Alanyl-PNA homoduplex: A-T pairing with the N7-regioisomer of adenine

Bioorganic and Medicinal Chemistry Letters

Volumn 8, Issue 2, 1998, Pages 165-168

  Diederichsen, Ulf ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; NUCLEIC ACID BASE; OLIGOMER;

ARTICLE; CONFORMATION; ISOMER; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACID SYNTHESIS; ULTRAVIOLET SPECTROSCOPY;

ADENINE; ALANINE; BASE SEQUENCE; CIRCULAR DICHROISM; ISOMERISM; PEPTIDE NUCLEIC ACIDS; SPECTROPHOTOMETRY, ULTRAVIOLET;

EID: 0032548440     PISSN: 0960894X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0960-894X(97)10210-4     Document Type: Article

References (13)

1. 1. a) Diederichsen, U.; Angew. Chem. Int. Ed. Engl. 1996, 35, 445-448.
2. b) Diederichsen, U.; Angew. Chem. Int. Ed. Engl. 1997, 36, 1886-1889.
3. c) Diederichsen, U.; Bioorg. Med. Chem. Lett. 1997, 7, 1743-1746.
4. d) Diederichsen, U.; manuscript in preparation.
5. 2. Diederichsen, U; Schnitt, H. W.; Tetrahedron Lett. 1996, 37, 475-478.
6. 3. Diederichsen, U; Schmitt, H. W.; Angew. Chem. Int. Ed. in press.
7. 4. a) Lohse, P.; Oberhauser, B.; Oberhauser-Hofbauer, B.; Baschang, G.; Eschenmoser, A.; Croatica Chim. Acta 1996, 69, 535-562.
8. b) Lohse, P.; 'Synthese und Eigenschaften von oligomeren Nukleodipeptamidinium-Salzen', Dissertation, ETH 9937, Zürich, 1992. The synthesis of Bocthyminyl alanine follows a similar procedure and is also described in ref. 4a,b.
9. 2 (lysine amide introduced for solubility).
10. 2+.
11. 7. Rotation of the Cα-Cβ-bond by 180° also provides a reversed donor/acceptor pattern but this conformer is disfavored by eclipsed bonds and a 1,5-repulsion. For further discussion compare ref. 2.
12. 8. Antiparallel strand orientation in general seems to be favored in the alanyl-PNA series. Alanyl-PNA sequences with alternating N9-adenine and thymine most likely favor a Hoogsteen A-A and a reverse Watson-Crick T-T pairing 1. Since we can exclude Hoogsteen pairing for N7-adenine A-A, T-T pairing is also very unlikely. The backbone distance in case of Watson-Crick A-A is much larger than T-T.
13. m = 19°C at 5 μM, 23°C at 12 μM, 26°C at 24 μM concentration) which excludes an intramolecular process.