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DNA Bending Propensity in the Presence of Base Mismatches:Implications for DNA Repair.

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Title: DNA Bending Propensity in the Presence of Base Mismatches:Implications for DNA Repair.
Authors: Sharma, Monika1, Predeus, Alexander V.1, Mukherjee, Shayantani1, Feig, Michael1
Source: Journal of Physical Chemistry B. May2013, Vol. 117 Issue 20, p6194-6205. 12p.
Subjects: DNA bending, DNA repair, Nucleotide sequence, Purines, Canonical coordinates, Free energy (Thermodynamics), Molecular recognition
Abstract: DNAbending is believed to facilitate the initial recognition ofthe mismatched base for repair. The repair efficiencies are dependenton both the mismatch type and neighboring nucleotide sequence. Wehave studied bending of several DNA duplexes containing canonicalmatches: A:T and G:C; various mismatches: A:A, A:C, G:A, G:G, G:T,C:C, C:T, and T:T; and a bis-abasic site: X:X. Free-energy profileswere generated for DNA bending using umbrella sampling. The highestenergetic cost associated with DNA bending is observed for canonicalmatches while bending free energies are lower in the presence of mismatches,with the lowest value for the abasic site. In all of the sequences,DNA duplexes bend toward the major groove with widening of the minorgroove. For homoduplexes, DNA bending is observed to occur via smoothdeformations, whereas for heteroduplexes, kinks are observed at themismatch site during strong bending. In general, pyrimidine:pyrimidinemismatches are the most destabilizing, while purine:purine mismatcheslead to intermediate destabilization, and purine:pyrimidine mismatchesare the least destabilizing. The ease of bending is partially correlatedwith the binding affinity of MutS to the mismatch pairs and subsequentrepair efficiencies, indicating that intrinsic DNA bending propensitiesare a key factor of mismatch recognition. [ABSTRACT FROM AUTHOR]
Copyright of Journal of Physical Chemistry B is the property of American Chemical Society and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
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DbLabel: Engineering Source
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  Data: DNA Bending Propensity in the Presence of Base Mismatches:Implications for DNA Repair.
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  Data: <searchLink fieldCode="AR" term="%22Sharma%2C+Monika%22">Sharma, Monika</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Predeus%2C+Alexander+V%2E%22">Predeus, Alexander V.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Mukherjee%2C+Shayantani%22">Mukherjee, Shayantani</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Feig%2C+Michael%22">Feig, Michael</searchLink><relatesTo>1</relatesTo>
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  Data: <searchLink fieldCode="JN" term="%22Journal+of+Physical+Chemistry+B%22">Journal of Physical Chemistry B</searchLink>. May2013, Vol. 117 Issue 20, p6194-6205. 12p.
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  Data: <searchLink fieldCode="DE" term="%22DNA+bending%22">DNA bending</searchLink><br /><searchLink fieldCode="DE" term="%22DNA+repair%22">DNA repair</searchLink><br /><searchLink fieldCode="DE" term="%22Nucleotide+sequence%22">Nucleotide sequence</searchLink><br /><searchLink fieldCode="DE" term="%22Purines%22">Purines</searchLink><br /><searchLink fieldCode="DE" term="%22Canonical+coordinates%22">Canonical coordinates</searchLink><br /><searchLink fieldCode="DE" term="%22Free+energy+%28Thermodynamics%29%22">Free energy (Thermodynamics)</searchLink><br /><searchLink fieldCode="DE" term="%22Molecular+recognition%22">Molecular recognition</searchLink>
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  Data: DNAbending is believed to facilitate the initial recognition ofthe mismatched base for repair. The repair efficiencies are dependenton both the mismatch type and neighboring nucleotide sequence. Wehave studied bending of several DNA duplexes containing canonicalmatches: A:T and G:C; various mismatches: A:A, A:C, G:A, G:G, G:T,C:C, C:T, and T:T; and a bis-abasic site: X:X. Free-energy profileswere generated for DNA bending using umbrella sampling. The highestenergetic cost associated with DNA bending is observed for canonicalmatches while bending free energies are lower in the presence of mismatches,with the lowest value for the abasic site. In all of the sequences,DNA duplexes bend toward the major groove with widening of the minorgroove. For homoduplexes, DNA bending is observed to occur via smoothdeformations, whereas for heteroduplexes, kinks are observed at themismatch site during strong bending. In general, pyrimidine:pyrimidinemismatches are the most destabilizing, while purine:purine mismatcheslead to intermediate destabilization, and purine:pyrimidine mismatchesare the least destabilizing. The ease of bending is partially correlatedwith the binding affinity of MutS to the mismatch pairs and subsequentrepair efficiencies, indicating that intrinsic DNA bending propensitiesare a key factor of mismatch recognition. [ABSTRACT FROM AUTHOR]
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  Data: <i>Copyright of Journal of Physical Chemistry B is the property of American Chemical Society and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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        Value: 10.1021/jp403127a
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      – Code: eng
        Text: English
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        PageCount: 12
        StartPage: 6194
    Subjects:
      – SubjectFull: DNA bending
        Type: general
      – SubjectFull: DNA repair
        Type: general
      – SubjectFull: Nucleotide sequence
        Type: general
      – SubjectFull: Purines
        Type: general
      – SubjectFull: Canonical coordinates
        Type: general
      – SubjectFull: Free energy (Thermodynamics)
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      – SubjectFull: Molecular recognition
        Type: general
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      – TitleFull: DNA Bending Propensity in the Presence of Base Mismatches:Implications for DNA Repair.
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            NameFull: Sharma, Monika
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            NameFull: Predeus, Alexander V.
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            NameFull: Mukherjee, Shayantani
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            NameFull: Feig, Michael
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              M: 05
              Text: May2013
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              Y: 2013
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