Influence of N6‐methylation of residue A(5) on the conformational behaviour of d(C‐C‐G‐A‐A‐T‐T‐C‐G‐G) in solution studied by 1H‐NMR spectroscopy

Rinkel, Lambertus J.; Marel, Gijs A. van der; Boom, Jacques H. van; Altona, C.

doi:10.1111/j.1432-1033.1987.tb10799.x

Cited by 31 publications

(20 citation statements)

References 22 publications

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“…This finding parallels earlier results reported from this laboratory [24, 26,361. Comparison of the average values of % S of Y and R residues in the two octamers indicates that, on average, the sugar rings of purine residues have a greater preference to adopt the S-type sugar conformation than those of the pyrimidine residues: d(G-A-G-A-T-C-T-C)2 %S(R),,,, 88, "/oS(Y),,,, 82 (see also Table 7).…”

Section: Pseudorotation Analysis Jbr Octamerssupporting

confidence: 82%

“…Comparison of the average values of % S of Y and R residues in the two octamers indicates that, on average, the sugar rings of purine residues have a greater preference to adopt the S-type sugar conformation than those of the pyrimidine residues: d(G-A-G-A-T-C-T-C)2 %S(R),,,, 88, "/oS(Y),,,, 82 (see also Table 7). Similar interesting correlations are seen in other B-DNA duplexes [24,26,361. The total collection of available data will be reviewed elsewhere.…”

Section: Pseudorotation Analysis Jbr Octamerssupporting

confidence: 67%

“…Similar effects are seen for the base signals of core residues in d(G-A-G-A-T-C-T-C)2. Chemical shift changes for 'H and 31P resonances of nuclei located in the core of intact duplexes have been reported for other DNA oligonucleotides [26,36,41,43,46, 47, 51, 521. These findings suggest that small and local conformational changes occur in the core of the intact duplex before melting takes place.…”

Section: Temperature-dependent Conformational Behaviourmentioning

confidence: 99%

“…In other words, upon warming up, 'early melting' of the 3'-terminal dC residue occurs when the 3'-terminal consists of the sequence -C-C, whereas two residues appear to be involved in such behaviour when the DNA is terminated by -C-T-C. At this point it should be stressed that: (a) 3'-terminal DNA sequences of the type -R-R, -R-Y or -Y-R appear to display shift profiles like those of the core residues, see e.g. d(C-A-C-A-T-G-T-G)2 and 126, 42,45 -501; (b) from results obtained thus far, it is judged that no 'early melting' occurs at the 5' terminals of DNA duplexes, including 5'-terminal C-C-sequences [26,42,451; (c) stacking appears to remain relatively intact at 5' R-R-ends, although the opposing 3' -Y-Y end at the same time may be involved in a rapid stack =+ unstack equilibrium. More details are given in the following sections.…”

Section: Temperature-dependent Conformational Behaviourmentioning

confidence: 99%

“…However, the preference of the sugar ring to adopt either the N-or the S-type sugar pucker should not be interpreted in an absolute sense, at least not in the cases of B-and Z-DNA type helices in solution. In recent papers [21,22,24,26,36,541, it was shown that the sugar ring of B-DNA duplex fragments in aqueous solution actually occurs as a blend of N-and S-type conformers, which exist side-by-side in a fast ring-flip equilibrium situation, with a preference for the S-type sugar pucker. Thus the preference of a given sugar ring for either N or S means that this particular sugar spends the larger part of the time in the preferred type of sugar conformation.…”

Section: General Considerationsmentioning

confidence: 99%

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Influence of the base sequence on the conformational behaviour of DNA polynucleotides in solution

Rinkel¹,

Marel²,

Boom³

et al. 1987

Eur J Biochem

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. Assignments, based upon one-dimensional NOE and homonucleardecoupling and two-dimensional correlated and NOE spectroscopies are given of the resonances of most of the base and sugar protons. Chemical shift vs temperature profiles, constructed for all samples, yielded insight into the temperature-and concentration-dependent conformational behaviour of the compounds and were used to obtain thermodynamic parameters pertaining to the stacked-single-strand + random-coil and duplex randomcoil equilibria. Vicinal proton-proton couplings were analyzed in terms of the conformation of the deoxyribose rings in the single-stranded tetramers and duplexed octamers.The NOE patterns, chemical shift profiles, imino-proton resonances and coupling data revealed that the compounds adopt B-DNA-like structures. The ratio duplexed/stacked-single-strand/random coil depends upon external conditions as well as upon base sequence. The thermodynamic data indicate that: (a) in terms of singlehelical stacking, the R-R steps ( T , 321 -328 K) appear more stable than the Y-R or R-Y steps (T, 308 -316 K) and the Y-Y steps score least (T, 290-300 K), and (b) the duplexes consisting of alternating, d(Y-R),, strands are more stable, in terms of AH", compared to the d(R-R), . d(Y-Y)" duplexes. The analyses of the couplings demonstrated that the sugars of the single-stranded tetramers and duplexed octamers occur as a blend of N -and S-type conformers, with a preference for the S-type (C2'-endo) sugar conformation: upon duplex formation, no significant shift in the N-type/S-type ratio was observed. The fraction S-type sugar conformation of a given residue, % S , in the stacked-single strands was found to depend upon the nature of its own base and that of the adjacent residues: sugars in an R-R stretch display high values of % S (90-loo), whereas those in Y-Y stretches show relatively low values (z 65). It appears that a good stacking interaction between bases goes hand-in-hand with high values of % S.

