LNA guanine and 2,6-diaminopurine. Synthesis, characterization and hybridization properties of LNA 2,6-diaminopurine containing oligonucleotides

• Published in: Bioorganic & medicinal chemistry Vol. 12; no. 9; pp. 2385 - 2396
• Main Authors: Rosenbohm, Christoph, Pedersen, Daniel Sejer, Frieden, Miriam, Jensen, Flemming R., Arent, Susan, Larsen, Sine, Koch, Troels
• Format: Journal Article
• Language: English
• Published: Oxford Elsevier Ltd 01.05.2004; Elsevier Science
• Subjects: 2-Aminopurine - analogs & derivatives; 2-Aminopurine - chemical synthesis; 2-Aminopurine - chemistry; Analytical, structural and metabolic biochemistry; Antisense agents; Biological and medical sciences; Bioorganic chemistry; Fundamental and applied biological sciences. Psychology; Guanine - chemical synthesis; Guanine - chemistry; Magnetic Resonance Spectroscopy; Nucleic Acid Hybridization; Nucleic acids; Nucleic bases, nucleotides; Nucleosides; Oligonucleotides; Oligonucleotides - chemistry; Spectrometry, Mass, Electrospray Ionization; Nucleosides; Bioorganic chemistry; Antisense agents; Oligonucleotides; Molecular rigidity; Purine nucleotide; DNA; Guanine derivatives; Organic phosphoramidite; Steric hindrance; Hybridization; Antisense oligonucleotide; Chemical synthesis
• ISSN: 0968-0896; 1464-3391
• DOI: 10.1016/j.bmc.2004.02.008

Graphic LNA guanine and 2,6-diaminopurine (D) phosphoramidites have been synthesized as building blocks for antisense oligonucleotides (ON). The effects of incorporating LNA D into ON were investigated. As expected, LNA D containing ON showed increased affinity towards complementary DNA (Δ T m +1.6 to +3.0 °C) and RNA (Δ T m +2.6 to +4.6 °C) ON. To evaluate if LNA D containing ON have an enhanced mismatch sensitivity compared to their complementary LNA A containing ON thermal denaturation experiments towards singly mismatched DNA and RNA ON were undertaken. Replacing one LNA A residue with LNA D, in fully LNA modified ON, resulted in higher mismatch sensitivity towards DNA ON (ΔΔ T m −4 to >−17 °C). The same trend was observed towards singly mismatched RNA ON (ΔΔ T m D–a = −8.7 °C and D–g = −4.5 °C) however, the effect was less clearcut and LNA A showed a better mismatch sensitivity than LNA D towards cytosine (Δ T m +5.5 °C).