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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:
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.
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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.
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
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Thank you! Your explanation was very useful for me.
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University