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We began analyzing https://link.springer.com/article/10.1007/s10858-020-00337-7, but it redirected us to https://link.springer.com/article/10.1007/s10858-020-00337-7. The analysis below is for the second page.

Title[redir]:
Probing conformational transitions towards mutagenic Watson–Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion | Journal of Biomolecular NMR
Description:
NMR off-resonance R1ρ relaxation dispersion measurements on base carbon and nitrogen nuclei have revealed that wobble G·T/U mismatches in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-abundance, and mutagenic Watson–Crick-like conformations. As Watson–Crick-like G·T mismatches have base pairing geometries similar to Watson–Crick base pairs, we hypothesized that they would mimic Watson–Crick base pairs with respect to the sugar-backbone conformation as well. Using off-resonance R1ρ measurements targeting the sugar C3′ and C4′ nuclei, a structure survey, and molecular dynamics simulations, we show that wobble G·T mismatches adopt sugar-backbone conformations that deviate from the canonical Watson–Crick conformation and that transitions toward tautomeric and anionic Watson–Crick-like G·T mismatches restore the canonical Watson–Crick sugar-backbone. These measurements also reveal kinetic isotope effects for tautomerization in D2O versus H2O, which provide experimental evidence in support of a transition state involving proton transfer. The results provide additional evidence in support of mutagenic Watson–Crick-like G·T mismatches, help rule out alternative inverted wobble conformations in the case of anionic G·T−, and also establish sugar carbons as new non-exchangeable probes of this exchange process.

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  • Education
  • Science
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Custom-built

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🏙️ Massive Traffic: 50M - 100M visitors per month


Based on our best estimate, this website will receive around 98,426,998 visitors per month in the current month.

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Many websites are intended to earn money, but some serve to share ideas or build connections. Websites exist for all kinds of purposes. This might be one of them. Doi.org has a secret sauce for making money, but we can't detect it yet.

Keywords {🔍}

google, scholar, wobble, mismatches, dna, exchange, wclike, sugar, chemical, supplementary, conformation, bps, nmr, mismatch, fig, base, data, shifts, kimsey, measurements, anionic, sugarbackbone, state, inverted, tautomeric, structures, nucleic, hoogsteen, figure, formation, ads, acids, chem, structure, relaxation, watsoncrick, pairs, methods, offresonance, shift, observed, ppm, obtained, expected, profiles, res, biol, canonical, form, parameters,

Topics {✒️}

c-g-c-g-a-a-t-t-c-a-c c-g-t-g-a-a-t-t-c-g-c base c6-h6/c2-h2/c8-h8 resonances canonical gua-cyt base-pairs watson-crick/hoogsteen breathing dynamics low-abundance short-lived wc n1-methyl deoxy guanosine canonical watson–crick sugar-backbone anti-hiv nucleoside 5-aza-5 low spin-lock fields longitudinal 13c/15n magnetization 13c/15n rf fields visualizing transient watson-crick 13c/15n spin-lock glen-pak dna cartridges gac/gc-cgc/gc-ggc resonance 13c/15n r1ρ article download pdf trna-mrna mini-helix uridine 5-oxyacetic acid n-site chemical exchange watson–crick base pairs sugar-backbone geometry typical unique sugar-backbone conformation hydrogen bond register full size image m1g6-c14+ hoogsteen bp favors anionic watson-crick sugar-backbone conformation differs polymerase active site canonical watson–crick conformation watson–crick duplex fragments t-c4′ chemical shifts rare tautomers form r2 free-precession relaxation canonical sugar-backbone conformations nucleic acid species dna damage repair c2′-endo sugar pucker nmr relaxation dispersion joung–cheatham ion parameters catalytically active conformations canonical c2′-endo conformation dna double helix dt form watson-crick g6-c14 hoogsteen bp disrupt a-rna structure gc-cgc/gc-ggc c8-h8 assignments bloch–mcconnell equations assuming

Questions {❓}

  • Brovarets OO, Hovorun DM (2015) How many tautomerization pathways connect Watson-Crick-like G*T DNA base mispair and wobble mismatches?
  • Hansen DF, Vallurupalli P, Lundstrom P, Neudecker P, Kay LE (2008b) Probing chemical shifts of invisible states of proteins with relaxation dispersion NMR spectroscopy: how well can we do?
  • Rangadurai A et al (2018) Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA?

