1,N⁶-etheno deoxy and ribo adenoGine and 3,N⁴-etheno deoxy and ribo cytidine phosphoramidites. Strongly fluorescent structures for selective introduction in defined sequence DNA and RNA molecules

Abstract

Synthesis of 1,N6-etheno-2'-deoxyadenosine, 3,N4-etheno-2'-deoxycytidine, and further chemistry on both deoxy and ribo series etheno nucleosides produces the corresponding phosphoramidites. These novel phosphoramidites are introduced selectively, quantitatively, and at specific positions at single or multiple sites into DNA or RNA sequences. The purification and chemistry involved in the synthesis of these products has been optimized to achieve the purity in excess of 99%. The resulting phosphoramidites were tested for their ability to couple and produce poly deoxy and ribonucleotides by solid phase chemistry. The coupling efficiency achieved was greater than 99% per step. Due to the instability of these etheno compounds in acidic and basic medium, various criteria to obtain pure oligomers have been established. The selective introduction of these fluorescent nucleosides into defined sequence DNA and RNA molecule will greatly facilitate the structure-function studies of various RNAs, protein-RNA structures, and DNA-RNA based diagnostics applications. The characteristic and high fluorescent intensity (detection below 1 x 10(-9) M for adenosine sites and below 1 x 10(-7) M for cytidine sites) is particularly suited for the biochemical and biological research and product development applications. The usefulness of these etheno containing modified sequences as sequencing and amplification primers is demonstrated by their full participation in polymerase chain reaction experiments.

Cloning of a yeast 8-oxoguanine DNA glycosylase reveals the existence of a base-excision DNA-repair protein superfamily

“…The radiolabeled strand of each duplex is the top strand as shown below. Phosphoramidites of 8-oxo-dG [39,40], 8-oxo-dA [41], 1,N 6 ⑀dA [42], THF [33],…”

The Extent of DNA Deformation in DNA Photolyase– Substrate Complexes: A Solution State Fluorescence Study

“…Fluorescent nucleobase analogs (32)(33)(34)(35)(36)(37)(38)(39) have been used to probe DNA structure and protein-DNA interactions. These modified bases typically provide comparable Watson-Crick base pairing and stability as the native bases they replace.…”

Preparation of Base-Deuterated 2?-Deoxyadenosine Nucleosides and Their Site-Specific Incorporation Into Dna

“…The synthetic route (Scheme 1) starts with 1,N 6 -ethenodeoxyadenosine (3), prepared by the reaction of 2 0 -deoxyadenosine with chloroacetaldehyde using a slight modification of a previously published protocol 9 . Reaction of 3 with NaOH at 23 C resulted in ring opening to yield 4.…”