Re: [ccp4bb] the structures of Nucleic acid

[Phoebe A. Rice]

For complex RNA structures,

  *   Molecular replacement can stumble
  *   If made by simple T7 transcription methods (the most common way), the RNA 
would have EVERY U replaced with 5-bromo-U
  *   Adding bromine to the 5 position of U could affect the structure (it 
would be replacing -H not -CH3)

~~~
Phoebe A. Rice
Dept. of Biochem & Mol. Biol. and
  Committee on Microbiology
https://voices.uchicago.edu/phoebericelab/


From: CCP4 bulletin board  on behalf of Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Date: Monday, September 18, 2023 at 4:44 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] the structures of Nucleic acid
I am afraid most scientists will use the most straightforward technique!
If SAD is available the PHOSPHATE backbone of DNA will provide sufficient 
signal to allow SAD to work, and you get an unambiguous answer to whether it is 
A-DNA or B or Z...
MR will usually work of course as well
Eleanor


On Mon, 18 Sept 2023 at 09:18, Natesh Ramanathan 
mailto:nat...@iisertvm.ac.in>> wrote:
Dear Fu Xingke,

 Depends on what Nucleic Acid you are talking of.  If it is RNA, you 
can expect some sequence to tertiary structure correspondence so you might be 
able to try more MR as compared to DNA.   DNA may have double helical 
architecture but less sequence to tertiary structure correspondence, and hence 
DNA is less likely to have a 3D structure like RNA specific structure for a 
sequence.

 SAD has become a straight forward method to avoid all these problems 
to get ab-initio structure.  So many go for it directly.

Hope that helps.
Best wishes,
Natesh

On Mon, 18 Sept 2023 at 13:36, fuxingke 
mailto:fuxingke0...@163.com>> wrote:
Dear Colleagues,
 Reacently, I find the structures of Nucleic acid are solved by 
single-wavelength anomalous diffraction(SAD). So, why molecular replacement 
(MR) not?

Regards



Best wishes,
Fu Xingke
Institute of Physics CAS



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1


--
--
"Live Simply and do Serious Things .. "
- Dorothy Mary Crowfoot Hodgkin OM, FRS

"In Science truth always wins"
- Max Ferdinand Perutz OM FRS
--
Dr. Ramanathan Natesh
Associate Professor,
School of Biology and Center for High-Performance Computing (CHPC),
Founding and Current President of Cryo Electron Microscopy and 3 Dimensional 
Image Processing Society of India (CEM3DIPSI),
Indian Institute of Science Education and Research Thiruvananthapuram 
(IISER-TVM),
Maruthamala P.O., Vithura,
Thiruvananthapuram,  695551, Kerala, India

nat...@iisertvm.ac.in<mailto:nat...@iisertvm.ac.in>
http://faculty.iisertvm.ac.in/natesh

Researcher ID: http://www.researcherid.com/rid/C-4488-2008
ORCID: http://orcid.org/-0002-1145-5962
Vidwan-ID : 94134: http://iisertvm.irins.org/profile/94134
PUBLONS: https://publons.com/author/1520837/ramanathan-natesh#profile

Office Ph. 0091- 471-2778087



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Re: [ccp4bb] the structures of Nucleic acid

[Harry Powell]

Hi

I am also reminded that I was involved in the data collection but not structure 
solution of a DNA cyclic octamer from a single wavelength dataset collected to 
atomic resolution (on image plate…), which was solved after locating a Ba 
(which turned out to be one of several with partial occupancy); the structure 
solution was actually carried out in the laboratory of one G.M. Sheldrick, 
using software that I think may have never been released to the public.

See 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC20809/

for details...

Harry

> On 19 Sep 2023, at 20:53, Diana Tomchick  
> wrote:
> 
> I have also found that there is significant anomalous signal from strontium 
> near the Se K-edge, which is useful if one uses strontium chloride instead of 
> potassium chloride (or in addition to KCl) during crystal growth.
> 
> Diana
> 
> **
> Diana R. Tomchick
> Professor
> Departments of Biophysics and Biochemistry
> UT Southwestern Medical Center
> 5323 Harry Hines Blvd.
