• Login
    View Item 
    •   Home
    • Research
    • Articles
    • View Item
    •   Home
    • Research
    • Articles
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Browse

    All of KAUSTCommunitiesIssue DateSubmit DateThis CollectionIssue DateSubmit Date

    My Account

    Login

    Quick Links

    Open Access PolicyORCID LibguideTheses and Dissertations LibguideSubmit an Item

    Statistics

    Display statistics

    Energetics and dynamics of the non-natural fluorescent 4AP:DAP base pair

    • CSV
    • RefMan
    • EndNote
    • BibTex
    • RefWorks
    Type
    Article
    Authors
    Chawla, Mohit cc
    Autiero, Ida cc
    Oliva, Romina cc
    Cavallo, Luigi cc
    KAUST Department
    Chemical Science Program
    KAUST Catalysis Center (KCC)
    Physical Science and Engineering (PSE) Division
    Date
    2018
    Permanent link to this record
    http://hdl.handle.net/10754/627251
    
    Metadata
    Show full item record
    Abstract
    The fluorescent non-natural 4-aminophthalimide (4AP) base, when paired to the complementary 2,4-diaminopyrimidine (DAP) nucleobase, is accommodated in a B-DNA duplex being efficiently recognized and incorporated by DNA polymerases. To complement the experimental studies and rationalize the impact of the above non-natural bases on the structure, stability and dynamics of nucleic acid structures, we performed quantum mechanics (QM) calculations along with classical molecular dynamics (MD) simulations. QM calculations were initially focused on the geometry and energetics of the 4AP:DAP non-natural pair and of H-bonded base pairs between 4AP and all the natural bases in their classical Watson-Crick geometries. The QM calculations indicate that the 4AP:DAP pair, despite the fact that it can form 3 H-bonds in a classic Watson-Crick geometry, has a stability comparable to the A:T pair. Then, we extended the study to reverse Watson-Crick geometries, characteristic of parallel strands. MD simulations were carried out on two 13-mer DNA duplexes, featuring a central 4AP:DAP or A:T pair, respectively. No major structural deformation of the duplex was observed during the MD simulation. Snapshots from the MD simulations were subjected to QM calculations to investigate the 4AP:DAP interaction energy when embedded into a duplex structure, and to investigate the impact of the two non-natural bases on the stacking interactions with adjacent bases in the DNA duplex. We found a slight increase in stacking interactions involving the 4AP:DAP pair, counterbalanced by a moderate decrease in H-bonding interactions of the 4AP:DAP and of the adjacent base pairs in the duplex. The results of our study are in agreement with experimental data and complement them by providing an insight into which factors contribute positively and which factors contribute negatively to the structural compatibility of the fluorescent 4AP:DAP pair with a B-DNA structure.
    Citation
    Chawla M, Autiero I, Oliva R, Cavallo L (2018) Energetics and dynamics of the non-natural fluorescent 4AP:DAP base pair. Physical Chemistry Chemical Physics 20: 3699–3709. Available: http://dx.doi.org/10.1039/c7cp07400j.
    Sponsors
    LC thanks the King Abdullah University of Science and Technology for supporting this work. For computer time, this research used the resources of the Supercomputing Laboratory at King Abdullah University of Science and Technology (KSL) in Thuwal, Saudi Arabia.
    Publisher
    Royal Society of Chemistry (RSC)
    Journal
    Physical Chemistry Chemical Physics
    DOI
    10.1039/c7cp07400j
    PubMed ID
    29345270
    Additional Links
    http://pubs.rsc.org/en/Content/ArticleLanding/2018/CP/C7CP07400J#!divAbstract
    ae974a485f413a2113503eed53cd6c53
    10.1039/c7cp07400j
    Scopus Count
    Collections
    Articles; Physical Science and Engineering (PSE) Division; Chemical Science Program; KAUST Catalysis Center (KCC)

    entitlement

    Related articles

    • Theoretical insights into the structural and fluorescence properties of DNA containing fluorescent nucleobases.
    • Authors: Wang W, Sheng X, Zhang S, Huang F, Sun C, Liu J, Chen D
    • Issue date: 2018 Jun 20
    • An Isosteric and Fluorescent DNA Base Pair Consisting of 4-aminophthalimide and 2,4-diaminopyrimidine as C-Nucleosides.
    • Authors: Merkel M, Dehmel L, Ernsting NP, Wagenknecht HA
    • Issue date: 2017 Jan 2
    • How do hydrophobic nucleobases differ from natural DNA nucleobases? Comparison of structural features and duplex properties from QM calculations and MD simulations.
    • Authors: Negi I, Kathuria P, Sharma P, Wetmore SD
    • Issue date: 2017 Jun 28
    • Effect of Watson-Crick and Hoogsteen base pairing on the conformational stability of C8-phenoxyl-2'-deoxyguanosine adducts.
    • Authors: Millen AL, Churchill CD, Manderville RA, Wetmore SD
    • Issue date: 2010 Oct 14
    • Replacing thymine with a strongly pairing fifth Base: A combined quantum mechanics and molecular dynamics study.
    • Authors: Chawla M, Gorle S, Shaikh AR, Oliva R, Cavallo L
    • Issue date: 2021
    DSpace software copyright © 2002-2022  DuraSpace
    Quick Guide | Contact Us | KAUST University Library
    Open Repository is a service hosted by 
    Atmire NV
     

    Export search results

    The export option will allow you to export the current search results of the entered query to a file. Different formats are available for download. To export the items, click on the button corresponding with the preferred download format.

    By default, clicking on the export buttons will result in a download of the allowed maximum amount of items. For anonymous users the allowed maximum amount is 50 search results.

    To select a subset of the search results, click "Selective Export" button and make a selection of the items you want to export. The amount of items that can be exported at once is similarly restricted as the full export.

    After making a selection, click one of the export format buttons. The amount of items that will be exported is indicated in the bubble next to export format.