title: Preparation of DNA containing 5-hydroxymethyl-2'-deoxycytidine modification through phosphoramidites with TBDMS as 5-hydroxymethyl protecting group.
abstract: This unit describes procedures for preparation of two phosphoramidite building blocks III and IV, both containing a TBDMS as 5-CH(2)OH-protecting group. Phosphoramidites III and IV allow efficient incorporation of 5-hmC into DNA and a "one-step" deprotection procedure to cleanly remove all the protecting groups. A "two-step" deprotection strategy is compatible with ultramild DNA synthesis, which enables the synthesis of 5 hmC-containing DNA with additional modifications. Methods are also presented for their incorporation into oligonucleotides by solid-phase synthesis, subsequent deprotection, and HPLC analysis.
authors.affiliation: Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA.
authors.forename: Qing
authors.initials: Q
authors.lastname: Dai
authors.forename: Chuan
authors.initials: C
authors.lastname: He
mesh_terms: D002851:Chromatography, High Pressure Liquid; D004247:DNA / Q000138:chemical synthesis* / Q000737:chemistry; D003841:Deoxycytidine / Q000031:analogs & derivatives* / Q000737:chemistry; D008956:Models, Chemical; D015394:Molecular Structure; D009943:Organophosphorus Compounds / Q000737:chemistry*; D012833:Siloxanes / Q000737:chemistry*; D013343:Styrenes / Q000737:chemistry*
chemical_list: C506477:4-(tert-butyldimethylsiloxy)styrene; C540838:5-hydroxymethyl-2'-deoxycytidine; D009943:Organophosphorus Compounds; D012833:Siloxanes; D013343:Styrenes; C434331:phosphoramidite; D003841:Deoxycytidine; D004247:DNA