> Rm. ND10.214A
> Dallas, TX 75390-8816
> diana.tomch...@utsouthwestern.edu
> (214) 645-6383 (phone)
> (214) 645-6353 (fax)
> 
> 
> 
>> On Sep 19, 2023, at 1:32 PM, Wagner, Armin (DLSLtd,RAL,LSCI) 
>> <ada38eff8538-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> 
>> EXTERNAL MAIL
>> 
>> Dear Fu Xingke,
>>  
>> Indeed P-SAD is quite attractive but requires high resolution as the number 
>> of anomalous scatterers (1 P per nucleotide) is rather large, but the unit 
>> cells are typically quite small, resulting in a rather small number of 
>> anomalous differences per scatterer. Based on the very nice publication from 
>> Tom Terwilliger et al. ( https://doi.org/10.1107/S2059798315019269) we wrote 
>> a little web app to predict the success for S-SAD phasing at the 
>> long-wavelength beamline I23 at Diamond. 
>> https://www.diamond.ac.uk/Instruments/Mx/I23/resolution-requirement-phasing-app.html
>> While the predictions are pretty reliable for S-SAD, there is a (not heavily 
>> tested) option to also submit DNA or RNA sequences, which can give you a 
>> hint on what you are against, or what resolution you should aim for. 
>> Unfortunately, we have not had many successful examples to far, but 
>> basically all the P-SAD projects which were predicted not to work at the 
>> resolutions the crystals diffracted to didn’t solve, so we are very 
>> interested in projects which are predicted to work to fine tune this also 
>> for P-SAD as there will be continuous need for experimental phasing in 
>> particular for non-canonical RNA/DNA structures.
>>  
>> 5-Br-U is a good alternative and works well, but we have also managed to 
>> solve RNA/DNA by K-SAD or Co-SAD (https://doi.org/10.1093/nar/gkaa439) and 
>> Ca could be attractive as a potential anomalous scatter as well.
>>  
>> Best regards,
>>  
>> Armin
>>  
>>  
>>  
>>  
>> From: CCP4 bulletin board  on behalf of Mark J. van 
>> Raaij 
>> Date: Tuesday, 19 September 2023 at 12:31
>> To: CCP4BB@JISCMAIL.AC.UK 
>> Subject: Re: [ccp4bb] the structures of Nucleic acid
>> 
>> This just appeared and may be relevant:
>> https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad726/7272628
>>  
>> Critical Reviews and Perspectives
>> When will RNA get its AlphaFold moment? 
>> Mark van Raaij
>> Dpto de Estructura de Macromoleculas, lab 20B
>> Centro Nacional de Biotecnologia - CSIC
>> calle Darwin 3
>> E-28049 Madrid, Spain
>> tel. +34 91 585 4616 (internal 432092)
>> 
>> 
>> 
>> On 18 Sep 2023, at 18:07, William G. Scott 
>> <2844d921eb97-dmarc-requ...@jiscmail.ac.uk> wrote:
>>  
>> The phosphorus absorption edge is about 5.8Å.
>> 
>> I've had much better luck with 5-Br-U for anomalous phasing.
>> 
>> Molecular replacement with sub-structural fragments can also work:
>> <https://scottlab.ucsc.edu/scottlab/reprints/2010_Scott_Methods.pdf>
>> 
>> 
>> Yours sincerely,
>> 
>> William G. Scott
>> Professor, Department of Chemistry and Biochemistry
>> and The Center for the Molecular Biology of RNA
>> University of California at Santa Cruz
>> Santa Cruz, California 95064  
>> USA
>> 
>> 
>> On Sep 18, 2023, at 2:43 AM, Eleanor Dodson 
>> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> I am afraid most scientists will use the most straightforward technique! 
>> If SAD is available the PHOSPHATE backbone of DNA will provide sufficient 
&

Re: [ccp4bb] the structures of Nucleic acid

[Harry Powell]

Hi folks

just my two ha’porth.

Back in the mid 1990s, when MAD was becoming common and tunable beamlines were 
being installed at every synchrotron you could shake a stick at, I was involved 
in several successful projects involving 5-Br-U in oligo-DNA crystallography. 
In my (very, very) naïve hands at the time it worked like magic (I remember my 
shock at seeing the base stacking in the first map I calculated for one of the 
structures) - and this was using data collected on image plates with each image 
spanning rather more than 1 degree - so not how it would be done now.

