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The post-SCF quantum chemistry characteristics of inter- and intra-strand stacking interactions in d(CpG) and d(GpC) steps found in B-DNA, A-DNA and Z-DNA crystals

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Abstract

The energies of intra- and inter-strand stacking interactions in model d(GpC) and d(CpG) two-base-pair steps were estimated by MP2/aug-cc-pVDZ single point calculations corrected for basis superposition errors. The stacked two-nucleobase pairs were constructed using experimental values of base pair and base step parameters taken from Nucleic Acid Database (http://ndbserver.rutgers.edu/). Three distinct polymorphic forms were analysed, namely A-, B- and Z-DNA. The applied methodology enables statistical analysis of structural and energetic diversities. The structural relationships between polymorphic forms are quite complex and depend on the sequence of pairs. The variability of parameters such as shift and tilt is almost the same irrespective of the polymorphic form and sequence of steps analysed. In contrast, shift and twist distributions easily discriminate all three polymorphic forms of DNA. Interestingly, despite significant structural diversities, the energies of the most frequent energy ranges are comparable irrespective of the polymorphic form and base sequence. There was observed compensation of inter- and intra-strand interactions, especially for d(GpC) and d(CpG) steps found in A- and B-DNA. Thus, among many other roles, these pairs act as a kind of energetic buffer, balancing the double helix.

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Acknowledgements

The technical assistance of Ms. A. Cieślińska is greatly appreciated. The results were partly obtained based on computational grants from PCSS (Poznań Supercomputing and Networking Centre, Poland).

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Authors and Affiliations

  1. Department of Physical Chemistry, Collegium Medicum, Nicolaus Copernicus University, Kurpińskiego 5, 85-950, Bydgoszcz, Poland

    Piotr Cysewski

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Correspondence to Piotr Cysewski.

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Table S1

List of the NDB and PDB file names of oligo-nucleotides used in this paper for description of interactions in model d(GpC) and d(CpG) steps. NR Nominal resolution in Å (DOC 148 kb)

Table S2

The intermolecular interaction energies (IIE, in kcal/mol) of CG and GC stacked pairs found in B-DNA. The NDB file names were used along with the pair position in the oligo-nucleotide sequence. Notation for interactions within d(CpG) steps is as follows: ΔE12 5′-C/G-3′ in stand I; ΔE13 5′-C|C-5′, ΔE24 3′-G|G-3′ and ΔE34 5′-C/G-3′ in stand II. By analogy, the IIE in d(GpC) steps are denoted as follows: ΔE12 5′-G/C-3′ in stand II, ΔE13 5′-G|G-5′, ΔE24 3′-C|C-3′ and ΔE34 5′-G/C-3′ in stand II. The energies of hydrogen bonded pairs are symbolised as ΔE14 for 5′-G-C-3′ and ΔE23 3′-G-C-5′, respectively (DOC 407 kb).

Table S3

Intermolecular interaction energies (IIE in kcal/mol) in model d(CpG) and d(GpC) found in A-DNA. Notation as in Table S2 (DOC 290 kb).

Table S4

Intermolecular interaction energies (IIE in kcal/mol) in model d(CpG) and d(GpC) steps found in Z-DNA. Notation as in Table S2 (DOC 168 kb).

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Cysewski, P. The post-SCF quantum chemistry characteristics of inter- and intra-strand stacking interactions in d(CpG) and d(GpC) steps found in B-DNA, A-DNA and Z-DNA crystals. J Mol Model 15, 597–606 (2009). https://doi.org/10.1007/s00894-008-0378-9

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