A Standard Reference Frame for the Description
of Nucleic Acid Base-pair Geometry
The report is available at Journal
of Molecular Biology (2001) 313: 229 - 237 and The Nucleic Acid
- Cartesian coordinates for A, C, G, T,
and U in the optimized reference frame
Standard chemical structures taken from Clowney
et al. (1996), J. Am. Chem. Soc., 118, 509-518). These data
do not include C1' atoms, which are placed here in the least-squares
plane of the base atoms, with the purine C1'-N9 bond length and
C1'-N9-C4 valence angle set respectively to 1.46 Å and 126.5°
and the pyrimidine C1'-N1 bond and C1-N1-C2 angle to 1.47 Å
and 118.1°. These distances and angles are based on the average
glycosyl geometries of purines and pyrimidines in high
resolution crystal structures of nucleic acid analogs from the
Cambridge Structure Database (John Westbrook and Helen M. Berman,
- Schematic representation of base-pair,
dimer step and helical parameters
If a base or base-pair is taken as a rigid block,
six parameters are required to describe rigorously the position
and orientation of one base-pair relative to another. There are
two sets of local parameters commonly in use in nucleic acid conformational
analysis: step parameters (Shift, Slide, Rise, Tilt, Roll and Twist)
which show the stacking geometry between neighboring base-pairs,
and helical parameters (x-displacement, y-displacement, helical
rise, inclination, tip, and helical twist) which demonstrate the
position and orientation of a base-pair relative to the helical
axis, defined here by the repetitive of a two-base-pair unit. These
two sets of parameters are obviously interrelated: from one set,
the other can be deduced and vice versa. The values of local vs.
helical rise and twist from these two sets of parameters can be
quite different in DNAs which deviate significantly from B-DNA.
- Comparative analysis of DNA base-pair
parameters in the TATA-box protein-DNA crystal structure
Y. Kim, J. H. Geiger, S. Hahn & P. B. Sigler (1993) ``Crystal
structure of a yeast TBP/TATA-box complex,'' Nature 365, 512-520.)
- Starting from the same base reference
frame, all methods of analysis give similar numerical values,
and show the same sequence-dependent patterns. This similarity
holds more for base-pair
parameters than for dimer
step or helical parameters, since the base-pair reference
frame is derived differently by the various methods.
- Slight variations in the imposed configurational
constraints have a limited and systematic influence on the
base reference frame, and thus affect base-pair parameters but
do not affect step and helical parameters. More specifically,
changing the O
H-N distance (dO-N) from 3.0 Å
to 2.9 Å increases stretch by about 0.1 Å, and changing
lambda0 from 54.5° to 55.5° decreases Opening
by about 2°. This is illustrated using the
AA/TT (base-pairs 8 and 9) from pdt012 as an example.
values and dispersion (in parentheses) of base-pair, dimer step,
and helical parameters in high resolution A-DNA
structures surveyed in this study.
These parameters are calculated for different analysis schemes with
the newly recommended base reference frame.
- Intrinsic correlations
By definition, there are four
sets of intrinsic correlations between base-pair parameters
and dimer step parameters associated with the current reference
frame (illustrated here using
pdt012 as an example):
Since the variations in Shear, Stagger, Opening,
Tilt and Shift are normally small, they are often ignored in DNA conformational
analysis. Not surprisingly, the last three correlations have never
been previously uncovered. These correlations, however, exist in the
CompDNA and RNA programs, but not in the original FREEHELIX, CEHS and
NUPARM programs, where the base-pair reference frame is defined
by the RC8-YC6 line and the base-pair normal vector rather than the
"middle-frame" of the two complementary bases. The discrepancy in
Twist between heavily sheared base-pairs has been reported in the
- Negative correlation between Rise and
the difference of Buckle. Since base-pair distortion by buckling
is both large and frequent, this correlation is strong and has
been known for many years.
- Negative correlation between Tilt and
the difference of Stagger.
- Positive correlation between Shift
and the difference of Opening.
- Positive correlation between Twist
and the difference of Shear.
By contrast, Slide and Roll, two of the most
important parameters, are much less sensitive to base-pair distortions,
and are thus more reliably defined in a comparable way among the
currently available analysis programs.
Last modified: Wed Apr 25 14:35:47 2001