title: In vitro selection of optimal DNA substrates for ligation by a water-soluble carbodiimide.
abstract: We have used in vitro selection to investigate the sequence requirements for efficient template-directed ligation of oligonucleotides at 0 degrees C using a water-soluble carbodiimide as condensing agent. We find that only 2 bp at each side of the ligation junction are needed. We also studied chemical ligation of substrate ensembles that we have previously selected as optimal for ligation by RNA ligase or by DNA ligase. As anticipated, we find that substrates selected with DNA ligase ligate efficiently with a chemical ligating agent, and vice versa. Substrates selected using RNA ligase are not ligated by the chemical condensing agent and vice versa. The implications of these results for prebiotic chemistry are discussed.
authors.affiliation: Salk Institute for Biological Studies, San Diego, CA 92186-5800.
authors.forename: K
authors.initials: K
authors.lastname: Harada
authors.forename: L E
authors.initials: LE
authors.lastname: Orgel
mesh_terms: D001483:Base Sequence; D002234:Carbodiimides / Q000494:pharmacology*; D003854:Deoxyribonucleotides / Q000737:chemistry; D008969:Molecular Sequence Data; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis* / Q000737:chemistry; D012995:Solubility; D013379:Substrate Specificity; D013698:Templates, Genetic; D014867:Water
chemical_list: D002234:Carbodiimides; D003854:Deoxyribonucleotides; D009838:Oligodeoxyribonucleotides; D014867:Water; C074139:1-ethyl-3-(3-dimethylaminoethyl)carbodiimide