Double stranded DNA

People,

I have two complementary strands of DNA (three bases each) lying close
to each other - how do make the hydrogen bonds so that the two strands
line up properly when I click “Optimize Geometry”? (I saw that hydrogen
bonds are supposed to be possible but couldn’t see how to set them
manually).

Thanks,

Phil.

Philip Rhoades

GPO Box 3411
Sydney NSW 2001
Australia
E-mail: phil@pricom.com.au

I have two complementary strands of DNA (three bases each) lying close
to each other - how do make the hydrogen bonds so that the two strands
line up properly when I click “Optimize Geometry”?

If you’re using the MMFF94 method for optimizing geometry (this is the default), then hydrogen bonding is included in the method itself – you don’t need to do anything.

If you want to see the hydrogen bonds, click on the “Display Types” button, and enable “Hydrogen Bonds” as an option.

Hope that helps,
-Geoff


Prof. Geoffrey Hutchison
Assistant Professor, Department of Chemistry
University of Pittsburgh


Office: (412) 648-0492

Geoff,

On 2010-05-25 01:51, Philip Rhoades wrote:

People,

I have two complementary strands of DNA (three bases each) lying
close to each other - how do make the hydrogen bonds so that the
two strands line up properly when I click “Optimize Geometry”? (I
saw that hydrogen bonds are supposed to be possible but couldn’t
see how to set them manually).

Thanks,

Phil.

If you’re using the MMFF94 method for optimizing geometry (this is
the default), then hydrogen bonding is included in the method itself
– you don’t need to do anything.

If you want to see the hydrogen bonds, click on the "Display Types"
button, and enable “Hydrogen Bonds” as an option.

Hope that helps, -Geoff

The strands are close to each other but not in the correct, double
stranded position - I thought I would be able to “make” the hydrogen
bonds somehow and then click on “Optimize Geometry” which would drag the
strands into the correct position . .

Thanks,

Phil.

Philip Rhoades

GPO Box 3411
Sydney NSW 2001
Australia
E-mail: phil@pricom.com.au

On May 28, 2010, at 9:39 AM, Philip Rhoades wrote:

The strands are close to each other but not in the correct, double
stranded position - I thought I would be able to “make” the hydrogen
bonds somehow and then click on “Optimize Geometry” which would drag the
strands into the correct position . .

If you are using MMFF94, it will recognize hydrogen bonds without any work on your part. Whether that will be enough to “zipper” a double strand, I don’t know. You could also specify some constraints to enforce specific distances between pairs of atoms.

Hope that helps,
-Geoff


Prof. Geoffrey Hutchison
Assistant Professor, Department of Chemistry
University of Pittsburgh


Office: (412) 648-0492

Geoff,

On 2010-05-29 00:46, Geoffrey Hutchison wrote:

On May 28, 2010, at 9:39 AM, Philip Rhoades wrote:

The strands are close to each other but not in the correct, double
stranded position - I thought I would be able to “make” the hydrogen
bonds somehow and then click on “Optimize Geometry” which would drag the
strands into the correct position . .

If you are using MMFF94, it will recognize hydrogen bonds without any work on your part. Whether that will be enough to “zipper” a double strand, I don’t know. You could also specify some constraints to enforce specific distances between pairs of atoms.

Hope that helps,
-Geoff

The best I can do is get one H bond per peptide pair ie in my example of
three pairs - three H bonds. If I select and drag/rotate etc some parts
of a single strand to make the second H bond by pair, it will show the H
bond but as soon I as I “Optimize Geometry” it separates the strands and
breaks the second bond . . (I am using three A-T peptide pairs).

It would be nice to be able to do what I said before - indicate where
the H bonds should be and then clicking “Optimize Geometry” changes the
conformation of the strands to allow the correct structure . . doesn’t
look like this is possible at the moment . .

Thanks anyway,

Phil.


Philip Rhoades

GPO Box 3411
Sydney NSW 2001
Australia
E-mail: phil@pricom.com.au

Geoff,

On 2010-05-29 02:08, Philip Rhoades wrote:

Geoff,

On 2010-05-29 00:46, Geoffrey Hutchison wrote:

On May 28, 2010, at 9:39 AM, Philip Rhoades wrote:

The strands are close to each other but not in the correct, double
stranded position - I thought I would be able to “make” the hydrogen
bonds somehow and then click on “Optimize Geometry” which would drag the
strands into the correct position . .

If you are using MMFF94, it will recognize hydrogen bonds without any
work on your part. Whether that will be enough to “zipper” a double
strand, I don’t know. You could also specify some constraints to
enforce specific distances between pairs of atoms.

Hope that helps,
-Geoff

The best I can do is get one H bond per peptide pair ie in my example of
three pairs - three H bonds. If I select and drag/rotate etc some parts
of a single strand to make the second H bond by pair, it will show the H
bond but as soon I as I “Optimize Geometry” it separates the strands and
breaks the second bond . . (I am using three A-T peptide pairs).

It would be nice to be able to do what I said before - indicate where
the H bonds should be and then clicking “Optimize Geometry” changes the
conformation of the strands to allow the correct structure . . doesn’t
look like this is possible at the moment . .

I couldn’t see how to use the constraints to enforce distances - I will
play with it some more . . I am still getting odd things happening like
"Optimize Geometry" and “Molecular Mechanics” disappearing off the menu
and only uninstalling and reinstalling Avogadro restores them.

Thanks,

Phil.

Philip Rhoades

GPO Box 3411
Sydney NSW 2001
Australia
E-mail: phil@pricom.com.au