The Quantitative Separation of Stacking and Self-Association Phenomena in a Dinucleoside Monophosphate by Means of NMR Concentration-Temperature Profiles: 6-N-(Dimethyl)Adenylyl- (3′,5′)-Uridine

Altona, C.; Hartel, Arnold J.; Olsthoorn, Cornelis S. M.; Leeuw, Harry P. M. de; Haasnoot, C. A. G.

doi:10.1007/978-94-009-9882-7_7

Cited by 20 publications

(3 citation statements)

References 31 publications

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“…The experimental stacking populations of DNMPs that we compared with here – those due to the Danyluk & Sarma groups 2b, 2c – were obtained by comparing J 3 ′ 4 ′ coupling constants in RNA DNMPs with those of corresponding 3′ and 5′ mononucleotides. Unfortunately, while corresponding J 3 ′ 4 ′ coupling constants were also subsequently reported by the same group for the DNA DNMPs, 46 it appears that the significant assumptions 47 used to convert these to stacking populations for RNAs do not hold for DNAs, 2d which means that a direct comparison of DNA and RNA stacking populations using the 1 H NMR data cannot be carried out.…”

Section: Discussionmentioning

confidence: 99%

Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment

Brown

Andrews

Elcock

2015

J. Chem. Theory Comput.

126

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We report the results of a series of 1 μs-long explicit-solvent molecular dynamics (MD) simulations performed to compare the free energies of stacking (ΔGstack) of all possible combinations of DNA and RNA nucleoside (NS) pairs and dinucleoside-monophosphates (DNMPs). For both NS-pairs and DNMPs we show that the computed stacking free energies are in reasonable qualitative agreement with experimental measurements, and appear to provide the closest correspondence with experiment yet found among computational studies; in all cases, however, the computed stacking free energies are too favorable relative to experiment. Comparisons of NS-pair systems indicate that stacking interactions are very similar in RNA and DNA systems except when a thymine or uracil base is involved: the presence of a thymine base favors stacking by ~0.3 kcal/mol relative to a uracil base. One exception is found in the self-stacking of cytidines, which are found to be significantly more favorable for the DNA form; an analysis of the rotational orientations sampled during stacking events suggests that this is likely to be due to more favorable sugar-sugar interactions in stacked complexes of deoxycytidines. Comparisons of the DNMP systems indicate that stacking interactions are more favorable in RNA than in DNA except, again, when thymine or uracil bases are involved. Finally, additional simulations performed using a previous generation of the AMBER force field – in which the description of glycosidic bond rotations was less than optimal – produce computed stacking free energies that are in poorer agreement with experimental data. Overall, the simulations provide a comprehensive view of stacking thermodynamics in NS pairs and in DNMPs as predicted by a state-of-the-art MD force field.

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Section: Discussionmentioning

confidence: 99%

Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment

Brown

Andrews

Elcock

2015

J. Chem. Theory Comput.

126

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“…The earlier proposal of a more complicated mechanism suggested by NMR (516) and kinetic experiments (517) for ApA has been criticized (520). If the more recent circular dichroism and NMR data are considered, then the two-state mechanism appears to be sufficient.…”

Section: Thermodynamic Description Of Stacking Interactionsmentioning

confidence: 99%

“…In most cases a simple two-state process (514)(515)(516)(517)(518)(519)(520)(521)(522) helical (stacked)~random coil (unstacked), is sufficient to explain the helix formation behavior of single-stranded oligomers. Thermodynamic parameters for some oligonucleotides are given in Table 6-7, aH, as, and T m for Ap U and ApA are virtually identical, and apparently the above given sequence-stacking rule does not apply strictly to oligonucleotides that short.…”

Section: Thermodynamic Description Of Stacking Interactionsmentioning

confidence: 99%

Principles of Nucleic Acid Structure

Saenger

1984

Springer Advanced Texts in Chemistry

5,968

312

6,279

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Calorimetric study of 2U:1A three‐stranded complexes formed between poly(U) and adenine dinucleotides: ApA and diastereoisomers of nonionic adenine dideoxyribonucleoside methyl phosphonate

1984

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SynopsisMelting parameters of 2U:lA complexes formed by polyuridylic acid [poly(U)] and three adenine dinucleotides, diribonucleoside monophosphonate ApA and diastereoisomers of dideoxyribonucleoside methyl phosphonate [(dAp A), and (dAp A),], in 1M NaCl and at a number of dinucleotide concentrations were obtained from differential scanning microcalorimetric data and interpreted in terms of the theory of helix-coil equilibrium in oligonucleotide-polynucleotide systems. The apparent binding constant, l/cm, a t 39°C and melting temperatures, Tm, at 1 x 10-3M dinucleotide concentration indicate the following order of thermodynamic stability of the complexes: 2 poly(U). (dApA), (2.27x 103M-l, 44.2"C) > 2 poly(U). (dApA), (9.9 x 102M1, 39.2"C) > 2 poly(U). (ApA) (5.9x 102M-I, 35.8"C). Corresponding calorimetric enthalpies of melting, AHm: 13.5, 12.7, and 12.8 kcal/mol (UUA base triplets) were found to be considerably lower than the van't Hoff enthalpies, AH,,,: 29.4, 16.2, and 16.2 kcal/mol, respectively, evaluated from the dependence of the melting temperatures on dinucleotide concentration. Self-association of dinucleotides and their simultaneous binding as monomers, dimers, and higher-order associated species is suggested as the most probable cause of the differences between AH,,, and AH,,, values. The differences in thermodynamic properties of the complexes formed by (dAp A), and (dApA)2 diastereoisomers are discussed in connection with their known conformational properties. The higher and essentially enthalpic stability of the 2 poly(U) . (dApA), complex correlates with a lower degree of intramolecular stacking of the (dApA), isomer. The hydrophobically enhanced strong self-association of the latter greatly influences the thermodynamics of its complex formation with poly(U) and results in AHapp/AHm = 2.3.

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The Quantitative Separation of Stacking and Self-Association Phenomena in a Dinucleoside Monophosphate by Means of NMR Concentration-Temperature Profiles: 6-N-(Dimethyl)Adenylyl- (3′,5′)-Uridine

Cited by 20 publications

References 31 publications

Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment

Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment

Principles of Nucleic Acid Structure

Calorimetric study of 2U:1A three‐stranded complexes formed between poly(U) and adenine dinucleotides: ApA and diastereoisomers of nonionic adenine dideoxyribonucleoside methyl phosphonate

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