Ahn, DR Mosimann, M Leumann, CJ 2024-01-21T08:06:42Z 2024-01-21T08:06:42Z 2021-09-01 2003-10-03 0022-3263 https://pubs.kist.re.kr/handle/201004/138149 We recently reported on the synthesis and pairing properties of the DNA analogue bicyclo[3.2.1]-amide DNA (bca-DNA). In this analogue the nucleobases are attached via a linear, 4-bond amide-linker to a structurally preorganized sugar-phosphate backbone unit. To define the importance of the degree of structural rigidity of the bca-backbone unit on the pairing properties, we designed the structurally simpler cyclopentane amide DNA (cpa-DNA), in which the bicyclo[3.2.1]-scaffold was reduced to a cyclopentane unit while the base-linker was left unchanged. Here we present a synthetic route to the enantiomerically pure cpa-DNA monomers and the corresponding phosphoramidites containing the bases A and T, starting from a known, achiral precursor in 9 and 12 steps, respectively. Fully modified oligodeoxynucleotides were synthesized by standard solid-phase oligonucleotide chemistry, and their base-pairing properties with complementary oligonucleotides of the DNA-, RNA-, bca-DNA-, and cpa-DNA-backbones were assessed by UV melting curves and CD-spectroscopic methods. We found that cpa-oligoadenylates form duplexes with complementary DNA that are less stable by -2.7 degreesC/mod. compared to DNA. The corresponding cpa-oligothymidylates do not participate in complementary base-pairing with any of the investigated backbone systems except with its own (homo-duplex). As its congener bca-DNA, cpa-DNA seems to prefer left-handed helical duplex structures with DNA or with itself as indicated by the CD spectra. English AMER CHEMICAL SOC CHIRAL ACYCLIC ANALOGS OLIGONUCLEOTIDES RECOGNITION PRINCIPLES BACKBONE Synthesis of cyclopentane amide DNA (cpa-DNA) and its pairing properties Article 10.1021/jo034143q 1 JOURNAL OF ORGANIC CHEMISTRY, v.68, no.20, pp.7693 - 7699 JOURNAL OF ORGANIC CHEMISTRY 68 20 7693 7699 scie scopus 000185609000017 Chemistry, Organic Chemistry Article CHIRAL ACYCLIC ANALOGS OLIGONUCLEOTIDES RECOGNITION PRINCIPLES BACKBONE cyclopentane cpa DNA bicyclic DNA