Adenine Protonation in Domain B of the Hairpin Ribozyme
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- 作者：Sapna Ravindranathan ; Samuel E. Butcher ; and Juli Feigon
- 刊名：Biochemistry
- 出版年：2000
- 出版时间：December 26, 2000
- 年：2000
- 卷：39
- 期：51
- 页码：16026 - 16032
- 全文大小：119K
- 年卷期：v.39,no.51(December 26, 2000)
- ISSN：1520-4995
文摘
Protein enzymes often use ionizable side chains, such as histidine, for general acid-basecatalysis because the imidazole pKa is near neutral pH. RNA enzymes, on the other hand, are comprisedof nucleotides which do not have apparent pKa values near neutral pH. Nevertheless, it has been recentlyshown that cytidine and adenine protonation can play an important role in both nucleic acid structure andcatalysis. We have employed heteronuclear NMR methods to determine the pKa values and time scalesof chemical exchanges associated with adenine protonation within the catalytically essential B domain ofthe hairpin ribozyme. The large, adenine-rich internal loop of the B domain allows us to determine adeninepKa values for a variety of non-Watson-Crick base pairs. We find that adenines within the internal loophave pKa values ranging from 4.8 to 5.8, significantly higher than the free mononucleotide pKa of 3.5.Adenine protonation results in potential charge stabilization, hydrogen bond formation, and stackinginteractions that are expected to stabilize the internal loop structure at low pH. Fast proton exchangetimes of 10-50 
s were determined for the well-resolved adenines. These results suggest that shifted pKavalues may be a common feature of adenines in non-Watson-Crick base pairs, and identify two adenineswhich may participate in hairpin ribozyme active site chemistry.
s were determined for the well-resolved adenines. These results suggest that shifted pKavalues may be a common feature of adenines in non-Watson-Crick base pairs, and identify two adenineswhich may participate in hairpin ribozyme active site chemistry.