Since just about everything to do with data collection and processing and 
structure solution has improved by leaps and bounds since then, I would back 
Br-SAD to yield a structure.

If anyone’s interested, they can see my contribution regarding this at the 1997 
CCP4 Study Weekend proceedings (this was prior to them appearing in Acta D), 
available at - 

https://legacy.ccp4.ac.uk/courses/proceedings/1997/h_powell/main.html

Contributions at the same meeting by others whose names will be instantly 
recognizable may well be more use than mine…

Best wishes

Harry

> On 19 Sep 2023, at 19:32, Wagner, Armin (DLSLtd,RAL,LSCI) 
> <ada38eff8538-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> 5-Br-U is a good alternative and works well, but we have also managed to 
> solve RNA/DNA by K-SAD or Co-SAD (https://doi.org/10.1093/nar/gkaa439) and Ca 
> could be attractive as a potential anomalous scatter as well.
>  
> Best regards,
>  
> Armin
>  
>  
>  
>  
> From: CCP4 bulletin board  on behalf of Mark J. van 
> Raaij 
> Date: Tuesday, 19 September 2023 at 12:31
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] the structures of Nucleic acid
> 
> This just appeared and may be relevant:
> https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad726/7272628
>  
> Critical Reviews and Perspectives
> When will RNA get its AlphaFold moment? 
> Mark van Raaij
> Dpto de Estructura de Macromoleculas, lab 20B
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. +34 91 585 4616 (internal 432092)
> 
> 
> 
> On 18 Sep 2023, at 18:07, William G. Scott 
> <2844d921eb97-dmarc-requ...@jiscmail.ac.uk> wrote:
>  
> The phosphorus absorption edge is about 5.8Å.
> 
> I've had much better luck with 5-Br-U for anomalous phasing.
> 
> Molecular replacement with sub-structural fragments can also work:
> <https://scottlab.ucsc.edu/scottlab/reprints/2010_Scott_Methods.pdf>
> 
> 
> Yours sincerely,
> 
> William G. Scott
> Professor, Department of Chemistry and Biochemistry
> and The Center for the Molecular Biology of RNA
> University of California at Santa Cruz
> Santa Cruz, California 95064  
> USA
> 
> 
> On Sep 18, 2023, at 2:43 AM, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> I am afraid most scientists will use the most straightforward technique! 
> If SAD is available the PHOSPHATE backbone of DNA will provide sufficient 
> signal to allow SAD to work, and you get an unambiguous answer to whether it 
> is A-DNA or B or Z...
> MR will usually work of course as well
> Eleanor
> 
> 
> On Mon, 18 Sept 2023 at 09:18, Natesh Ramanathan  
> wrote:
> Dear Fu Xingke,
> 
> Depends on what Nucleic Acid you are talking of.  If it is RNA, you 
> can expect some sequence to tertiary structure correspondence so you might be 
> able to try more MR as compared to DNA.   DNA may have double helical 
> architecture but less sequence to tertiary structure correspondence, and 
> hence DNA is less likely to have a 3D structure like RNA specific structure 
> for a sequence.
> 
> SAD has become a straight forward method to avoid all these problems 
> to get ab-initio structure.  So many go for it directly.
> 
> Hope that helps.
> Best wishes,
> Natesh
> 
> On Mon, 18 Sept 2023 at 13:36, fuxingke  wrote:
> Dear Colleagues,
> 
> Reacently, I find the structures of Nucleic acid are solved by 
> single-wavelength anomalous diffraction(SAD). So, why molecular replacement 
> (MR) not?
> 
> Regards
> 
> 
> 
> Best wishes,
> 
> Fu Xingke
> 
> Institute of Physics CAS
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
> 
> 
> -- 
> --
> "Live Simply and do Serious Things .. "
> - Dorothy Mary Crowfoot Hodgkin OM, FRS
> 
> "In Science truth always wins"
> - Max Ferdinand Perutz OM FRS
> --
> D

Re: [ccp4bb] the structures of Nucleic acid

[Diana Tomchick]

I have also found that there is significant anomalous signal from strontium 
near the Se K-edge, which is useful if one uses strontium chloride instead of 
potassium chloride (or in addition to KCl) during crystal growth.

