Matches in SemOpenAlex for { <https://semopenalex.org/work/W4229021887> ?p ?o ?g. }
- W4229021887 abstract "Abstract The Hoogsteen (HG) base pairing (bp) conformation, commonly observed in damaged and mutated DNA helices, facilitates DNA repair and DNA recognition. The free energy difference between HG and Watson-Crick (WC) base pairs has been computed in previous studies. However, the mechanism of the conformational transition is not well understood. A detailed understanding of the process of WC to HG base pair transition can provide deeper understanding of DNA repair and recognition. In an earlier study, we explored the free energy landscape for this process using extensive computer simulation with the CHARMM36 force field. In this work, we study the impact of force field models in describing the WC to HG base pairing transition using meta-eABF enhanced sampling, quasi-harmonic entropy calculation, and non-bonded energy analysis. The secondary structures of both base pairing forms and the topology of the free energy landscapes were consistent over different force field models, although the relative free energy, entropy and the interaction energies tend to vary. The relative stability of the WC and HG conformations is dictated by a delicate balance between the enthalpic stabilization and the reduced entropy of the structurally rigid HG structure. These findings highlight the impact that subtleties in force field models can have on accurately modeling DNA base pair dynamics and should stimulate further computational investigations into other dynamically important motions in DNA. Graphical TOC Entry" @default.
- W4229021887 created "2022-05-08" @default.
- W4229021887 creator A5033374983 @default.
- W4229021887 creator A5056815405 @default.
- W4229021887 creator A5085371660 @default.
- W4229021887 date "2022-05-04" @default.
- W4229021887 modified "2023-09-26" @default.
- W4229021887 title "Force Field Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA" @default.
- W4229021887 cites W1031578623 @default.
- W4229021887 cites W1927152389 @default.
- W4229021887 cites W1967737979 @default.
- W4229021887 cites W1970335347 @default.
- W4229021887 cites W1972758026 @default.
- W4229021887 cites W1976499671 @default.
- W4229021887 cites W1980322667 @default.
- W4229021887 cites W1988529738 @default.
- W4229021887 cites W1993177346 @default.
- W4229021887 cites W1999784224 @default.
- W4229021887 cites W2005298772 @default.
- W4229021887 cites W2009026487 @default.
- W4229021887 cites W2011691446 @default.
- W4229021887 cites W2014727583 @default.
- W4229021887 cites W2029667189 @default.
- W4229021887 cites W2038758364 @default.
- W4229021887 cites W2043578603 @default.
- W4229021887 cites W2051278359 @default.
- W4229021887 cites W2052221476 @default.
- W4229021887 cites W2052246375 @default.
- W4229021887 cites W2057806291 @default.
- W4229021887 cites W2058971275 @default.
- W4229021887 cites W2062013630 @default.
- W4229021887 cites W2065152187 @default.
- W4229021887 cites W2065466631 @default.
- W4229021887 cites W2069247446 @default.
- W4229021887 cites W2073380384 @default.
- W4229021887 cites W2076497939 @default.
- W4229021887 cites W2080461436 @default.
- W4229021887 cites W2082490524 @default.
- W4229021887 cites W2093257892 @default.
- W4229021887 cites W2117208578 @default.
- W4229021887 cites W2118233996 @default.
- W4229021887 cites W2126466006 @default.
- W4229021887 cites W2135963245 @default.
- W4229021887 cites W2136729627 @default.
- W4229021887 cites W2140154727 @default.
- W4229021887 cites W2149655632 @default.
- W4229021887 cites W2150981663 @default.
- W4229021887 cites W2153954238 @default.
- W4229021887 cites W2159634882 @default.
- W4229021887 cites W2160341881 @default.
- W4229021887 cites W2169528473 @default.
- W4229021887 cites W2246932694 @default.
- W4229021887 cites W2327880765 @default.
- W4229021887 cites W2433523887 @default.
- W4229021887 cites W2463208053 @default.
- W4229021887 cites W2503596412 @default.
- W4229021887 cites W2600380703 @default.
- W4229021887 cites W2783073729 @default.
- W4229021887 cites W2797346249 @default.
- W4229021887 cites W2800772006 @default.
- W4229021887 cites W2883234896 @default.
- W4229021887 cites W2885128148 @default.
- W4229021887 cites W2903272752 @default.
- W4229021887 cites W2905003304 @default.
- W4229021887 cites W2982532206 @default.
- W4229021887 cites W2992752060 @default.
- W4229021887 cites W3023686201 @default.
- W4229021887 cites W3025988887 @default.
- W4229021887 cites W3046751266 @default.
- W4229021887 cites W3083604952 @default.
- W4229021887 cites W3086381040 @default.
- W4229021887 cites W3087727766 @default.
- W4229021887 cites W3135162129 @default.
- W4229021887 cites W3205128990 @default.
- W4229021887 doi "https://doi.org/10.1101/2022.05.04.490579" @default.
- W4229021887 hasPublicationYear "2022" @default.
- W4229021887 type Work @default.
- W4229021887 citedByCount "0" @default.
- W4229021887 crossrefType "posted-content" @default.
- W4229021887 hasAuthorship W4229021887A5033374983 @default.
- W4229021887 hasAuthorship W4229021887A5056815405 @default.
- W4229021887 hasAuthorship W4229021887A5085371660 @default.
- W4229021887 hasBestOaLocation W42290218871 @default.
- W4229021887 hasConcept C106301342 @default.
- W4229021887 hasConcept C10803110 @default.
- W4229021887 hasConcept C119621388 @default.
- W4229021887 hasConcept C121332964 @default.
- W4229021887 hasConcept C121864883 @default.
- W4229021887 hasConcept C128747166 @default.
- W4229021887 hasConcept C14103023 @default.
- W4229021887 hasConcept C147597530 @default.
- W4229021887 hasConcept C185581394 @default.
- W4229021887 hasConcept C185592680 @default.
- W4229021887 hasConcept C54101563 @default.
- W4229021887 hasConcept C552990157 @default.
- W4229021887 hasConcept C55493867 @default.
- W4229021887 hasConcept C59593255 @default.
- W4229021887 hasConcept C62520636 @default.
- W4229021887 hasConcept C97355855 @default.
- W4229021887 hasConceptScore W4229021887C106301342 @default.