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Section: Pseudorotation Analysis Jbr Octamerssupporting

confidence: 82%

Section: Pseudorotation Analysis Jbr Octamerssupporting

confidence: 67%

Section: Temperature-dependent Conformational Behaviourmentioning

confidence: 99%

Section: Temperature-dependent Conformational Behaviourmentioning

confidence: 99%

Section: General Considerationsmentioning

confidence: 99%

See 3 more Smart Citations

Influence of the base sequence on the conformational behaviour of DNA polynucleotides in solution

Rinkel¹,

Marel²,

Boom³

et al. 1987

Eur J Biochem

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Thermodynamics of the various forms of the dodecamer d(ATTACCGGTAAT) and of its constituent hexamers from proton nmr chemical shifts and UV melting curves: Three‐state and four‐state thermodynamic models

Pieters

Mellema²,

Elst

et al. 1989

Biopolymers

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Chemical shifts of base and H1' protons of the single-stranded hexamers d(ATTACC) and d(GGTAAT), of the 1:1 mixtures of these complementary hexamers, and of the self-complementary dodecamer d(ATTACCGGTAAT) were measured at various temperatures in aqueous solution. Four different sample concentrations were used in the case of the dodecamer and of the mixture of the complementary hexamers; the individual hexamers were measured at two different DNA concentrations. Absorbance temperature profiles at five different NaCl concentrations were measured for the dodecamer in order to quantify the effect of the ionic strength on the duplex formation. Under suitable conditions of nucleotide concentration, temperature, and ionic strength, the dodecamer adopts either a B-DNA duplex or a hairpin-loop structure. Chemical shift vs temperature profiles, constructed for all samples, were used to obtain thermodynamic parameters either for the various stacking interactions in the single strands or for the duplex or the hairpin-loop formation. In the analysis of the duplex formation of the hexamers, a two-state approach appeared too simple, because systematic deviations were revealed. Therefore, a new three-state model (DUPSTAK) was developed. In order to investigate the magnitude of error arising from the use of the two-state approach in cases where the DUPSTAK model appears more appropriate, a series of test calculations was made. The magnitude of error in the enthalpy and in the entropy of duplex melting is found to depend linearly upon the actual melting temperature and not upon the individual delta Hd degrees and delta Sd degrees values. Thermodynamic analysis of the chemical shift vs temperature profiles in D2O solution (no added salt) yields an average Tmd value of 341 K (1M DNA) and delta Hd degrees of - 121 kJ.mol-1 for the dimer/random-coil transition of the hexamer duplex d(ATTACC).d(GGTAAT). For the duplex in equilibrium random-coil transition of the 12-mer d(ATTACCGGTAAT) an average Tmd value of 336 K (1M DNA) and delta Hd degrees of -372 kJ.mol-1 are found. The hairpin/random-coil transition of d(ATTACCGGTAAT) is characterized by a rather large delta Hh degrees value, -130 kJ.mol-1, and an average Tmh value of 304 K.

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Slow conformational exchange in DNA minihairpin loops: A conformationalstudy of the circular dumbbell d〈pCGC‐TT‐GCG‐TT〉

et al. 1995

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In recent years various examples of highly stable two-residue hairpin loops (miniloops) in DNA have been encountered. As the detailed structure and stability of miniloops appear to be determined not only by the nature and sequence of the two bases in the loop, but also by the closing base pair, it is desirable to carry out in-depth studies of especially designed small model DNA compounds. Therefore, a circular DNA dumbbell-like molecule is tailored to consist of a stem of three Watson-Crick base pairs, flanked on each side by a minihairpin loop. The resulting circular DNA decamer 5'-d-3' (I) is studied in solution by means of nmr spectroscopy. At a temperature of 269 K the molecule occurs in a 50/50 mixture of two dumbbell structures (denoted L2L2 and L2L4). L2L2 contains three Watson-Crick C-G base pairs and two two-residue loops (H2-family type) in opposite parts of the molecule. On raising the temperature from 269 to 314 K, the L2L4 conformer becomes increasingly dominant (95% at 314 K). This conformer has a partially disrupted closing G-C base pair in the 5'-GTTC-3' loop with only one remaining solvent-accessible hydrogen bond between NH alpha of the cytosine C(1) and O6 of the guanine G(8), whereas the opposite 5'-CTTG-3' loop remains stable. The disruption of the C(1)-G(8) base pair in the L2L4 form is correlated with the presence of a syn orientation for the C(1) base at the 5'-3' loop-stem junction in the 5'-GTTC-3' loop. The two conformers, L2L2 and L2L4, occur in slow equilibrium (2-20 s-1). Moderate line broadening of specific 1H, 13C, and 31P resonances of residues C(1), G(8), T(9), and T(10) at low temperatures, due to chemical exchange between L2L2 and L2L4, show that the interconversion from an anti to syn conformer in residue C(1) has a small local effect on the structure of the dumbbell. T1 relaxation measurements, chemical-shift considerations, and complete band-shape calculations of the exchange process of the G(8) imino proton reveal a possibility for the existence of multiconformational states in the anti-syn equilibrium.

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Influence of N⁶‐methylation of residue A(5) on the conformational behaviour of d(C‐C‐G‐A‐A‐T‐T‐C‐G‐G) in solution studied by ¹H‐NMR spectroscopy

Cited by 31 publications

References 22 publications

Influence of the base sequence on the conformational behaviour of DNA polynucleotides in solution

Influence of the base sequence on the conformational behaviour of DNA polynucleotides in solution

Thermodynamics of the various forms of the dodecamer d(ATTACCGGTAAT) and of its constituent hexamers from proton nmr chemical shifts and UV melting curves: Three‐state and four‐state thermodynamic models

Slow conformational exchange in DNA minihairpin loops: A conformationalstudy of the circular dumbbell d〈pCGC‐TT‐GCG‐TT〉

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