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu>
(214) 645-6383 (phone)
(214) 645-6353 (fax)



On Sep 19, 2023, at 1:32 PM, Wagner, Armin (DLSLtd,RAL,LSCI) 
<ada38eff8538-dmarc-requ...@jiscmail.ac.uk<mailto:ada38eff8538-dmarc-requ...@jiscmail.ac.uk>>
 wrote:


EXTERNAL MAIL

Dear Fu Xingke,

Indeed P-SAD is quite attractive but requires high resolution as the number of 
anomalous scatterers (1 P per nucleotide) is rather large, but the unit cells 
are typically quite small, resulting in a rather small number of anomalous 
differences per scatterer. Based on the very nice publication from Tom 
Terwilliger et al. ( 
https://doi.org/10.1107/S2059798315019269<https://urldefense.com/v3/__https://doi.org/10.1107/S2059798315019269__;!!MznTZTSvDXGV0Co!FVcv4z-85T4vC7VbHq9ovFGb90t3epudF1WV4ZvkXWqf51jVB7EfNZAHkQnf77TODeUSY5TVKsfEQoPZFt8d0q4Ldoubul1hBmZxnowSdSNrDrk$>)
 we wrote a little web app to predict the success for S-SAD phasing at the 
long-wavelength beamline I23 at Diamond. 
https://www.diamond.ac.uk/Instruments/Mx/I23/resolution-requirement-phasing-app.html<https://urldefense.com/v3/__https://www.diamond.ac.uk/Instruments/Mx/I23/resolution-requirement-phasing-app.html__;!!MznTZTSvDXGV0Co!FVcv4z-85T4vC7VbHq9ovFGb90t3epudF1WV4ZvkXWqf51jVB7EfNZAHkQnf77TODeUSY5TVKsfEQoPZFt8d0q4Ldoubul1hBmZxnowSvD5csvg$>
While the predictions are pretty reliable for S-SAD, there is a (not heavily 
tested) option to also submit DNA or RNA sequences, which can give you a hint 
on what you are against, or what resolution you should aim for. Unfortunately, 
we have not had many successful examples to far, but basically all the P-SAD 
projects which were predicted not to work at the resolutions the crystals 
diffracted to didn’t solve, so we are very interested in projects which are 
predicted to work to fine tune this also for P-SAD as there will be continuous 
need for experimental phasing in particular for non-canonical RNA/DNA 
structures.

5-Br-U is a good alternative and works well, but we have also managed to solve 
RNA/DNA by K-SAD or Co-SAD 
(https://doi.org/10.1093/nar/gkaa439<https://urldefense.com/v3/__https://doi.org/10.1093/nar/gkaa439__;!!MznTZTSvDXGV0Co!FVcv4z-85T4vC7VbHq9ovFGb90t3epudF1WV4ZvkXWqf51jVB7EfNZAHkQnf77TODeUSY5TVKsfEQoPZFt8d0q4Ldoubul1hBmZxnowSr-TWaw8$>)
 and Ca could be attractive as a potential anomalous scatter as well.

Best regards,

Armin




From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Mark J. van Raaij 
mailto:mjvanra...@cnb.csic.es>>
Date: Tuesday, 19 September 2023 at 12:31
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] the structures of Nucleic acid
This just appeared and may be relevant:
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad726/7272628<https://urldefense.com/v3/__https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad726/7272628__;!!MznTZTSvDXGV0Co!FVcv4z-85T4vC7VbHq9ovFGb90t3epudF1WV4ZvkXWqf51jVB7EfNZAHkQnf77TODeUSY5TVKsfEQoPZFt8d0q4Ldoubul1hBmZxnowSyfBOklU$>

Critical Reviews and Perspectives
When will RNA get its AlphaFold moment?
Mark van Raaij
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)


On 18 Sep 2023, at 18:07, William G. Scott 
<2844d921eb97-dmarc-requ...@jiscmail.ac.uk<mailto:2844d921eb97-dmarc-requ...@jiscmail.ac.uk>>
 wrote:

The phosphorus absorption edge is about 5.8Å.

I've had much better luck with 5-Br-U for anomalous phasing.

