Messages

1

General discussions (Q&As) / Re: Base Pair Step Parameters

« on: February 18, 2009, 03:59:55 pm »

Thanks for your answer and sorry for the little info.

    Maybe I should make myself more clear. I simulated a 12 mer A-RNA with one modified nucleotide in the middle.  The modification caused a perturbation in the following base-pair which is still watson-Crick. One of them is quite appart from its natural position (compared to the wild-type ) . The base-pair parameters are quite different from the control specially propeller, stragger and bucke. I don´t know if such values allow me to use the   step parameters (Roll , Rise, Tilt) since they are calculated from irregular  base pairs .


 I´m sending an attachment the output of  modified duplex to explain my point. THe modification is the U7 of Strand II, notice that  the effect is seen in the base of the C6 of strand 2 which shows to be quite affected.

  Hope this help u to understand my problem

Best Reagads.

Rodrigo

2

General discussions (Q&As) / Base Pair Step Parameters

« on: February 16, 2009, 02:41:54 pm »

I´m analyzing an double helix RNA with a modified nucleotide. The effect of the modification pushes one of the bases but doesnt affect complementary one. stragger, proppeler and Buckle are very affected. Since  it affects only one base of the base pair I dont know if  it is correct two analyze roll and tilt. May be its a wrong average of a non-averageble structure.
It would be great If you could tell me if I should take in consideration the base pair step parameters in my analysis.

  Thanks

Regads