what does helix-form mean?

[febos]

Good afternoon Dr. Xiang-Jun Lu

Could you please explain to me what does helix-form mean and how do you create it?

Some examples:

Code: [Select]

strand-1 5'-ACC-3'
 bp-type    |||
strand-2 3'-UGG-5'
helix-form  .A

strand-1 5'-GACGGACAAGUU-3'
  bp-type    |||...|||||.
strand-2 3'-CUGAAAGUUCGA-5'
helix-form  A...xx.AAAx

strand-1 5'-CCGUAU-3'
 bp-type    ||||||
strand-2 3'-GGCAUG-5'
helix-form  AAA..

strand-1 5'-CC-3'
 bp-type    ||
strand-2 3'-GG-5'
helix-form  .

strand-1 5'-CCACCGUAUACCG-3'
  bp-type    ||.|||||||||.
strand-2 3'-GGUGGCAUGUGGC-5'
helix-form  ...AAA..x.A.

strand-1 5'-GGC-3'
 bp-type    |||
strand-2 3'-CCG-5'
helix-form  AA

strand-1 5'-CAAGU-3'
 bp-type    |||||
strand-2 3'-GUUCG-5'
helix-form  .AAA

strand-1 5'-UCUG-3'
 bp-type    ||||
strand-2 3'-AGAC-5'
helix-form  A.A

strand-1 5'-CCC-3'
 bp-type    |||
strand-2 3'-GGG-5'
helix-form  ..

Best regards,
Eugene.

[xiangjun]

Hi Eugene,

DSSR classifies each double-helical dinucleotide step into a helix-form of A/B/Z/./x, standing for A-form, B-form, Z-form, undecided (.), or with backbone breaks (x), respectively.

Code: [Select]

            123456789012
strand-1 5'-GACGGACAAGUU-3'
 bp-type    |||...|||||.
strand-2 3'-CUGAAAGUUCGA-5'
helix-form  A...xx.AAAx
In the above example, the strand-1 row gives base sequence in 5' to 3' direction, and the strand-2 row corresponds to the pairing sequence in 3' to 5' direction. The bp-type row has a symbol of '|' for each canonical pair  (Watson-Crick or wobble), and '.' otherwise. The helix-form row has number-of-base – 1 terms, corresponding to the number of dinucleotide steps, and the last column is alway empty. Here the first dinucleotide step, GA/UC, is classified as A-form. The following three steps have proper backbone linkage, but cannot be assigned to A-, B- or Z-form, thus '.'. The fifth step, GA/AA, has backbone break(s), thus 'x'. The following steps have similar meanings.

The method used in DSSR for classifying a double-helical step into A-, B-, or Z-form is experimental, and more details will be reported later. It's worth noting that the method is different from the Zp-based one used in the original 3DNA analyze program.

THT,

Xiang-Jun

[febos]

Thank you! Your explanation was very useful for me.