New imidazopyridopyrimidine:naphthyridine base-pairing motif, ImNN:NaOO, consisting of a DAAD:ADDA hydrogen bonding pattern, markedly stabilize DNA duplexes

Abstract

Synthesis of phosphoramidite units. 170.9, 170.6, 163.8, 159.5, 155.2, 148.0, 139.7, 132.6, 126.5, 118.5, 110.0, 82.4, 77.3, 77.0, 64.5, 52.3, 46.1, 40.1, 31.4, 29.3, 21.1, 21.0, 20.5, 19.9, 14.0, 13.8. 3-(3,5-Di-O-acetyl-2-deoxy--D-ribofuranosyl)-2-(N,N

Faithful PCR Amplification of an Unnatural Base‐Pair Analogue with Four Hydrogen Bonds

“…In addition, we have demonstrated that ImN O :NaO N and ImO N :NaN O are recognized by DNA polymerases as complementary base pairs 10. Inspired by these successful results, we have recently developed a new Im:Na pair, that is, ImN N :NaO O 11. This newly designed base pair has a DAAD:ADDA hydrogen‐bonding pattern, as illustrated in Scheme , which is distinct from our two previous pairs having alternating hydrogen‐bonding patterns.…”

“…Meanwhile, we have been developing a series of unnatural base‐pair analogues with four non‐canonical hydrogen bonds 9–11. Thus far, we have designed imidazopyridopyrimidine:naphthyridine (Im:Na) base pairs, that is, ImN O :NaO N and ImO N :NaN O , having alternating hydrogen‐bonding patterns of DADA:ADAD and ADAD:DADA (A=acceptor, D=donor), respectively (Schemes ) 9a,b.…”

Unnatural Base Pairs for Synthetic Biology

“…In a similar manner as for 1, 6 is converted into the corresponding phosphoramidite unit and 5′-triphosphate for enzymatic evaluation. 39,45) …”

“…To improve efficiency and selectivity, a new Im : Na pair, i.e., ImN N : NaO O , has been envisioned 39,44) (Fig. 5c).…”

“…To answer this, we have explored four H-bonding base pairs. [37][38][39][40][41] , which have alternate H-bonding geometries, were developed. As can be seen in Fig.…”