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 <CCP4BB@JISCMAIL.AC.UK> on behalf of Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> Date: Monday, September 18, 2023 at 4:44 AM To: CCP4BB@JISCMAIL.AC.UK <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 <nat...@iisertvm.ac.in<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 <fuxingke0...@163.com<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/0000-0002-1145-5962 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: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
