Browsing by Subject "fidelity"
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Item Exonuclease Removal Of Dideoxycytidine (Zalcitabine) By The Human Mitochondrial DNA Polymerase(2008-01) Hanes, Jeremiah W.; Johnson, Kenneth A.; Hanes, Jeremiah W.; Johnson, Kenneth A.The toxicity of nucleoside analogs used for the treatment of human immunodeficiency virus infection is due primarily to the inhibition of replication of the mitochondrial genome by the human mitochondrial DNA polymerase (Pol gamma). The severity of clinically observed toxicity correlates with the kinetics of incorporation versus excision of each analog as quantified by a toxicity index, spanning over six orders of magnitude. Here we show that the rate of excision of dideoxycytidine (zalcitabine; ddC) was reduced fourfold (giving a half-life of similar to 2.4 h) by the addition of a physiological concentration of deoxynucleoside triphosphates (dNTPs) due to the formation of a tight ternary enzyme-DNA-dNTP complex at the polymerase site. In addition, we provide a more accurate measurement of the rate of excision and show that the low rate of removal of ddCMP results from both the unfavorable transfer of the primer strand from the polymerase to the exonuclease site and the inefficient binding and/or hydrolysis at the exonuclease site. The analogs ddC, stavudine, and ddATP (a metabolite of didanosine) each bind more tightly at the polymerase site during incorporation than normal nucleotides, and this tight binding contributes to slower excision by the proofreading exonuclease, leading to increased toxicity toward mitochondrial DNA.Item A self-verifying theorem prover(2009-12) Davis, Jared Curran; Moore, J Strother, 1947-; Emerson, E. Allen; Harrison, John; Hunt, Jr., Warren A.; Kaufmann, Matt; Lifschitz, VladimirPrograms have precise semantics, so we can use mathematical proof to establish their properties. These proofs are often too large to validate with the usual "social process" of mathematics, so instead we create and check them with theorem-proving software. This software must be advanced enough to make the proof process tractable, but this very sophistication casts doubt upon the whole enterprise: who verifies the verifier? We begin with a simple proof checker, Level 1, that only accepts proofs composed of the most primitive steps, like Instantiation and Cut. This program is so straightforward the ordinary, social process can establish its soundness and the consistency of the logical theory it implements (so we know theorems are "always true"). Next, we develop a series of increasingly capable proof checkers, Level 2, Level 3, etc. Each new proof checker accepts new kinds of proof steps which were not accepted in the previous levels. By taking advantage of these new proof steps, higher-level proofs can be written more concisely than lower-level proofs, and can take less time to construct and check. Our highest-level proof checker, Level 11, can be thought of as a simplified version of the ACL2 or NQTHM theorem provers. One contribution of this work is to show how such systems can be verified. To establish that the Level 11 proof checker can be trusted, we first use it, without trusting it, to prove the fidelity of every Level n to Level 1: whenever Level n accepts a proof of some phi, there exists a Level 1 proof of phi. We then mechanically translate the Level 11 proof for each Level n into a Level n - 1 proof---that is, we create a Level 1 proof of Level 2's fidelity, a Level 2 proof of Level 3's fidelity, and so on. This layering shows that each level can be trusted, and allows us to manage the sizes of these proofs. In this way, our system proves its own fidelity, and trusting Level 11 only requires us to trust Level 1.