Conformation and Flexibility of GpC and CpG in Neutral Aqueous Solution using 1H Nuclear-Magnetic-Resonance and Spin-Lattice-Relaxation Time Measurements

Abstract

The average conformations of guanylyl(3'-5')cytidine (GpC) and cytidylyl(3'-5')guanosine (CpG) in neutral aqueous solution have been investigated by proton-proton and proton-phosphorus coupling constants and by TI relaxation time measurements at 250 MHz.The temperature effect on the chemical shifts and coupling constants has been studied in the temperature interval between 25 "C and 65 "C. Apart from the H-5 of the pC residue in GpC, which shows a downfield shift of about 0.18 ppm, no dramatic changes in chemical shift have been observed for other protons. On the other hand, the couplings JH-H and JP-H of both dinucleoside monophosphates are quite sensitive to temperature. The results indicate that the temperature effect is larger for GpC than for CpG. The N conformer is favoured at low temperature. At 25 "C its proportion is preponderant and is more important for the C than for the G residue in both dimers. When the temperature increases from 25 "C to 65 "C, the N proportions decrease and approach those of the corresponding mononucleotides. The largest change in N/S equilibrium with temperature is observed in the G p residue of GpC.The conformers gauche-gauche and gauche -(or gauche +) are favoured in both dinucleoside monophosphates. At 25 "C, the proportion of the gg rotamer of pC in GpC is almost equal to 100 %.This indicates that the rotation about the phosphodiester linkage of this molecule is very reduced. The rotamer distribution of the 3' residue exocyclic groups of both GpC and CpG is virtually unchanged, while that of the 5' residues is notably affected by the temperature variation. The conformation of the base around the glycosidic bond was studied by TI proton relaxation time measurement before and after deuteration of H-8 of the G residue. In the case of GpC, the syn conformation is predominant in the Gp, while the anti conformation is highly favoured in the pC residue. In the case of CpG, the guanine base is close to the sugar of the Cp moiety at least part of the time. The syn and anti conformations appear equally probable in both residues. As far as the temperature effect and conformational analysis are concerned, both residues of CpG behave similarly to the corresponding mononucleotides, suggesting a great flexibility of this dimer.The continuing interest in the conformation of dinucleoside phosphates can be divided into three main areas : (a) solid-state studies of self-complementary dinucleoside phosphates, highlighted by the recent minihelices ApU [l] and GpC [ 2 ] ; (b) solution studies on all 16 dinucleoside phosphates [3 -51 which quite clearly indicated that even at ambient temperature only small parts of these compounds are stacked, in equilibrium with several other extended Abbreviations. GpC, guanylyl(3'-5')cytidine; CpG, cytidylyl-(3'-5')guanosine; NMR, nuclear magnetic resonance. conformations; (c) studies on the interaction of selfcomplementary dinucleotides and oligonucleotides [6 -121 with intercalating drugs in order to obtain precise details of their interactions with nuclei...

The structures and relative stabilities of d(G · G) reverse hoogsteen, d(G·T) reverse wobble, and d(G · C) reverse watson-crick base-pairs in DNA crystals 1 1Edited by I. Tinoco

“…The relative instability of the rwGT base-pair likely results from the disfavored syn conformation adopted by this pyrimidine base (Haschemeyer & Rich, 1967;Neumann et al, 1979). Furthermore, no water molecule was observed bridging the guanine and thymine bases, as has been observed in the structures of``normal'' d(G ÁT) wobble base-pairs (Ho et al, 1985;Kneale et al 1985;Hunter et al, 1986).…”

Principles of Nucleic Acid Structure

“…In general, the N2 amino group of guanosine and alternating purine-pyrimidine sequences appear to be essential prerequisites for Z-DNA. The former provides for favorable solvent interaction and the latter assists Z-DNA formation because purines adopt the syn conformation easier than pyrimidines (923).…”

Stacking-unstacking of the dinucleoside monophosphate guanylyl-3',5'-uridine studied with molecular dynamics

“…GpU has been extnsively investigated by nuclear magntic resonance experments (Chachaty et al, 1977;Ts'o et al, 1969). From proton magnetic resonance data it has first been concluded that all dinucleoside monophosphates are in a right-handed anti-anti-conformation (Ts'o et al, 1969) but later some exceptions have been shown to exist, for instance GpU and GpC (Chachaty et al, 1977;Neumann et al, 1979), where it has been quite clearly shown that the orientation is predominantly syn for the Guo moiety and anti for the Urd moiety (Chachaty et aL., 1977). At room temperature and neutral pH an unusual perpendicular structure of GpU has been proposed (Guschlbur et al, 1971;Guschlbauer et al, 1972) with Guo in syn and Urd in anti.…”