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Author Topic: DNA unwinding  (Read 5495 times)

Offline kgoodwin

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DNA unwinding
« on: April 11, 2007, 03:47:01 pm »
I am trying to calculate the structural properties of a DNA sequence bound to an intercalating compound.  The DNA is a 15-mer with 7 correct base pairs on each side of a T-T mismatch in the middle of the sequence.  There is also a break in the DNA 5' to each of the Ts in the mismatched pair.  I would like to calculate the unwinding of the DNA using the global parameters based on C1'-C1' vectors.  I was able to obtain the global parameters for the unbound DNA, but 3DNA did not calculate them for the DNA with the compound bound (the output file only shows the deviation from regular linear helix).  Do you have any suggestions about how I might formulate my input file in order to obtain these parameters for the bound DNA?  Or do you have any suggestions for how I might be able to calculate the degree of unwinding using the other parameters?

Offline xiangjun

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« Reply #1 on: April 12, 2007, 12:21:05 am »
Hi,

There is a default cut-off threshold (0.6) used in 3DNA to decide if a structure is too curved to calculate the global parameters based on C1'-C1' vector. It is defined in the file "misc_3dna.par" (under directory $X3DNA/BASEPARS) on the 7th line -- increase the value (based on your data) will make 3DNA output the parameters you request.

Needless to say, the file "misc_3dna.par" is a bit cryptic -- the parameters were added while 3DNA was under actively development. In the coming new release of 3DNA v2.0, the file is much easer to understand, as show below.
Code: [Select]
# Section 4: is this double helix curved?
std_curved: 0.6         # criterion to decide if a helix is curved (0.6)


HTH,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline kgoodwin

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« Reply #2 on: April 12, 2007, 10:40:18 am »
My "misc_3dna.par" file does not have a 7th line.  It looks like this:
 
4.0  ON  A1  # upper H-bond length limit/atom, alternative location
8.5      # max. distance between paired base origins (FIND_PAIR)
2.5      # max. vertical distance between paired base origins (FIND_PAIR)
65.0    # max. angle between paired bases [0-90] (FIND_PAIR)
6.0      # MIN. distance between RN9/YN1 atoms (FIND_PAIR)
7.5      # max. distance criterion for helix break [0-12] (FIND_PAIR)

Do I need to add a new line, and if so, how should it read?

Thanks,
KDG

Offline xiangjun

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« Reply #3 on: April 12, 2007, 09:16:19 pm »
Hi,

Please down the 3DNA v1.5 from its homepage. The Linux version, as I checked it just a moment ago, has the content of file "misc_3dna.par" as follows:

Code: [Select]
4.0 0.0 ON A1 # upper H-bond length limits/atoms, alternative location
15.0          # max. distance between paired base origins (FIND_PAIR)
2.5           # max. vertical distance between paired base origins (FIND_PAIR)
65.0          # max. angle between paired bases [0-90] (FIND_PAIR)
4.5           # MIN. distance between RN9/YN1 atoms (FIND_PAIR)
7.5           # max. distance criterion for helix break (FIND_PAIR)
0.6           # r7 criterion to decide if a helix is curved
3.2           # r8 H-bond distance for water molecules with base N/O atoms
4.5           # r9 maximum O3'--P distance for linkage (REBUILD)


So it seems you are using an earlier version.

HTH,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.