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Table 1 List of used sets of structural parameters

From: The role of structural parameters in DNA cyclization

Parameter set name Reference Derivation approach Number of nucleotides Tilt Roll Twist Shift Slide Rise
SET1 (Zhou et al., 2013) [43] All-atom Monte Carlo simulations Pentanucleotides No Yes Yes No No No
SET2 (Gabrielian and Pongor, 1996) [45] Computationally combining SET3 and SET4 Trinucleotides No Yes No No No No
SET3 (Brukner et al., 1995) [44] Endonuclease experiments Trinucleotides No Yes No No No No
SET4 (Goodsell and Dickerson, 1994) [40] Nucleosome positioning Trinucleotides No Yes No No No No
SET5 (Ulyanov and James, 1995) [46] NMR spectroscopy Dinucleotides Yes Yes Yes Yes Yes Yes
SET6 (Rachofsky et al., 2001) [47] Computational analysis of X-ray crystallography Dinucleotides Yes Yes Yes Yes Yes Yes
SET7 (Olson et al., 1998) [48] Computational analysis of X-ray crystallography Dinucleotides Yes Yes Yes Yes Yes Yes
  1. Reference information, derivation approach, and number of nucleotides are provided for each set of parameters. Additionally, the table denotes with “Yes” which of the six types of parameters is provided in the respective references. “No” is equivalent to using a default value for all nucleotide combinations. Default values: tilt = 0.00°; helix twist = 34.30°; shift = 0.00 Å; slide = 0.00 Å; rise = 3.40 Å. The exact values for each set of parameters are provided in Additional file 1: Tables S3 through S9 respectively for SET1 through SET7