Molecular replacement with sub-structural fragments can also work:
<https://scottlab.ucsc.edu/scottlab/reprints/2010_Scott_Methods.pdf><https://urldefense.com/v3/__https://scottlab.ucsc.edu/scottlab/reprints/2010_Scott_Methods.pdf*3E__;JQ!!MznTZTSvDXGV0Co!FVcv4z-85T4vC7VbHq9ovFGb90t3epudF1WV4ZvkXWqf51jVB7EfNZAHkQnf77TODeUSY5TVKsfEQoPZFt8d0q4Ldoubul1hBmZxnowS8KUir6c$>


Yours sincerely,

William G. Scott
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064
USA


On Sep 18, 2023, at 2:43 AM, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto:176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>>
 wrote:

I am afraid most scientists will use the most straightforward technique!
If SAD is available the PHOSPHATE

Re: [ccp4bb] the structures of Nucleic acid

[Wagner, Armin (DLSLtd,RAL,LSCI)]

Dear Fu Xingke,

Indeed P-SAD is quite attractive but requires high resolution as the number of 
anomalous scatterers (1 P per nucleotide) is rather large, but the unit cells 
are typically quite small, resulting in a rather small number of anomalous 
differences per scatterer. Based on the very nice publication from Tom 
Terwilliger et al. ( https://doi.org/10.1107/S2059798315019269) we wrote a 
little web app to predict the success for S-SAD phasing at the long-wavelength 
beamline I23 at Diamond. 
https://www.diamond.ac.uk/Instruments/Mx/I23/resolution-requirement-phasing-app.html
While the predictions are pretty reliable for S-SAD, there is a (not heavily 
tested) option to also submit DNA or RNA sequences, which can give you a hint 
on what you are against, or what resolution you should aim for. Unfortunately, 
we have not had many successful examples to far, but basically all the P-SAD 
projects which were predicted not to work at the resolutions the crystals 
diffracted to didn’t solve, so we are very interested in projects which are 
predicted to work to fine tune this also for P-SAD as there will be continuous 
need for experimental phasing in particular for non-canonical RNA/DNA 
structures.

5-Br-U is a good alternative and works well, but we have also managed to solve 
RNA/DNA by K-SAD or Co-SAD (https://doi.org/10.1093/nar/gkaa439) and Ca could 
be attractive as a potential anomalous scatter as well.

Best regards,

Armin




From: CCP4 bulletin board  on behalf of Mark J. van 
Raaij 
Date: Tuesday, 19 September 2023 at 12:31
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] the structures of Nucleic acid
This just appeared and may be relevant:
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad726/7272628

Critical Reviews and Perspectives
When will RNA get its AlphaFold moment?
Mark van Raaij
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)


On 18 Sep 2023, at 18:07, William G. Scott 
<2844d921eb97-dmarc-requ...@jiscmail.ac.uk> wrote:

The phosphorus absorption edge is about 5.8Å.

I've had much better luck with 5-Br-U for anomalous phasing.

Molecular replacement with sub-structural fragments can also work:
<https://scottlab.ucsc.edu/scottlab/reprints/2010_Scott_Methods.pdf>


Yours sincerely,

William G. Scott
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064
USA


On Sep 18, 2023, at 2:43 AM, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

I am afraid most scientists will use the most straightforward technique!
If SAD is available the PHOSPHATE backbone of DNA will provide sufficient 
signal to allow SAD to work, and you get an unambiguous answer to whether it is 
A-DNA or B or Z...
MR will usually work of course as well
Eleanor


On Mon, 18 Sept 2023 at 09:18, Natesh Ramanathan  wrote:
Dear Fu Xingke,

Depends on what Nucleic Acid you are talking of.  If it is RNA, you can 
expect some sequence to tertiary structure correspondence so you might be able 
to try more MR as compared to DNA.   DNA may have double helical architecture 
but less sequence to tertiary structure correspondence, and hence DNA is less 
likely to have a 3D structure like RNA specific structure for a sequence.

SAD has become a straight forward method to avoid all these problems to 
get ab-initio structure.  So many go for it directly.

Hope that helps.
