Comprehensive Bending Classification of Nucleic Acid Double Helix Structures
Bending classification of helical axis - Single-kink lineA definitive conclusion about the preferred model for the description of the helix axis can only be drawn for structures with 13 or more base pairs because fitting a double-kink line requires structures with 13 base pairs at least. Therefore, in the following compilations structures with 12 or less and with 13 or more base pairs are separately listed. It is, however, very likely that in almost all cases also for structures with 12 or less base pairs listed in Tables 4 and 5 a single-kink line is the most appropriate model .
Structures with 13 or more base pairs
Table 1:
Structures with 13 or more base pairs for which the
helical axis is best described by a single-kink line.
Sigma2 of a single-kink
line is only slightly smaller (< 0.2) than for the next best
model(s). All structures have 13 or more base pairs. Therefore, all
of them can be unambigiously classified as single-kink structures, in
principle. Note, however, that for all structures the single-kink
goodness-of-fit is only marginally smaller than for the next-best
model. This Table includes 30 structures.
Structures with 13 or more base pairs for which the
helical axis is best described by a single-kink line and the
alternative double-kink model has a short central segment with 0 or 1
base pairs.
These duplexes are classified as single-kink structures
by the automatic approach. The alternative double-kink model has a
short central segment consisting of 0 or 1 base pairs. In this case
the difference in the goodness-of fit values between the best and the
next best models is not used as a classification criterion. Because of
the small number of structures different listings are not given. This
Table includes 9 structures.
Structures with 13 or more base pairs for which a
double-kink helical axis is selected as the most appropriate
description by the automatic approach, but the central segment consists
of 0 or 1 base pairs only. In these cases the double-kink geometrical
parameters make no sense. Therefore, these structures have to be viewed
as single-kink structures.
The difference in the goodness-of fit values between the
best and the next best models is here not used as a classification
criterion. Because of the small number of structures different listings
are not given. This Table includes 21 structures. If these
structures occur in other classification schemes they are indicated by
a *.
Structures with 12 or less base pairs
Table 4: Structures with
an automatically assigned single-kink helical axis.
Sigma2 of a single-kink
line is significantly smaller (> 0.2) than sigma2 of the
next best model.
All structures
of Table 4 have 12 or less base pairs. Therefore, fitting a double-kink
helical axis is not possible in these cases. Visual inspection shows
that almost all of these structures have in fact a single-kink
helical axis even though, especially for small kink angles, a
non-ambigious manual classification is impossible. This Table includes 54 structures.
Table 5: Structures with
an automatically assigned single-kink helical axis.
Sigma2 of a single-kink
line is only slightly smaller (< 0.2) than for the next best
model(s). All structures of Table 5 have 12 or less base
pairs. Therefore, fitting a
double-kink helical axis is not possible in these cases. For small kink angles it is not possible to differentiate
between single-kink or double-kink helical axes by visual inspection.
This Table includes 179 structures.
An example of a single-kink structure with 20 base pairs is shown below.
| PDB code | 1tup |
| image |
|
| molecule type | DNA part of a p53 tumor suppressor-DNA complex |
| kink angle | 22 ° |
| base pairs | 20 |
| JPEG | |
Here two single-kink structures with 10 and 12 base pairs are shown.
| PDB code | 410d |
1d88 |
| image |
|
|
| molecule type | duplex[5'-D(GCGTA+TACGC)]2 with incorporated 2'-O-ethoxymethylene ribonucleoside | DNA/RNA chimeric duplex |
| kink angle | 29 ° |
29 ° |
| base pairs | 10 |
12 |
| JPEG | ||