Schema {🗺️}

WebPage:
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         headline:Probing conformational transitions towards mutagenic Watson–Crick-like G¡T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion
         description:NMR off-resonance R1ρ relaxation dispersion measurements on base carbon and nitrogen nuclei have revealed that wobble G¡T/U mismatches in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-abundance, and mutagenic Watson–Crick-like conformations. As Watson–Crick-like G¡T mismatches have base pairing geometries similar to Watson–Crick base pairs, we hypothesized that they would mimic Watson–Crick base pairs with respect to the sugar-backbone conformation as well. Using off-resonance R1ρ measurements targeting the sugar C3′ and C4′ nuclei, a structure survey, and molecular dynamics simulations, we show that wobble G¡T mismatches adopt sugar-backbone conformations that deviate from the canonical Watson–Crick conformation and that transitions toward tautomeric and anionic Watson–Crick-like G¡T mismatches restore the canonical Watson–Crick sugar-backbone. These measurements also reveal kinetic isotope effects for tautomerization in D2O versus H2O, which provide experimental evidence in support of a transition state involving proton transfer. The results provide additional evidence in support of mutagenic Watson–Crick-like G¡T mismatches, help rule out alternative inverted wobble conformations in the case of anionic G¡T−, and also establish sugar carbons as new non-exchangeable probes of this exchange process.
         datePublished:2020-08-12T00:00:00Z
         dateModified:2020-08-12T00:00:00Z
         pageStart:457
         pageEnd:471
         license:http://creativecommons.org/licenses/by/4.0/
         sameAs:https://doi.org/10.1007/s10858-020-00337-7
         keywords:
            Tautomers
            Anions
            Replication error
            Nucleic acid dynamics
            Chemical exchange
            Sugar pucker
            Biological and Medical Physics
            Biophysics
            Biochemistry
            general
            Spectroscopy/Spectrometry
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                     address:
                        name:Department of Biochemistry, Duke University School of Medicine, Durham, USA
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                        name:Department of Chemistry, Duke University, Durham, USA
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      headline:Probing conformational transitions towards mutagenic Watson–Crick-like G¡T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion
      description:NMR off-resonance R1ρ relaxation dispersion measurements on base carbon and nitrogen nuclei have revealed that wobble G¡T/U mismatches in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-abundance, and mutagenic Watson–Crick-like conformations. As Watson–Crick-like G¡T mismatches have base pairing geometries similar to Watson–Crick base pairs, we hypothesized that they would mimic Watson–Crick base pairs with respect to the sugar-backbone conformation as well. Using off-resonance R1ρ measurements targeting the sugar C3′ and C4′ nuclei, a structure survey, and molecular dynamics simulations, we show that wobble G¡T mismatches adopt sugar-backbone conformations that deviate from the canonical Watson–Crick conformation and that transitions toward tautomeric and anionic Watson–Crick-like G¡T mismatches restore the canonical Watson–Crick sugar-backbone. These measurements also reveal kinetic isotope effects for tautomerization in D2O versus H2O, which provide experimental evidence in support of a transition state involving proton transfer. The results provide additional evidence in support of mutagenic Watson–Crick-like G¡T mismatches, help rule out alternative inverted wobble conformations in the case of anionic G¡T−, and also establish sugar carbons as new non-exchangeable probes of this exchange process.
      datePublished:2020-08-12T00:00:00Z
      dateModified:2020-08-12T00:00:00Z
      pageStart:457
      pageEnd:471
      license:http://creativecommons.org/licenses/by/4.0/
      sameAs:https://doi.org/10.1007/s10858-020-00337-7
      keywords:
         Tautomers
         Anions
         Replication error
         Nucleic acid dynamics
         Chemical exchange
         Sugar pucker
         Biological and Medical Physics
         Biophysics
         Biochemistry
         general
         Spectroscopy/Spectrometry
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         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1007%2Fs10858-020-00337-7/MediaObjects/10858_2020_337_Fig1_HTML.png
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            name:Atul Rangadurai
            affiliation:
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                     name:Department of Biochemistry, Duke University School of Medicine, Durham, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Eric S. Szymanski
            affiliation:
                  name:Duke University School of Medicine
                  address:
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            name:Isaac Kimsey
            affiliation:
                  name:Duke University School of Medicine
                  address:
                     name:Department of Biochemistry, Duke University School of Medicine, Durham, USA
                     type:PostalAddress
                  type:Organization
                  name:Nymirum
                  address:
                     name:Nymirum, Durham, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Honglue Shi
            affiliation:
                  name:Duke University
                  address:
                     name:Department of Chemistry, Duke University, Durham, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Hashim M. Al-Hashimi
            url:http://orcid.org/0000-0003-0681-1747
            affiliation:
                  name:Duke University School of Medicine
                  address:
                     name:Department of Biochemistry, Duke University School of Medicine, Durham, USA
                     type:PostalAddress
                  type:Organization
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               name:Nymirum, Durham, USA
               type:PostalAddress
            type:Organization
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      affiliation:
            name:Duke University
            address:
               name:Department of Chemistry, Duke University, Durham, USA
               type:PostalAddress
            type:Organization
      name:Hashim M. Al-Hashimi
      url:http://orcid.org/0000-0003-0681-1747
      affiliation:
            name:Duke University School of Medicine
            address:
               name:Department of Biochemistry, Duke University School of Medicine, Durham, USA
               type:PostalAddress
            type:Organization
            name:Duke University
            address:
               name:Department of Chemistry, Duke University, Durham, USA
               type:PostalAddress
            type:Organization
      email:[email protected]
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      name:Department of Biochemistry, Duke University School of Medicine, Durham, USA
      name:Department of Biochemistry, Duke University School of Medicine, Durham, USA
      name:Nymirum, Durham, USA
      name:Department of Biochemistry, Duke University School of Medicine, Durham, USA
      name:Nymirum, Durham, USA
      name:Department of Chemistry, Duke University, Durham, USA
      name:Department of Biochemistry, Duke University School of Medicine, Durham, USA
      name:Department of Chemistry, Duke University, Durham, USA

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