2PIS

Efforts toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs

2PIS の概要

• エントリーDOI: 10.2210/pdb2pis/pdb
• 分子名称: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3'), MAGNESIUM ION (2 entities in total)
• 機能のキーワード: nucleic acid, duplex, replication, unnatural base, dna
• タンパク質・核酸の鎖数: 12
• 化学式量合計: 48343.47

構造登録者

Matsuda, S.,Fillo, J.D.,Henry, A.A.,Wilkins, S.J.,Rai, P.,Dwyer, T.J.,Geierstanger, B.H.,Wemmer, D.E.,Schultz, P.G.,Spraggon, G.,Romesberg, F.E. (登録日: 2007-04-13, 公開日: 2007-10-30, 最終更新日: 2024-02-21)

主引用文献

Matsuda, S.,Fillo, J.D.,Henry, A.A.,Rai, P.,Wilkens, S.J.,Dwyer, T.J.,Geierstanger, B.H.,Wemmer, D.E.,Schultz, P.G.,Spraggon, G.,Romesberg, F.E.
Efforts toward expansion of the genetic alphabet: structure and replication of unnatural base pairs.
J.Am.Chem.Soc., 129:10466-10473, 2007

PubMed Abstract: Expansion of the genetic alphabet has been a long-time goal of chemical biology. A third DNA base pair that is stable and replicable would have a great number of practical applications and would also lay the foundation for a semisynthetic organism. We have reported that DNA base pairs formed between deoxyribonucleotides with large aromatic, predominantly hydrophobic nucleobase analogues, such as propynylisocarbostyril (dPICS), are stable and efficiently synthesized by DNA polymerases. However, once incorporated into the primer, these analogues inhibit continued primer elongation. More recently, we have found that DNA base pairs formed between nucleobase analogues that have minimal aromatic surface area in addition to little or no hydrogen-bonding potential, such as 3-fluorobenzene (d3FB), are synthesized and extended by DNA polymerases with greatly increased efficiency. Here we show that the rate of synthesis and extension of the self-pair formed between two d3FB analogues is sufficient for in vitro DNA replication. To better understand the origins of efficient replication, we examined the structure of DNA duplexes containing either the d3FB or dPICS self-pairs. We find that the large aromatic rings of dPICS pair in an intercalative manner within duplex DNA, while the d3FB nucleobases interact in an edge-on manner, much closer in structure to natural base pairs. We also synthesized duplexes containing the 5-methyl-substituted derivatives of d3FB (d5Me3FB) paired opposite d3FB or the unsubstituted analogue (dBEN). In all, the data suggest that the structure, electrostatics, and dynamics can all contribute to the extension of unnatural primer termini. The results also help explain the replication properties of many previously examined unnatural base pairs and should help design unnatural base pairs that are better replicated.

PubMed: 17685517
DOI: 10.1021/ja072276d

実験手法

X-RAY DIFFRACTION (2.8 Å)