Flow linear dichroism and fourier transform IR spectra reveal geometry for X‐form DNA

Ab initio (MP2/6-31G*(0.25)) interaction energies were calculated for almost 240 geometries of 10 stacked nucleic acid−base pairs: A···A, C···C, G···G, U···U, A···C, G···A, A···U, G···C, C···U, and G···U; in some cases uracil was replaced by thymine. The most stable stacked pair is the G···G dimer (−11.3 kcal/mol), and the least stable is the uracil dimer (−6.5 kcal/mol). The interaction energies of H-bonded base pairs range from −25.8 kcal/mol (G···C) to −10.6 kcal/mol (T···T). The stability of stacked pairs originates in the electron correlation, while all the H-bonded pairs are dominated by the HF energy. The mutual orientation of the stacked bases is, however, primarily determined by the HF interaction energy. The ab initio base stacking energies are well reproduced by the empirical potential calculations, provided the atomic charges are derived by the same method as used in the ab initio calculations. Some contributions previously postulated to significantly influence base stacking (induction interactions, π−π interactions) were not found. Base stacking was also investigated in six B-DNA and two Z-DNA base pair steps; their geometries were taken from the oligonucleotide crystal data. The many-body correction was estimated at the HF/MINI-1 level. The sequence-dependent variations of the total base pair step stacking energies range from −9.9 to −14.7 kcal/mol. The range of the calculated many-body corrections to the stacking energy is 2 kcal/mol. The ab initio calculations exclude the consideration that the unusual conformational properties of the CpA(TpG) steps might be associated with attractive induction interactions of the exocyclic groups of DNA bases and the aromatic rings of bases.

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The Unusual X-Form DNA in Oligodeoxynucleotides: Dependence of Stability on the Base Sequence and Length

Kypr

Chládková²,

Arnold³

et al. 1996

Journal of Biomolecular Structure and Dynamics

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X-form is an unusual double helix of DNA adopted by poly(dA-dT) or (dT-dA)4 at high concentrations of CsF. On the other hand, poly(dA), poly(dT), (dA-dT)4 and most other DNAs do not adopt this conformer. Here we demonstrate that the X-form is strongly destabilized by GC pairs or even minute perturbations of the alternating pyrimidinepurine sequence. For example, the 30-mer d(TATAAT)5, containing five tandem repeats of the Pribnow box, fails to isomerize into the X-form. After (dT-dA)4, the 16-mer (dT-dA)8 is shown to be the second most predisposed oligodeoxynucleotide in the (dT-dA)n series to isomerize into the X-form while the duplex lengths corresponding to n = 3,5,6,7,9,12 and 20 make the X-form unstable even in the strictly alternating (dT-dA)n sequence. Consequently, the (dT-dA)n duplex length is also a crucial factor of the X-form stability on the oligodeoxynucleotide level. We discuss a possibility that the X-form is a solution counterpart of the D-form adopted in dehydrated poly(dA-dT) fibers because properties of these two conformers are remarkably similar in many respects.

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Flow linear dichroism and fourier transform IR spectra reveal geometry for X‐form DNA

Cited by 3 publications

References 33 publications

Experimental detection of conformational transitions between forms of DNA: problems and prospects

Experimental detection of conformational transitions between forms of DNA: problems and prospects

Nature of Nucleic Acid−Base Stacking: Nonempirical ab Initio and Empirical Potential Characterization of 10 Stacked Base Dimers. Comparison of Stacked and H-Bonded Base Pairs

The Unusual X-Form DNA in Oligodeoxynucleotides: Dependence of Stability on the Base Sequence and Length

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