increasing the percent 2E of the nucleoside than the addition of 5′-deoxycytidylic acid and 5′-thymidylic acid. On the other hand, the 3′-nucleotidyl unit exerts little effect on the sugar conformation of the 5′-nucleosidyl unit. Thus, the residue at the 3′ end (with free 3′-0H group) always has a lower percent 2E than the internal residues adjacent to a 5′-purine nucleotidyl unit. The rotation of the C4′-C5′ bond (Ψ angle) is in favor of the gg conformation (55–85%), the rotation of the C5′-O5′ bonds (ϕ angle) is highly in favor oi g′g′ (75–90%), and the rotation of the C3′-O3′, bond (ϕ′ angle) is restricted to the domain of ϕ ≃ 200°. Also, the percent gg of the nucleotidyl unit of the free 3′ end are higher than those of the free 5′ end, indicating the restricted rotation of the C4′-C5′ bond of the 3′ end. The population distributions of these three bonds, Ψ, ϕ, and ϕ′, are relatively insensitive to temperature (25–75 °C), indicating that the rotation of these angles is considerably restricted to their favored conformations. The achievement in the complete assignments of all nonexchangeable protons of these two complementary pentamers paves the way for assignment of all the protons of the helical duplex of d-(CCAAG + CTTGG) as well as assignment of the 13C resonances and 31P resonances for these two pentamers by the heterodecoupling technique.

Original languageEnglish (US)
Pages (from-to)621-630
Number of pages10
Issue number4
StatePublished - 1982
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry


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