The Synthesis of N4‐(6‐Aminopyridin‐2‐yl)‐2′‐deoxycytidine for Recognizing the CG Base Pair at Neutral pH by Oligodeoxyribonucleotide‐Directed Triple Helix Formation

• DOI: 10.1002/jccs.199900103
• Publication Date: 2015-05-01T20:15:51Z
• Authors: T.‐M. Chin; K.‐Y. Chung; J.‐J. Chen; W.‐C. Lin; L.‐S. Kan
• Keywords: Synthon; Sequence (biology); Triad (sociology); Base (topology); Phosphoramidite

Abstract The sequence‐specific recognition of double‐helical DNA by oligodeoxyribonucleotide‐directed triple helix (triplex) formation is limited mostly to purine tracts. To interrupt the tract in a target sequence, non‐natural deoxyribonucleoside N 4 ‐(6‐aminopyridin‐2‐yl)‐2′‐deoxycytidine ( p C) was designed interact with C base CG pair. protected phosphoramidite synthon synthesized seven steps and then incorporated into an oligodeoxyribonucleotide automatic synthesizer. Two 22‐mers, designated as C2 P , common sequence 5′‐d‐T m CTXT CTTCTGTCTCCAGACAG were this study. 5‐methyl‐2′‐deoxycytidine X either 2′‐deoxycytidine (C) or for respectively. able form paper clip type triplex one · mismatched triad slightly acidic conditions but not at neutral pH. On other hand, forms stable under both conditions. This indicates that triplex. Their physical properties studied UV thermal melting experiments circular dichorism spectroscopy (CD). results imply + GC pH 6.0, helps preferably In addition hydrogen bonding interaction pair, hydrophobic may also play important role stabilizing oligodeoxyribonucleotides. presence spermine 5.0 temperature third strand elevated about 30 21 °C, Thus, can enhance stability triple‐helical structure.