Conformational analysis of a modified ribotetranucleoside triphosphate: m62A-U-m62A-U studied in aqueous solution by nuclear magnetic resonance at 500 MHz1

Hartel, Arnold J.; Wille-Hazeleger, Gerrie; Boom, Jacques H. van; Altona, C.

doi:10.1093/nar/9.6.1405

Cited by 33 publications

(17 citation statements)

References 11 publications

(2 reference statements)

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“…These conclusions regarding the N/S distribution agree with Lee and Tinoco's analysis based on the ribose H1'-H2' coupling constants (4). (4,6,11,36,37) have argued from 1 H-nmr data that RYR sequences (R stands for purine, Y for pyrimidine) have substantial populations of structures withY bulged out and the two R bases stacked on each other. Such a structure for AUG should have large changes in the ribose-phosphate backbone as compared to AAA and AAG.…”

Section: Chemical Shifts Of the Ribose Carbonssupporting

confidence: 87%

¹³C-NMR of Ribosyl ApApA, ApApG and ApUpG

Stone

Winkle

Borer

1986

Journal of Biomolecular Structure and Dynamics

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The chemical shifts as well as the 13C-31P coupling constants of the carbon-13 nuclei in single-stranded ApApA, ApApG, and ApUpG are sensitive to sequence and temperature. ApApA and ApApG have similar properties with large shielding (up to 1.7 ppm) of many of the base carbons upon decreasing the temperature from 70 degrees C to 11 degrees C; the base carbons have smaller shielding changes in ApUpG. Large shielding and deshielding effects are observed for the 1', 3', 4' and 5'-carbons over this temperature range. Analysis of the 13C-31P couplings measured at the 4' ribose carbons show that the population of the anti rotamer about O5'-C5' varies from 98 to 75%, and is higher in ApApA and ApApG than in ApUpG. The CCOP coupling data at 2' and 4' is consistent with a blend of the -antiperiplanar/-synclinal nonclassical rotamers about the C3'-O3' bond, varying from 89/11% in ApApG to 55/45% in ApUpG. The coupling and chemical shift data support the thesis that ApUpG is stacked much less than the other two molecules. The stacked forms of all three trinucleotides is most easily interpreted by a standard A-RNA model. It is not necessary to invoke the "bulged base" hypothesis [Lee, C.-H. and Tinoco, Jr., I. (1981) Biophysical Chemistry 1, 283-294; Lankhorst, P.P., Wille, G., van Boom., J.H., Altona, C., and Haasnoot, C.A.G. (1983) Nucleic Acids Research 11, 2839-2856] to explain the contrast in 13C spectroscopic properties of ApUpG in comparison to ApApG and ApApA.

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Section: Chemical Shifts Of the Ribose Carbonssupporting

confidence: 87%

¹³C-NMR of Ribosyl ApApA, ApApG and ApUpG

Stone

Winkle

Borer

1986

Journal of Biomolecular Structure and Dynamics

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“…Protonphosphorus coupling along p can be translated into torsion angles and vice-versa by means of a Karplus-type equation, Eqn (5) [71]:…”

Section: Backbone Conformations Of D(t-a-t-a)mentioning

confidence: 99%

“…Classical angles (60") were assumed for the gauche rotamers. The appropriate limiting couplings were then obtained by means of Eqn (5). The p' populations thus obtained at 8 "C and at 22 "C are shown in Table 6.…”

Section: Backbone Conformations Of D(t-a-t-a)mentioning

confidence: 99%

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Sequence‐dependent structural variation in single‐helical DNA Proton NMR studies of d(T‐A‐T‐A) and d(A‐T‐A‐T) in aqueous solution

Mellema

Pieters

Marel

et al. 1984

European Journal of Biochemistry

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The two deoxyribotetranucleoside triphosphates d(T‐A‐T‐A) and d(A‐T‐A‐T) were investigated in aqueous solution by one‐ and two‐dimensional proton NMR at 300 and 500 MHz. It is demonstrated that both compounds occur predominantly in the single‐helical form. Accurate coupling constants are obtained by computer simulation of several 500‐MHz spectra. The data are interpreted in terms of N and S pseudorotational ranges. The geometry of the major S‐type conformers displays a clear sequence dependence, as expressed by variation of the endocyclic backbone angle δ (C5′‐C4′‐C3′‐O3′). A simple sum rule is proposed to predict δ variation in single‐helical DNA fragments. Comparisons are made with other sequence‐dependent geometries as observed in a double‐helical B‐DNA fragment in the crystalline state. Furthermore, one‐ and two‐dimensional nuclear Overhauser effect (NOE) spectroscopy was carried out on d(T‐A‐T‐A). An inventory is made of the observed intra‐ and inter‐residue NOEs. The NOE data confirm the presence of a highly stacked single‐helical conformation of d(T‐A‐T‐A) in solution. No indications are found for the formation of a bulge‐out structure as observed for analogous alternating purine‐pyrimidine oligoribonucleotides.

