Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · Reproduce DSSR · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Author Topic: Circular DNA and Groove Information  (Read 48 times)

Offline ry54451

  • regular
  • *
  • Posts: 11
    • View Profile
Circular DNA and Groove Information
« on: March 08, 2019, 03:20:45 pm »
Thanks for an absolutely fantastic software package. I've been able to devote more time to understanding it while improving my own programming skills and you've done a brilliant job with 3DNA.

I wanted to know if you had any plans on incorporating circular analysis? I ask as I work with 336bp and 1014bp circles and would like to get minor-/major-groove data. However, the first and last few entries lack values. I've been looking at the cited paper to get a better idea with maybe calculating it on my own, but I wanted to know if circular analysis was on the radar.

Again, thanks for your time.

Note: I've posted a simple planar circle as an example.

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1356
    • View Profile
    • 3DNA homepage
Re: Circular DNA and Groove Information
« Reply #1 on: March 08, 2019, 05:05:18 pm »
Hi,

Thanks a lot for your kind words about 3DNA!

Yes, I'd like to incorporate the analysis of circular DNA or RNA into 3DNA. Your attached example looks beautiful and serves as a good starting point. Timewise, I'm recently busy with a deadline, but would hopefully get back to the topic late next week. I'll have a follow-up along this thread once I've something concrete to share.

Best regards,

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

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1356
    • View Profile
    • 3DNA homepage
Re: Circular DNA and Groove Information
« Reply #2 on: March 18, 2019, 12:15:35 pm »
In addition to groove dimensions for circular DNA or RNA, as you asked in your starting post, do you have any preference on how to list the base-pair step parameters? I am planning to add a new option, tentatively named '--circular', to the 3DNA analyze program. Does it sound good?

Best regards,

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

Offline ry54451

  • regular
  • *
  • Posts: 11
    • View Profile
Re: Circular DNA and Groove Information
« Reply #3 on: March 19, 2019, 10:34:39 am »
That sounds great!
It's been my experience that there doesn't need to be a new way of arranging the base pair nor the base pair step parameters except that the first base pair will need to be repeated at the end (N base pairs so N base pair steps) in order to collect the last base pair step data.

 

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.