Best wishes,
Natesh

On Mon, 18 Sept 2023 at 13:36, fuxingke  wrote:
Dear Colleagues,

Reacently, I find the structures of Nucleic acid are solved by 
single-wavelength anomalous diffraction(SAD). So, why molecular replacement 
(MR) not?

Regards



Best wishes,

Fu Xingke

Institute of Physics CAS

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



--
--
"Live Simply and do Serious Things .. "
- Dorothy Mary Crowfoot Hodgkin OM, FRS

"In Science truth always wins"
- Max Ferdinand Perutz OM FRS
--
Dr. Ramanathan Natesh
Associate Professor,
School of Biology and Center for High-Performance Computing (CHPC),
Founding and Current President of Cryo Electron Microscopy and 3 Dimensional 
Image Processing Society of India (CEM3DIPSI),
Indian Institute of Science Education and Research Thiruvananthapuram 
(IISER-TVM),
Maruthamala P.O., Vithura,
Thiruvananthapuram,  695551, Kerala, India

nat...@iisertvm.ac.in
http://faculty.iisertvm.ac.in/natesh

Researcher ID: http://www.researcherid.com/rid/C-4488-2008
ORCID: http://orcid.org/-0002-1145-5962
Vidwan-ID : 94134: http://iisertvm.irins.org/profile/94134
PUBLONS: https://publons.com/author/1520837/

Re: [ccp4bb] the structures of Nucleic acid

[Mark J. van Raaij]

This just appeared and may be relevant:
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad726/7272628

Critical Reviews and Perspectives
When will RNA get its AlphaFold moment? 

Mark van Raaij
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)


> On 18 Sep 2023, at 18:07, William G. Scott 
> <2844d921eb97-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> The phosphorus absorption edge is about 5.8Å.
> 
> I've had much better luck with 5-Br-U for anomalous phasing.
> 
> Molecular replacement with sub-structural fragments can also work:
> 
> 
> 
> Yours sincerely,
> 
> William G. Scott
> Professor, Department of Chemistry and Biochemistry
> and The Center for the Molecular Biology of RNA
> University of California at Santa Cruz
> Santa Cruz, California 95064  
> USA
> 
>> On Sep 18, 2023, at 2:43 AM, Eleanor Dodson 
>> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> I am afraid most scientists will use the most straightforward technique! 
>> If SAD is available the PHOSPHATE backbone of DNA will provide sufficient 
>> signal to allow SAD to work, and you get an unambiguous answer to whether it 
>> is A-DNA or B or Z...
>> MR will usually work of course as well
>> Eleanor
>> 
>> 
>> On Mon, 18 Sept 2023 at 09:18, Natesh Ramanathan  
>> wrote:
>> Dear Fu Xingke,
>> 
>> Depends on what Nucleic Acid you are talking of.  If it is RNA, you 
>> can expect some sequence to tertiary structure correspondence so you might 
>> be able to try more MR as compared to DNA.   DNA may have double helical 
>> architecture but less sequence to tertiary structure correspondence, and 
>> hence DNA is less likely to have a 3D structure like RNA specific structure 
>> for a sequence.
>> 
>> SAD has become a straight forward method to avoid all these problems 
>> to get ab-initio structure.  So many go for it directly.
>> 
>> Hope that helps.
>> Best wishes,
>> Natesh
>> 
>> On Mon, 18 Sept 2023 at 13:36, fuxingke  wrote:
>> Dear Colleagues,
>> 
>> Reacently, I find the structures of Nucleic acid are solved by 
>> single-wavelength anomalous diffraction(SAD). So, why molecular replacement 
>> (MR) not?
