How DNA Polymerases Catalyze DNA Replication, Repair, and Mutation

Tsai, Ming‐Daw

doi:10.1021/bi500417m

Cited by 16 publications

(11 citation statements)

References 37 publications

(55 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, various tricks have to be applied to alter reaction processes so that individual intermediate steps can be analyzed and their occurrence rate measured [8–13]. Similar to kinetic studies, to obtain three-dimensional structures of enzyme-substrate complexes, chemical reactions have to be manipulated and stopped by using non-reactive substrate mimics, enzymes inactivated by mutations, or non-permissible cofactors [14–19].…”

Section: Introductionmentioning

confidence: 99%

A new paradigm of DNA synthesis: three-metal-ion catalysis

2016

View full text Add to dashboard Cite

Enzyme catalysis has been studied for over a century. How it actually occurs has not been visualized until recently. By combining in crystallo reaction and X-ray diffraction analysis of reaction intermediates, we have obtained unprecedented atomic details of the DNA synthesis process. Contrary to the established theory that enzyme-substrate complexes and transition states have identical atomic composition and catalysis occurs by the two-metal-ion mechanism, we have discovered that an additional divalent cation has to be captured en route to product formation. Unlike the canonical two metal ions, which are coordinated by DNA polymerases, this third metal ion is free of enzyme coordination. Its location between the α- and β-phosphates of dNTP suggests that the third metal ion may drive the phosphoryltransfer from the leaving group opposite to the 3′-OH nucleophile. Experimental data indicate that binding of the third metal ion may be the rate-limiting step in DNA synthesis and the free energy associated with the metal-ion binding can overcome the activation barrier to the DNA synthesis reaction.Electronic supplementary materialThe online version of this article (doi:10.1186/s13578-016-0118-2) contains supplementary material, which is available to authorized users.

show abstract

Section: Introductionmentioning

confidence: 99%

A new paradigm of DNA synthesis: three-metal-ion catalysis

2016

View full text Add to dashboard Cite

show abstract

“…78 Overall, elucidation of the novel mechanisms of the tautomerisation of DNA bases eventually gives a theoretical background for the experimental observations, [73][74][75][76][77] allowing us to suppose that DNA-polymerase is able to make errors due to the formation of the rare tautomers, incorporated into the structure of the wrong mispairs, mimicking the shape of the canonical Watson-Crick pairs. 79 So, ultimately these mismatches can be accommodated without obstacles into the structure of the DNA double helix.…”

Section: Discussionmentioning

confidence: 99%

Novel physico-chemical mechanism of the mutagenic tautomerisation of the Watson–Crick-like A·G and C·T DNA base mispairs: a quantum-chemical picture

Brovarets’

Hovorun

2015

RSC Adv.

View full text Add to dashboard Cite

The newly discovered physico-chemical mechanism of the mutagenic tautomerisation of the long A$G and short C$T Watson-Crick DNA base mispairs was revealed for the first time. The tautomerisation of each mismatch occurs via four topologically and energetically different ways through highly stable transition states -H-bonded tight ion pairs containing protonated and deprotonated bases. These processes are accompanied by a significant rebuilding of the base mispairs with a Watson-Crick architecture into wobble mismatches, which are shifted towards both the minor and major DNA grooves and vice versa. Moreover, it was established that these tautomerisation reactions occur non-dissociatively and are accompanied by the consequent replacement of the unique patterns of the specific intermolecular interactions along the IRC. Finally, we briefly discuss the possible biological significance of the obtained results for clarifying the microstructural foundations of the origin of the spontaneous point mutations within the framework of the classical Watson-Crick tautomeric hypothesis. † Electronic supplementary information (ESI) available: (i) Energetic characteristics of the investigated DNA mispairs; (ii) proles of the glycosidic parameters along the IRC of tautomerisation; (iii) energetic proles and parameters of the mismatch planarization. See

show abstract

“…Of course, the details of the process cannot be certainly established but general idea seems to be worthy of confidence, otherwise it would not be possible to explain magnetic effects. In terms of commonly accepted two-magnesium-ion mechanism of the DNA synthesis [16][17][18][19][20][21] one of the ions is supposed to be tightly bound with pyrophosphate group of the incoming nucleotide and assists the departure of this group from the catalytic site after the insertion of the nucleotide into the growing DNA strand is completed. Another ion coordinates 3´O ribose ion of the DNA and P α atom of the incoming nucleotide to facilitate nucleophilic in-line attack of 3´O on the P α atom.…”

Section: Nuclear Magnetic Control Of the Polymerase Chain Reactionmentioning

confidence: 99%