- University of Hamburg - Faculty of Biology - Biocenter Klein Flottbek

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Nucleic Acid Basepair Geometry Nomenclature

Basepairing is a fundamental concept in biology - lots of regulative events depend on it. In this respect there is not the ideal basepair important, regultion rather depends on deviations from ideality to enable differentiated reactions on a molecular level.

In the idealized basepair the bases lie in a common plane in a distance corresponding to the energetically most favourable hydrogen bond length. This geometry, however, will hardly be found in 'real' DNA double helices, and much less in RNA structures. Analysis of structure-mechanism relationships requires a precise description of both the relative positions of bases in a pair and the relationship of adjoining pairs in larger structures. A unifying proposal for the description of nucleic acid basepairing and stacking is presented here according to a document of the Joint Commission on Biochemical Nomenclature.

In the table the basepairs are abstracted to rectangles to demonstrate the geometric features described. The average numerical values given for the features found in A-DNA and B-DNA were computed from crystal structures found in the Nucleic Acid Database ('canonical' DNA).

basepair features:
 

Shear
Sx
(Å)


A-DNA:  0.01
B-DNA:  0.00

Stretch
Sy
(Å)


A-DNA: -0.18
B-DNA: -0.15

Stagger
Sz
(Å)


A-DNA:  0.02
B-DNA:  0.09

Buckle
kappa
(°)


A-DNA: -0.1
B-DNA:  0.5

Propeller
pi
(°)


A-DNA: -11.8
B-DNA: -11.4

Opening
sigma
(°)


A-DNA:  0.6
B-DNA:  0.6

basepair step features:
 

Shift
Dx
(Å)


A-DNA:  0.00
B-DNA: -0.02

Slide
Dy
(Å)


A-DNA: -1.53
B-DNA:  0.23

Rise
Dz
(Å)


A-DNA:  3.32
B-DNA:  3.32

Tilt
tau
(°)


A-DNA:  0.1
B-DNA: -0.1

Roll
rho
(°)


A-DNA:  8.0
B-DNA:  0.6

Twist
omega
(°)


A-DNA:  31.1
B-DNA:  36.0

An example of a functional DNA with widely varying geometric values is a TATA-box containing stem-loop to which a regulatory protein (TBP) binds. Shown here is the TATA-box binding protein from yeast with its cognate DNA:

Literature:
WK Olson et al, A standard reference frame for the description of nucleic acid base-pair geometry, J. Mol. Biol. 313 (2001) 229-237
HM Berman et al, The Nucleic Acid Database - a comprehensive relational database of three-dimensional structures of nucleic acids, Biophys. J. 63 (1992) 751-759
http://ndbserver.rutgers.edu/NDB/archives/

Previous papers on a thorough mathematical description of nucleic acid structure:
MS Babcock & WK Olson, The effect of mathematics and coordinate system on comparability and "dependencies" of nucleic acid structure parameters, J. Mol. Biol. 237 (1994) 98-124
MS Babcock et al, Nucleic acid structure analysis. Mathematics for local cartesian and helical structure parameters that are truely comparable between structures, J. Mol. Biol. 237 (1994) 125-156

A historical description of nucleic acid structure elucidation:
RE Dickerson, DNA structure from A to Z, Meth. Enzymol. 211 (1992) 67-110

2-02 - Rolf Bergmann