>> 
>> Regards
>> 
>> 
>> 
>> Best wishes,
>> 
>> Fu Xingke
>> 
>> Institute of Physics CAS
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> 
>> 
>> 
>> -- 
>> --
>> "Live Simply and do Serious Things .. "
>> - Dorothy Mary Crowfoot Hodgkin OM, FRS
>> 
>> "In Science truth always wins"
>> - Max Ferdinand Perutz OM FRS
>> --
>> Dr. Ramanathan Natesh
>> Associate Professor, 
>> School of Biology and Center for High-Performance Computing (CHPC),
>> Founding and Current President of Cryo Electron Microscopy and 3 Dimensional 
>> Image Processing Society of India (CEM3DIPSI),
>> Indian Institute of Science Education and Research Thiruvananthapuram 
>> (IISER-TVM),
>> Maruthamala P.O., Vithura,
>> Thiruvananthapuram,  695551, Kerala, India
>> 
>> nat...@iisertvm.ac.in
>> http://faculty.iisertvm.ac.in/natesh
>> 
>> Researcher ID: http://www.researcherid.com/rid/C-4488-2008
>> ORCID: http://orcid.org/-0002-1145-5962
>> Vidwan-ID : 94134: http://iisertvm.irins.org/profile/94134
>> PUBLONS: https://publons.com/author/1520837/ramanathan-natesh#profile
>> 
>> Office Ph. 0091- 471-2778087
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> 
>> 
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>> 
> 
> 
> 
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Re: [ccp4bb] the structures of Nucleic acid

[William G. Scott]

The phosphorus absorption edge is about 5.8Å.

I've had much better luck with 5-Br-U for anomalous phasing.

Molecular replacement with sub-structural fragments can also work:



Yours sincerely,

William G. Scott
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064  
USA

> On Sep 18, 2023, at 2:43 AM, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> I am afraid most scientists will use the most straightforward technique! 
> If SAD is available the PHOSPHATE backbone of DNA will provide sufficient 
> signal to allow SAD to work, and you get an unambiguous answer to whether it 
> is A-DNA or B or Z...
> MR will usually work of course as well
> Eleanor
> 
> 
> On Mon, 18 Sept 2023 at 09:18, Natesh Ramanathan  
> wrote:
> Dear Fu Xingke,
> 
>  Depends on what Nucleic Acid you are talking of.  If it is RNA, you 
> can expect some sequence to tertiary structure correspondence so you might be 
> able to try more MR as compared to DNA.   DNA may have double helical 
> architecture but less sequence to tertiary structure correspondence, and 
> hence DNA is less likely to have a 3D structure like RNA specific structure 
> for a sequence.
> 
>  SAD has become a straight forward method to avoid all these problems 
> to get ab-initio structure.  So many go for it directly.
> 
> Hope that helps.
> Best wishes,
> Natesh
> 
> On Mon, 18 Sept 2023 at 13:36, fuxingke  wrote:
> Dear Colleagues,
> 
>  Reacently, I find the structures of Nucleic acid are solved by 
> single-wavelength anomalous diffraction(SAD). So, why molecular replacement 
> (MR) not?
> 
> Regards
> 
> 
> 
> Best wishes,
> 
> Fu Xingke
> 
> Institute of Physics CAS
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
> 
> 
> -- 
> --
> "Live Simply and do Serious Things .. "
> - Dorothy Mary Crowfoot Hodgkin OM, FRS
> 
> "In Science truth always wins"
> - Max Ferdinand Perutz OM FRS
> --
> Dr. Ramanathan Natesh
> Associate Professor, 
> School of Biology and Center for High-Performance Computing (CHPC),
> Founding and Current President of Cryo Electron Microscopy and 3 Dimensional 
> Image Processing Society of India (CEM3DIPSI),
> Indian Institute of Science Education and Research Thiruvananthapuram 
> (IISER-TVM),
> Maruthamala P.O., Vithura,
> Thiruvananthapuram,  695551, Kerala, India
> 
> nat...@iisertvm.ac.in
> http://faculty.iisertvm.ac.in/natesh
> 
> Researcher ID: http://www.researcherid.com/rid/C-4488-2008
> ORCID: http://orcid.org/-0002-1145-5962
> Vidwan-ID : 94134: http://iisertvm.irins.org/profile/94134
> PUBLONS: https://publons.com/author/1520837/ramanathan-natesh#profile
> 
> Office Ph. 0091- 471-2778087
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 



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Re: [ccp4bb] the structures of Nucleic acid

[Eleanor Dodson]

I am afraid most scientists will use the most straightforward technique!
If SAD is available the PHOSPHATE backbone of DNA will provide sufficient
signal to allow SAD to work, and you get an unambiguous answer to whether
it is A-DNA or B or Z...