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“…Comparison between the trimerization shifts of the base protons and the calculated composite chemical shifts based on the nearestneighbor interactions indicates the presence of these bulged structures for ApApA in solution. Evidence from other research groups also suggest the existence of the bulged structures in trimers [16,17] and in a tetramer [18]. Such bulged structures of nucleic acids have been proposed as the models for frameshift mutations [6,7,15].…”

Section: Resultsmentioning

confidence: 90%

Conformational studies of trinucleoside bisphosphates 2. Potential energy calculations

Lee

1983

European Journal of Biochemistry

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Semi-empirical potential energy calculations were carried out for the conformations of ApApA, a trinucleoside bisphosphate (trimer), as proposed in the preceding paper in this journal. Energy minimals were obtained for these conformers, i. e. conformers 1-1, 1-11, 111-1' and 1'-I' (the first Roman numeral represents the conformation of the ApAp-moiety and the second one the -pApA moiety of ApApA), of the nearest-neighbor interactions, and conformers B 1, B2 and B3 of bulged structures. The results show that the detailed conformations of the component dinuclotide (dimer) moieties in I-I,I-II, 111-1' and I/-[' are close (k lo'.) to the corresponding stable conformations of dinucleotides in solution proposed by Lee and coworkers. The bulged conformations B 1, B2 and B3 have open forms for each dinucleotide moiety. Their preferred local conformations are anti, y', /3+, E + (except for Ap-in B3, c -) , and 3'endo (except for Ap-in B3, 2'endo) for the glycosidic bond, C4'-C5', C5'-05', C3'-03' and the ribose moiety, respectively. The conformation of the phosphodiester linkage in -PAPA moiety is c2, L X~ for all the three bulged conformers, while that in ApAp-is (;, a : for BI, ( : a; for B2, and (:, a: for B3. The calculated composite chemical shifts of the base protons from ring-current effects agree with the corresponding observed trimerization shifts. Conformers 1-1 and I'-I' are helix-like structures and correspond to the right-handed and the'vertical-stacked'helices, respectively. The structure of 1-11 is similar to that observed in the ApApA single crystals. The bulged conformations may serve as models for frameshift mutations.Studies of molecular conformations are essential for understanding the relationship between the structures and functions of the molecules. This is especially important for flexible molecules which are capable of assuming many possible conformations in solution. High-field nuclear magnetic resonance spectroscopy has recently become available and is capable of generating structural and conformational data of complicated molecules at the atomic level. However, due to the dynamic nature of the molecules in solution, rationalization and interpretation of these data may not be straightforward and may sometimes be oversimplified [I]. It has been proposed that semi-empirical potential energy calculations may serve for this purpose to construct conformations which can explain the solution data. Meanwhile, the structures thus obtained are with minimal potential energy without unreasonably short contact between atoms [2 -41. Recently, this method, coupled with N M R data, was used successfully to compare the stabilities of many possible conformations proposed for dinucleotides [3,4]. This led to the postulation that the dinucleotides have four stable conformations (i.e. conformers I, 1', I1 and 111) in solution [3 -51. In this paper, the stable conformations of trinucleoside bisphosphates (i.e. 1-1, 1-11, 111-1', I'-I', BI, B2 and B3) proposed from the N M R data in the preceding papers of this serie...

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Conformational analysis of a modified ribotetranucleoside triphosphate: m⁶₂A-U-m⁶₂A-U studied in aqueous solution by nuclear magnetic resonance at 500 MHz¹

Cited by 33 publications

References 11 publications

¹³C-NMR of Ribosyl ApApA, ApApG and ApUpG

¹³C-NMR of Ribosyl ApApA, ApApG and ApUpG

Sequence‐dependent structural variation in single‐helical DNA Proton NMR studies of d(T‐A‐T‐A) and d(A‐T‐A‐T) in aqueous solution

Conformational studies of trinucleoside bisphosphates 2. Potential energy calculations

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Conformational analysis of a modified ribotetranucleoside triphosphate: m62A-U-m62A-U studied in aqueous solution by nuclear magnetic resonance at 500 MHz1

Cited by 33 publications

References 11 publications

13C-NMR of Ribosyl ApApA, ApApG and ApUpG

13C-NMR of Ribosyl ApApA, ApApG and ApUpG

Sequence‐dependent structural variation in single‐helical DNA Proton NMR studies of d(T‐A‐T‐A) and d(A‐T‐A‐T) in aqueous solution

Conformational studies of trinucleoside bisphosphates 2. Potential energy calculations

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Conformational analysis of a modified ribotetranucleoside triphosphate: m⁶₂A-U-m⁶₂A-U studied in aqueous solution by nuclear magnetic resonance at 500 MHz¹

¹³C-NMR of Ribosyl ApApA, ApApG and ApUpG

¹³C-NMR of Ribosyl ApApA, ApApG and ApUpG