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- W2105393940 abstract "The Jacobson-Stockmayer (JS) model is used in a number of standard programs for calculating the conformational entropy of RNA (and proteins). However, it is shown in this study that, in certain limiting cases, the current form of this model can lead to highly unphysical conclusions. The origin of this behavior can be traced to misunderstandings that occurred during the development of the model as applied to folded, single-stranded RNA. Here we show that an alternative model known as the cross linking entropy (CLE) model can overcome these issues. The principal object that causes entropy loss on a global scale in the CLE model is the <em>stem</em>, the primary measure of structural order in such coarse-grained calculations. The principal objects in the JS-model are various types of <em>loops</em>, and, with the exception of the hairpin loop, they are topologically local in character. To extract experimentally measurable variables, a simplified version of the CLE model is developed that resembles many features of the contact order model used in RNA and protein folding. These modifications are then applied to single molecule force-extension experiments (molecular tweezers) to extract quantitative information. It is further shown that a crude derivative of the CLE model itself can be derived directly from the JS-model when the misunderstandings are examined and corrected." @default.
- W2105393940 created "2016-06-24" @default.
- W2105393940 creator A5005766294 @default.
- W2105393940 creator A5029518682 @default.
- W2105393940 creator A5032544713 @default.
- W2105393940 date "2012-07-24" @default.
- W2105393940 modified "2023-10-16" @default.
- W2105393940 title "A new entropy model for RNA: part I. A critique of the standard Jacobson-Stockmayer model applied to multiple cross links" @default.
- W2105393940 cites W1487526850 @default.
- W2105393940 cites W1505352099 @default.
- W2105393940 cites W1519185585 @default.
- W2105393940 cites W1524134997 @default.
- W2105393940 cites W1530482967 @default.
- W2105393940 cites W1536769227 @default.
- W2105393940 cites W1543796220 @default.
- W2105393940 cites W1559047570 @default.
- W2105393940 cites W1582219327 @default.
- W2105393940 cites W1583149693 @default.
- W2105393940 cites W1975830725 @default.
- W2105393940 cites W1976384779 @default.
- W2105393940 cites W1977360446 @default.
- W2105393940 cites W1977765491 @default.
- W2105393940 cites W1978220465 @default.
- W2105393940 cites W1978696824 @default.
- W2105393940 cites W1981742364 @default.
- W2105393940 cites W1982720588 @default.
- W2105393940 cites W1986748899 @default.
- W2105393940 cites W1987218221 @default.
- W2105393940 cites W1989296116 @default.
- W2105393940 cites W1990351127 @default.
- W2105393940 cites W1990644981 @default.
- W2105393940 cites W1991645679 @default.
- W2105393940 cites W1994344559 @default.
- W2105393940 cites W1994978181 @default.
- W2105393940 cites W1995403172 @default.
- W2105393940 cites W1995764925 @default.
- W2105393940 cites W1999479012 @default.
- W2105393940 cites W2009818318 @default.
- W2105393940 cites W2010952782 @default.
- W2105393940 cites W2011120754 @default.
- W2105393940 cites W2011217803 @default.
- W2105393940 cites W2011684965 @default.
- W2105393940 cites W2013311969 @default.
- W2105393940 cites W2017302704 @default.
- W2105393940 cites W2022159242 @default.
- W2105393940 cites W2023793727 @default.
- W2105393940 cites W2023806120 @default.
- W2105393940 cites W2025763720 @default.
- W2105393940 cites W2027743880 @default.
- W2105393940 cites W2035783320 @default.
- W2105393940 cites W2039896604 @default.
- W2105393940 cites W2041483072 @default.
- W2105393940 cites W2041963112 @default.
- W2105393940 cites W2045872199 @default.
- W2105393940 cites W2048811303 @default.
- W2105393940 cites W2049370744 @default.
- W2105393940 cites W2051713039 @default.
- W2105393940 cites W2051753857 @default.
- W2105393940 cites W2051999592 @default.
- W2105393940 cites W2054252707 @default.
- W2105393940 cites W2059202194 @default.
- W2105393940 cites W2061559913 @default.
- W2105393940 cites W2064061853 @default.
- W2105393940 cites W2070418318 @default.
- W2105393940 cites W2077854862 @default.
- W2105393940 cites W2081407528 @default.
- W2105393940 cites W2089597488 @default.
- W2105393940 cites W2091118010 @default.
- W2105393940 cites W2093789041 @default.
- W2105393940 cites W2103250001 @default.
- W2105393940 cites W2105950741 @default.
- W2105393940 cites W2109969444 @default.
- W2105393940 cites W2112259833 @default.
- W2105393940 cites W2113368761 @default.
- W2105393940 cites W2116479507 @default.
- W2105393940 cites W2117243692 @default.
- W2105393940 cites W2123241418 @default.
- W2105393940 cites W2124162379 @default.
- W2105393940 cites W2135025383 @default.
- W2105393940 cites W2137334883 @default.
- W2105393940 cites W2139433006 @default.
- W2105393940 cites W2148599336 @default.
- W2105393940 cites W2148699366 @default.
- W2105393940 cites W2149801992 @default.
- W2105393940 cites W2162310257 @default.
- W2105393940 cites W2163226166 @default.
- W2105393940 cites W2163558891 @default.
- W2105393940 cites W2163638609 @default.
- W2105393940 cites W2169427967 @default.
- W2105393940 cites W2332949416 @default.
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- W2105393940 doi "https://doi.org/10.4081/jnai.2012.2650" @default.
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