MR will usually work of course as well
Eleanor


On Mon, 18 Sept 2023 at 09:18, Natesh Ramanathan 
wrote:

> Dear Fu Xingke,
>
>  Depends on what Nucleic Acid you are talking of.  If it is RNA,
> you can expect some sequence to tertiary structure correspondence so you
> might be able to try more MR as compared to DNA.   DNA may have double
> helical architecture but less sequence to tertiary structure
> correspondence, and hence DNA is less likely to have a 3D structure like
> RNA specific structure for a sequence.
>
>  SAD has become a straight forward method to avoid all these
> problems to get ab-initio structure.  So many go for it directly.
>
> Hope that helps.
> Best wishes,
> Natesh
>
> On Mon, 18 Sept 2023 at 13:36, fuxingke  wrote:
>
>> Dear Colleagues,
>>  Reacently, I find the structures of Nucleic acid are solved by
>> single-wavelength anomalous diffraction(SAD). So, why molecular
>> replacement (MR) not?
>>
>> Regards
>>
>>
>>
>> Best wishes,
>>
>> Fu Xingke
>> Institute of Physics CAS
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>
>
> --
> --
> "Live Simply and do Serious Things .. "
> - Dorothy Mary Crowfoot Hodgkin OM, FRS
>
> "In Science truth always wins"
> - Max Ferdinand Perutz OM FRS
> --
> Dr. Ramanathan Natesh
> Associate Professor,
> School of Biology and Center for High-Performance Computing (CHPC),
> Founding and Current President of Cryo Electron Microscopy and 3
> Dimensional Image Processing Society of India (CEM3DIPSI),
> Indian Institute of Science Education and Research Thiruvananthapuram
> (IISER-TVM),
> Maruthamala P.O., Vithura,
> Thiruvananthapuram,  695551, Kerala, India
>
> nat...@iisertvm.ac.in
> http://faculty.iisertvm.ac.in/natesh
>
> *Researcher ID*: http://www.researcherid.com/rid/C-4488-2008
> *ORCID*: http://orcid.org/-0002-1145-5962
> Vidwan-ID : 94134: http://iisertvm.irins.org/profile/94134
> *PUBLONS*: https://publons.com/author/1520837/ramanathan-natesh#profile
>
> Office Ph. 0091- 471-2778087
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] the structures of Nucleic acid

[Natesh Ramanathan]

Dear Fu Xingke,

 Depends on what Nucleic Acid you are talking of.  If it is RNA,
you can expect some sequence to tertiary structure correspondence so you
might be able to try more MR as compared to DNA.   DNA may have double
helical architecture but less sequence to tertiary structure
correspondence, and hence DNA is less likely to have a 3D structure like
RNA specific structure for a sequence.

 SAD has become a straight forward method to avoid all these
problems to get ab-initio structure.  So many go for it directly.

Hope that helps.
Best wishes,
Natesh

On Mon, 18 Sept 2023 at 13:36, fuxingke  wrote:

> Dear Colleagues,
>  Reacently, I find the structures of Nucleic acid are solved by
> single-wavelength anomalous diffraction(SAD). So, why molecular
> replacement (MR) not?
>
> Regards
>
>
>
> Best wishes,
>
> Fu Xingke
> Institute of Physics CAS
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>


-- 
--
"Live Simply and do Serious Things .. "
- Dorothy Mary Crowfoot Hodgkin OM, FRS

"In Science truth always wins"
- Max Ferdinand Perutz OM FRS
--
Dr. Ramanathan Natesh
Associate Professor,
School of Biology and Center for High-Performance Computing (CHPC),
Founding and Current President of Cryo Electron Microscopy and 3
Dimensional Image Processing Society of India (CEM3DIPSI),
Indian Institute of Science Education and Research Thiruvananthapuram
(IISER-TVM),
Maruthamala P.O., Vithura,
Thiruvananthapuram,  695551, Kerala, India

nat...@iisertvm.ac.in
http://faculty.iisertvm.ac.in/natesh

*Researcher ID*: http://www.researcherid.com/rid/C-4488-2008
*ORCID*: http://orcid.org/-0002-1145-5962
Vidwan-ID : 94134: http://iisertvm.irins.org/profile/94134
*PUBLONS*: https://publons.com/author/1520837/ramanathan-natesh#profile

Office Ph. 0091- 471-2778087



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