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Attaining the 2nd Chargaff Rule by Tandem Duplications

Jain, Siddharth and Raviv, Netanel and Bruck, Jehoshua (2018) Attaining the 2nd Chargaff Rule by Tandem Duplications. Parallel and Distributed Systems Group Technical Reports, 138. California Institute of Technology , Pasadena, CA. (Unpublished) http://resolver.caltech.edu/CaltechAUTHORS:20180105-092230028

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Abstract

Erwin Chargaff in 1950 made an experimental observation that the count of A is equal to the count of T and the count of C is equal to the count of G in DNA. This observation played a crucial rule in the discovery of the double stranded helix structure by Watson and Crick. However, this symmetry was also observed in single stranded DNA. This phenomenon was termed as 2nd Chargaff Rule. This symmetry has been verified experimentally in genomes of several different species not only for mononucleotides but also for reverse complement pairs of larger lengths up to a small error. While the symmetry in double stranded DNA is related to base pairing, and replication mechanisms, the symmetry in a single stranded DNA is still a mystery in its function and source. In this work, we define a sequence generation model based on reverse complement tandem duplications. We show that this model generates sequences that satisfy the 2nd Chargaff Rule even when the duplication lengths are very small when compared to the length of sequences. We also provide estimates on the number of generations that are needed by this model to generate sequences that satisfy 2nd Chargaff Rule. We provide theoretical bounds on the disruption in symmetry for different values of duplication lengths under this model. Moreover, we experimentally compare the disruption in the symmetry incurred by our model with what is observed in human genome data.


Item Type:Report or Paper (Technical Report)
Related URLs:
URLURL TypeDescription
http://www.paradise.caltech.edu/papers/etr138.pdfAuthorTechnical Report
ORCID:
AuthorORCID
Jain, Siddharth0000-0002-9164-6119
Additional Information:This work was supported in part by the NSF Expeditions in Computing Program - The Molecular Programming Project. The work of Netanel Raviv was supported in part by the postdoctoral fellowship of the Center for the Mathematics of Information (CMI), Caltech, and in part by the Lester-Deutsch postdoctoral fellowship.
Group:Parallel and Distributed Systems Group
Funders:
Funding AgencyGrant Number
NSFUNSPECIFIED
Center for the Mathematics of Information, CaltechUNSPECIFIED
Lester-Deutsch postdoctoral fellowshipUNSPECIFIED
Subject Keywords:reverse complement, inversion symmetry, balanced and unbalanced sequences, duplications
Other Numbering System:
Other Numbering System NameOther Numbering System ID
PARADISEETR-38
Record Number:CaltechAUTHORS:20180105-092230028
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20180105-092230028
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:84120
Collection:CaltechPARADISE
Deposited By: George Porter
Deposited On:05 Jan 2018 18:06
Last Modified:03 Apr 2018 21:23

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