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Theory of RNA branching and its rela...

Singaram, Surendra.

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Theory of RNA branching and its relation to packaging by viral capsid protein.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Theory of RNA branching and its relation to packaging by viral capsid protein./
Author:	Singaram, Surendra.
Description:	133 p.
Notes:	Source: Dissertation Abstracts International, Volume: 77-11(E), Section: B.
Contained By:	Dissertation Abstracts International77-11B(E).
Subject:	Biophysics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=10119117
ISBN:	9781339804330

Theory of RNA branching and its relation to packaging by viral capsid protein.
Singaram, Surendra.

Theory of RNA branching and its relation to packaging by viral capsid protein. - 133 p.

Source: Dissertation Abstracts International, Volume: 77-11(E), Section: B.

Thesis (Ph.D.)--University of California, Los Angeles, 2016.

We have developed coarse-grained models of RNA bound by capsid protein (CP) in response to recent in vitro studies on the self-assembly of viral RNA by capsid protein. Under typical in vitro self-assembly conditions and in particular for the case of many ssRNA viruses whose CP have cationic N-termini, the adsorption of CP onto the (anionic) RNA is non-specific because the CP concentration exceeds the Largest dissociation constant for CP-RNA binding. Following an introductory chapter, which recounts the history and physics of the in vitro self-assembly experiments, Chapters 2-4 of this dissertation explore simple lattice models of single-stranded (ss) RNA in the presence of interacting bound particles.

ISBN: 9781339804330Subjects--Topical Terms:

518360
Biophysics.

Theory of RNA branching and its relation to packaging by viral capsid protein.
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020 $a 9781339804330
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100 1 $a Singaram, Surendra. $3 3276608
245 1 0 $a Theory of RNA branching and its relation to packaging by viral capsid protein.
300 $a 133 p.
500 $a Source: Dissertation Abstracts International, Volume: 77-11(E), Section: B.
500 $a Adviser: WILLIAM M. GELBART.
502 $a Thesis (Ph.D.)--University of California, Los Angeles, 2016.
520 $a We have developed coarse-grained models of RNA bound by capsid protein (CP) in response to recent in vitro studies on the self-assembly of viral RNA by capsid protein. Under typical in vitro self-assembly conditions and in particular for the case of many ssRNA viruses whose CP have cationic N-termini, the adsorption of CP onto the (anionic) RNA is non-specific because the CP concentration exceeds the Largest dissociation constant for CP-RNA binding. Following an introductory chapter, which recounts the history and physics of the in vitro self-assembly experiments, Chapters 2-4 of this dissertation explore simple lattice models of single-stranded (ss) RNA in the presence of interacting bound particles.
520 $a In Chapter 2 our investigation opens with a simple model to account for the measured yield of packaged RNA (nucleocapsids) by CP. We treat the RNA as a 1D lattice, whose sites represent CP binding sites, to calculate the yield of RNA packaged as a function of the CP:RNA mol ratio. The measured yield of in vitro assembled nucleocapsids agrees exceptionally well with our simple 1D model.
520 $a In Chapters 3 and 4 we extend our 1D model to 2D to better account for the branched nature of RNA. Our theoretical work provides the statistical-thermodynamic grounding for understanding the in vitro "competition" experiments. In these experiments two RNAs compete for a limited amount of CP. The exchange of CP between the RNAs was found to be reversible at pH 7 and, separately, it was found that long RNAs were able to strip CPs from shorter ones. Our Monte Carlo simulations demonstrate that, for a given RNA mass, the sequence with the highest affinity for protein is the one with the most compact secondary structure arising from self-complementarity; similarly, a long RNA steals protein from an equal mass of shorter ones because of the energetic preference of forming one large cluster of CPs over forming two smaller clusters.
520 $a Finally, in chapter 5 we turn our attention away from the self-assembly experiments to focus on branched polymers. We show there that the 3D size of a branched polymer with N monomers can be directly calculated from a sequence of N -- 2 integers, known as the Prufer sequence. The calculation was performed numerically and shown to be far more efficient (memory-wise) than typical calculations of the 3D size.
590 $a School code: 0031.
650 4 $a Biophysics. $3 518360
650 4 $a Physical chemistry. $3 1981412
650 4 $a Mathematics. $3 515831
690 $a 0786
690 $a 0494
690 $a 0405
710 2 $a University of California, Los Angeles. $b Chemistry. $3 2104984
773 0 $t Dissertation Abstracts International $g 77-11B(E).
790 $a 0031
791 $a Ph.D.
792 $a 2016
793 $a English
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=10119117