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Local sequential minimization of double stranded B-DNA using Monte Carlo annealing

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Abstract

A software algorithm has been developed to investigate the folding process in B-DNA structures in vacuum under a simple and accurate force field. This algorithm models linear double stranded B-DNA sequences based on a local, sequential minimization procedure. The original B-DNA structures were modeled using initial nucleotide structures taken from the Brookhaven database. The models contain information at the atomic level allowing one to investigate as accurately as possible the structure and characteristics of the resulting DNA structures. A variety of DNA sequences and sizes were investigated containing coding and non-coding, random and real, homogeneous or heterogeneous sequences in the range of 2 to 40 base pairs. The force field contains terms such as angle bend, Lennard-Jones, electrostatic interactions and hydrogen bonding which are set up using the Dreiding II force field and defined to account for the helical parameters such as twist, tilt and rise. A close comparison was made between this local minimization algorithm and a global one (previously published) in order to find out advantages and disadvantages of the different methods. From the comparison, this algorithm gives better and faster results than the previous method, allowing one to minimize larger DNA segments. DNA segments with a length of 40 bases need approximately 4 h, while 2.5 weeks are needed with the previous method. After each minimization the angles between phosphate–oxygen-carbon A 1, the oxygen–phosphate–oxygen A 2 and the average helical twists were calculated. From the generated fragments it was found that the bond angles are A 1=150°±2°and A 2=130°±10°, while the helical twist is 36.6°±2° in the A strand and A 1=150°±6° and A 2=130±6° with helical twist 39.6°±2° in the B strand for the DNA segment with the same sequence as the Dickerson dodecamer.

Figure The final minimized DNA segment of the Dickerson dodecamer sequence represented by ball drawings and viewed (left) perpendicular and (right) down the helical axis

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Authors and Affiliations

  1. School of Biomedical and Life Sciences, Chemistry, University of Surrey, Guildford, GU2 7XH, UK

    Konstantinos Sfyrakis, David C. Povey & Brendan J. Howlin

  2. Institute of Physical Chemistry, National Research Center “Demokritos”, 15310, Athens, Greece

    Konstantinos Sfyrakis & Astero Provata

Authors
  1. Konstantinos Sfyrakis
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  2. Astero Provata
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  3. David C. Povey
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  4. Brendan J. Howlin
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Corresponding author

Correspondence to Astero Provata.

Appendices

Appendix A

Initial structures are shown in Tables 6 and 7.

Table 6 The values for the bonds, and angles and torsion angles for the B-DNA strand from the pdb file 166D.pdb
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Table 7 The values for the torsion angles for the B-DNA strand from the pdb file 166D.pdb
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Appendix B

The average starting and final energy values of the minimized double B-DNA strands are shown in Table 8.

Table 8 The average starting and final energy values of the minimized double B-DNA strands. The energy values are composed from the addition of all initials and final potentials of each base which composed the DNA fragments
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Sfyrakis, K., Provata, A., Povey, D.C. et al. Local sequential minimization of double stranded B-DNA using Monte Carlo annealing. J Mol Model 10, 185–197 (2004). https://doi.org/10.1007/s00894-004-0182-0

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  • DOI: https://doi.org/10.1007/s00894-004-0182-0

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