Synthesis and properties of oligodeoxyribonucleotides containing 2’-O-(2,3-dihydroxypropyl)- and 2’-O-(2-oxoethyl)arabinouridine residues

Abstract

2´ O (2,3 Dihydroxypropyl)arabinouridine containing oligodeoxyribonucleotides were synthesized starting from a new modified nucleoside, viz., 2´ O (2,3 dihydroxypropyl)arabino uridine, and the corresponding 3´ phosphoramidite. Oxidation of these oligodeoxyribo nucleotides with sodium periodate afforded oligonucleotides containing 2´ O (2 oxo ethyl)arabinouridine residues. Subsequent modification of the aldehyde containing oligonucle otides involved the reactions with 9 hydrazinoacridine and N aminooxyacetyl peptide and reductive amination by 4 (1 pyrenyl)butyrohydrazide and biotin hydrazide. Thermal stabilities of duplexes of modified oligodeoxyribonucleotides with complementary oligodeoxyribo nucleotides are slightly lower than those of natural duplexes. Duplexes with complementary oligoribonucleotides are substantially destabilized.Oligonucleotides including modified oligonucleotides find wide application in various fields of molecular biol ogy. They are used as primers for DNA sequencing and amplification, for the determination of DNA primary structures by hybridization, and also as potential thera peutics. 2,3 In particular, modified oligonucleotides are employed for the preparation of conjugates with various compounds, such as peptides, oligosaccharides, and fluo rescent dyes for studying the behavior of nucleic acids in vitro or in vivo. Affinity modification of DNA binding proteins is used to study the structures and functioning of the active sites of the latter. 4,5Conjugation of fluorophores or electrochemically ac tive compounds to oligonucleotides enables the use of such derivatives in the design of DNA detection systems by hybridization. 6-8 Marker groups substantially increase sensitivity of DNA detection. Many conjugates of oligo nucleotides with peptides, carbohydrates, and lipophilic compounds more easily penetrate cell membranes than native nucleic acids, and this fact can be used in antisense and antigene biotechnology. 9-11Covalent attachment of proteins to nucleic acids is the method of choice for solving a series of problems. First and foremost, it allows identification of the amino acids interacting with particular regions of nucleic acids in nucleic acid-protein complexes. In studies of multi protein complexes formed during the replication, transla tion, etc., one can determine a protein component inter acting with a region of nucleic acid recognition 12 and examine cell extracts with the aim of revealing proteins that selectively interact with particular nucleotide se quences. This approach is also applicable in the SELEX technology for the design of nucleic acid aptamers that irreversibly bind to proteins. 13,14 In recent years, consid erable progress has been achieved in crystallization of covalent nucleic acid-protein complexes and elucida tion of their structures by X ray diffraction. 15 Earlier, we have demonstrated that 2´ O (2 oxo ethyl)uridine containing DNA duplexes can successfully be used for the affinity modification of DNA binding proteins, such as transcription factor NF κB 1...