As of v2.3-2016jan01, the 3DNA analyze program outputs a list of new ‘simple’ base-pair and step parameters, by default. Shown below is a sample output for PDB entry 1xvk. This echinomycin-(GCGTACGC)2 complex has a single DNA strand as the asymmetric unit. 3DNA needs the the biological unit (1xvk.pdb1) to analyze the duplex (with the -symm option). This structure contains two Hoogsteen base pairs, and has popped up on the 3DNA Forum for the zero or negative Rise values. Note that the ‘simple’ Rise values are all positive; for the middle (#4) TA/TA step, it is now 3.09 Å instead of 0.
# find_pair -symm 1xvk.pdb1 1xvk.bps
# analyze -symm 1xvk.bps
# OR by combing the above two commands:
# find_pair -symm 1xvk.pdb1 | analyze -symm
# The output is in file '1xvk.out'
This structure contains 4 non-Watson-Crick (with leading *) base pair(s)
----------------------------------------------------------------------------
Simple base-pair parameters based on RC8--YC6 vectors
bp Shear Stretch Stagger Buckle Propeller Opening
* 1 G+C -3.07 1.55 -0.35 -6.98 0.29 67.33
2 C-G 0.27 -0.17 0.35 -22.34 3.33 -2.80
3 G-C -0.39 -0.17 0.41 22.91 1.81 -2.73
* 4 T+A -3.29 1.56 0.31 -8.03 1.59 -70.46
* 5 A+T -3.29 1.56 -0.31 -8.03 1.59 70.46
6 C-G 0.39 -0.17 0.41 -22.91 1.81 -2.72
7 G-C -0.27 -0.17 0.35 22.34 3.32 -2.80
* 8 C+G -3.07 1.55 0.35 -6.98 0.30 -67.33
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -1.59 0.69 0.19 -3.75 1.75 -1.38
s.d. 1.72 0.92 0.32 17.57 1.15 52.11
----------------------------------------------------------------------------
Simple base-pair step parameters based on consecutive C1'-C1' vectors
step Shift Slide Rise Tilt Roll Twist
* 1 GC/GC -0.55 0.39 7.41 6.40 -4.22 23.36
2 CG/CG -0.05 0.87 2.44 -0.55 3.94 -0.81
* 3 GT/AC 0.38 0.47 7.23 -8.62 3.75 25.70
* 4 TA/TA -0.00 4.73 3.09 -0.00 7.49 25.67
* 5 AC/GT -0.38 0.47 7.23 8.62 3.75 25.70
6 CG/CG 0.05 0.87 2.44 0.55 3.94 -0.82
* 7 GC/GC 0.55 0.39 7.41 -6.40 -4.22 23.36
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.00 1.17 5.32 -0.00 2.06 17.45
s.d. 0.39 1.59 2.50 6.21 4.49 12.52
The simple parameters are ‘intuitive’ for non-Watson-Crick base pairs and associated base-pair steps, where the existing standard-reference-frame-based 3DNA parameters may look weird. Note that these simple parameters are for structural description only, not to be fed into the ‘rebuild’ program. Overall, they complement the rigorous characterization of base-pair geometry, as demonstrated by the original analyze/rebuild pair of programs in 3DNA.
In short, the ‘simple’ base-pair parameters employ the YC6—RC8 vector as the y-axis whereas the ‘simple’ step parameters use consecutive C1’—C1’ vectors. As before, the z-axis is the average of two base normals, taking consideration of the M–N vs M+N base-pair classification. In essence, the ‘simple’ parameters make geometrical sense by introducing an ad hoc base-pair reference frame in each case. More details will be provided in a series of blog posts shortly.
Overall, this new section of ‘simple’ parameters should be taken as experimental. The output can be turned off by specifying the analyze -simple=false command-line option explicitly. As always, I greatly appreciate your feedback.
