Delphi on DNA

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letheve
Posts: 1
Joined: Thu Nov 12, 2015 4:39 am

Delphi on DNA

Post by letheve » Thu Nov 12, 2015 4:47 am

Dear users,

Until now, i used Delphi to obtain electrostatic potential from my whole DNA but now i want to calculate the potential only for DNA major groove .

Can someone knows how to do this kind of calculation ?

Sincerely

charlesarnot
Posts: 1
Joined: Thu Dec 24, 2015 1:06 pm

Re: Delphi on DNA

Post by charlesarnot » Thu Dec 24, 2015 1:22 pm

Hey Letheve,

I do not have any idea about this calculations, and I hope that you will not get the right details from the users here as well. This is absolutely a rare subject as far as I am concerned. If you ask about DNA structure and in general, then I could possible to help you. Do not think that I have joined here unnecessarily. I just shared with you about how people reacts to this question.

When I was unsure about this topic, I asked my friends and some other intelligent too, however I did not get the one you want here.

:(

Karina507
Posts: 1
Joined: Thu Sep 07, 2017 9:36 am

Re: Delphi on DNA

Post by Karina507 » Thu Sep 07, 2017 10:19 am

A direct connection between a groove width and electrostatic potential recently was established, providing a physical basis for this type of shape readout. Specifically, the magnitude of the electrostatic potential in the minor groove is controlled by the width of the groove3 with narrowing of the groove associated with more negative electrostatic potential. Many proteins have been found to take advantage of this property by inserting positively charged arginine side chains into the groove where it is narrow.
I'm not an specialist, but if I were you I would first set at which point I want to make the calculus (e.g. from Phosphate 3 to Phosphate 6') and calculate the width at every snapshot. This way you can provide the mean of the minor groove width +/- the standard deviation. First of all, what I told you is how to calculate the "groove width". The definition major/minor stands on which one is the largest and which one is the shortest. The i values in B-DNA +/- 4 for major groove. I am analyzing DNA minor groove width using Curve+.
Imagine we have a dsDNA and we are situated at the phosphate at position i (i.e. P(i)). If we increase the phosphate position in the complementary strand (i.e. P'(i+1), P'(i+2) ... P'(n)) and we calculate distances from those phosphates to P(i), we will observe that as the phosphate position increases, the distance between phosphates also gets larger, up to a maximum, but later, the distance starts decreasing until a minimum, and then it increases again. If we repeat the same procedure but decrasing phosphate positions, we will obtain another minimum. The larger of the two minimums is the width of the major groove and the smaller is the width of the minor groove. ;)
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stephanyortega
Posts: 1
Joined: Fri Sep 08, 2017 2:53 am

Re: Delphi on DNA

Post by stephanyortega » Fri Sep 08, 2017 7:53 am

do not have any idea about this calculations, and I hope that you will not get the right details from the users here as well. This is absolutely a rare subject as far as I am concerned. If you ask about DNA structure and in general, then I could possible to help you. Do not think that I have joined here unnecessarily. I just shared with you about how people reacts to this question.
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abriljoseph
Posts: 1
Joined: Wed Sep 13, 2017 4:22 am
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Re: Delphi on DNA

Post by abriljoseph » Wed Sep 13, 2017 4:27 am

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