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Definitions and Nomenclature of Nucleic Acid Structure Parameters

(R. E. Dickerson et al., J. Mol. Biol. (1989) 205, 787-791.)

Subsections: Rotation and Translation

Values below the pictures belong to

  1. an A-helix (Blackburn and Gait, Nucleic acids in chemistry and biology, Oxford University Press New York 1996)
  2. an Curves output from ideal A-RNA, letters in brackets denote the section.
  3. an B-DNA helix (Blackburn and Gait, Nucleic acids in chemistry and biology, Oxford University Press New York 1996)
  4. an Curves output from ideal B-DNA, letters in brackets denote the section.

The Curves reference files are available for


Rotation

Definitions of various rotations involving 2 bases of a pair (upper 2 picture rows) or 2 successive base-pairs (bottom picture row).

motions are co-coordinated

Co-ordinate frame Tip Inclination
Co-ordinate frame Tip Inclination
I -- 11.0 ° 12.0 °
II (C) -- 0.0 ° 15.8 °
III -- 0.0 ° 2.4 °
IV (C) -- 0.0 ° -6.0 °

motions are opposed

Opening Propeller Twist Buckle
Opening Propeller Twist Buckle
I -- -8.3 ° -2.4 °
II (D) -4.22 ° 14.42 ° 0.01 °
III -- -11.1 ° -0.2 °
IV (D) -3.90 ° 3.87 ° 0.00 °

two-base pair step

Twist Roll Tilt
Twist Roll Tilt
I 32.7 ° 6.3 ° 16 - 19 °
II (F) 32.7 ° 0.0 ° 0.0 °
III 36.1 ° 0.6 ° 0.0 °
IV (F) 36.0 ° 0.0 ° 0.0 °




Translation

Definitions of various translations involving 2 bases of a pair (upper 2 picture rows) or 2 successive base-pairs (bottom picture row).

motions are co-coordinated

P-P interstrand distance y displacement x displacement
Co-ordinate frame y_displ x_displ
I 11.5 - 11.9 Å 4.4 Å --
II (C) -- 0.0 Å -5.30 Å
III 8.8 - 14.0 Å -0.2 to -1.8 Å --
IV (C) -- 0.0 Å -0.7 Å

motions are opposed

Stagger Stretch Shear
Stagger Stretch Shear
I -- -- --
II (D) 0.21 Å -0.38 Å 0.00 Å
III -- -- --
IV (D) 0.06 Å 0.03 Å 0.0 Å

two-base pair step

Rise Slide Shift
Rise Slide Shift
I 2.8 Å -- -4.1 Å
II (F) 2.81 Å 0.00 Å 0.00 Å
III 3.36 Å 0.4 Å 0.8 Å
IV (F) 3.38 Å 0.0 Å 0.0 Å


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