Selenium derivatization and crystallization of DNA and RNA oligonucleotides for X-ray crystallography using multiple anomalous dispersion.
We report here the solid phase synthesis of RNA and DNA oligonucleotides containing the 2'-selenium functionality for X-ray crystallography using multiwavelength anomalous dispersion. We have synthesized the novel 2'-methylseleno cytidine phosphoramidite and improved the accessibility of the 2'-methylseleno uridine phosphoramidite for the synthesis of many selenium-derivatized DNAs and RNAs in large scales. The yields of coupling these Se-nucleoside phosphoramidites into DNA or RNA oligonucleotides were over 99% when 5-(benzylmercapto)-1H-tetrazole was used as the coupling reagent. The UV melting study of A-form dsDNAs indicated that the 2'-selenium derivatization had no effect on the stability of the duplexes with the 3'-endo sugar pucker. Thus, the stems of functional RNA molecules with the same 3'-endo sugar pucker appear to be the ideal sites for the selenium derivatization with 2'-Se-C and 2'-Se-U. Crystallization of the selenium-derivatized oligonucleotides is also reported here. The results demonstrate that this 2'-selenium functionality is suitable for RNA and A-form DNA derivatization in X-ray crystallography.
Carrasco
Nicolas
N
Department of Chemistry, Brooklyn College, and Program of Biochemistry and Chemistry, The Graduate School, The City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA.
Buzin
Yuri
Y
Tyson
Elizabeth
E
Halpert
Elizer
E
Huang
Zhen
Z
D001483:Base Sequence; D003460:Crystallization; D018360:Crystallography, X-Ray; D003545:Cysteine / Q000031:analogs & derivatives* / Q000737:chemistry; D004247:DNA / Q000737:chemistry; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D009843:Oligoribonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D009943:Organophosphorus Compounds / Q000138:chemical synthesis / Q000737:chemistry; D016566:Organoselenium Compounds / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D012643:Selenium / Q000737:chemistry*; D017279:Selenocysteine / Q000031:analogs & derivatives; D014529:Uridine / Q000031:analogs & derivatives
D009838:Oligodeoxyribonucleotides; D009843:Oligoribonucleotides; D009943:Organophosphorus Compounds; D016566:Organoselenium Compounds; C434331:phosphoramidite; D017279:Selenocysteine; D012313:RNA; D004247:DNA; D012643:Selenium; D003545:Cysteine; C002979:selenomethylselenocysteine; D014529:Uridine