DNA FORM A/B

[bciezah1]

Dear Dr. Xiang-Jun Lu

I have a question, I could see that in the section Classification of each dinucleotide step in a right-handed nucleic acid
structure: A-like; B-like; TA-like; intermediate of A and B, or other cases. in the output file there is a classification as A like or B-like. However, sometimes I see that the corresponding section appear empty. I copy my output to show you what I mean:

   8 GG/CC   -1.19    8.24    2.31   -9.23    7.09    4.72     A
   9 GG/CC   -1.30    8.29    1.93   -4.17    7.08    4.72     A
  10 GA/TC   -1.49    8.52    1.37   -2.55    8.53    1.31
  11 AG/CT   -1.31    8.33    2.80   -7.37    7.00    5.29     A
  12 GG/CC   -1.10    8.62    2.47   -3.32    8.96    0.43     A

Can you explain, please, what this mean for the software? I mean...I guess this is either not A or not B, what is this?

Thank you very much in advance,

Basilio.

[xiangjun]

Hi Basilio,

It means not A-, or B-, or TA-like, based on the criteria used in 3DNA. See the source code ana_fncs.c/print_PP() for details. Bear in mind that DNA has more conformational flexibility than the three types can cover.

HTH,

Xiang-Jun

[bciezah1]

I see, I understand. I will also review the source code.Thank you very much.