Synthesis of cyclopentane amide DNA (cpa-DNA) and its pairing properties

Ahn, D. R.; Mosimann, Markus; Leumann, Christian (2003). Synthesis of cyclopentane amide DNA (cpa-DNA) and its pairing properties. Journal of organic chemistry, 68(20), pp. 7693-7699. American Chemical Society 10.1021/jo034143q

[img] Text
reprint.pdf - Published Version
Restricted to registered users only
Available under License Publisher holds Copyright.

Download (135kB) | Request a copy

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 degrees C/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

Item Type:

Journal Article (Original Article)


08 Faculty of Science > Department of Chemistry, Biochemistry and Pharmaceutical Sciences (DCBP)

UniBE Contributor:

Mosimann, Markus (A), Leumann, Christian


500 Science > 570 Life sciences; biology
500 Science > 540 Chemistry




American Chemical Society




Christian Leumann

Date Deposited:

19 May 2015 08:10

Last Modified:

29 Mar 2023 23:34

Publisher DOI:


Additional Information:

Notes: Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, SwitzerlandFAU - Ahn, Dae-Ro

Uncontrolled Keywords:

amide Amides analogue backbone base Base Pairing Base Sequence BASE-PAIRING PROPERTIES bases CD chemical synthesis chemistry Circular Dichroism Cyclopentanes DNA duplex DUPLEXES methods modified monomers Nucleic Acid Conformation Nucleic Acid Denaturation nucleobases Oligodeoxynucleotides oligonucleotide Oligonucleotides PAIRING PROPERTIES phosphoramidite properties RNA solid phase Spectrophotometry,Ultraviolet Structure SUGAR-PHOSPHATE BACKBONE Support,Non-U.S.Gov't synthesis Temperature




Actions (login required)

Edit item Edit item
Provide Feedback