Molecular Dynamics Studies of Ion Distributions around DNA Duplexes and Duplex Dimers: Salt Effects and the Connection to Cooperative DNA Melting
Abstract We present extensive molecular dynamics simulations of DNA duplexes and duplex dimers based on the Amber force field to determine the distribution of ions as a function of salt (NaCl) concentration over the range 0.2–1.0M. Periodic boundary conditions are used to model an infinite DNA chain...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Long, Hai [verfasserIn] Schatz, George C. [verfasserIn] |
|---|
| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2002 |
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| Übergeordnetes Werk: |
Enthalten in: MRS online proceedings library - Warrendale, Pa. : MRS, 1998, 735(2002), 1 vom: Dez. |
|---|---|
| Übergeordnetes Werk: |
volume:735 ; year:2002 ; number:1 ; month:12 |
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| DOI / URN: |
10.1557/PROC-735-C10.1 |
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| 520 | |a Abstract We present extensive molecular dynamics simulations of DNA duplexes and duplex dimers based on the Amber force field to determine the distribution of ions as a function of salt (NaCl) concentration over the range 0.2–1.0M. Periodic boundary conditions are used to model an infinite DNA chain, and particle mesh Ewald summation is used to describe long range electrostatic interactions. We have used these simulations to determine the ion distributions associated with a 10 base pair duplex, and we find that the positive and negative ion distributions are identical for distances greater than a radius $ R_{counter} $ which is on the order of 25 Å from the DNA axis, and which decreases as the bulk salt concentration is varied. Based on the calculated $ R_{counter} $, we determine the local counterion concentration as a function of bulk salt concentration. Similar studies of DNA duplex dimers separated by 30–40 Å leads to a determination of the local counterion concentration around these dimers. Here we find that dimerization leads to greatly enhanced counterion concentrations. If this information is combined with the measured results concerning the dependence of DNA melting temperature on bulk salt concentration, we find that dimerization leads to a several degree increase in melting temperature, with the increase being 10°C for a dimer separation of 30 Å. This result provides justification for a recently developed cooperative melting model of DNA duplex aggregates. | ||
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10.1557/PROC-735-C10.1 doi (DE-627)SPR042513375 (DE-599)SPRPROC-735-C10.1-e (SPR)PROC-735-C10.1-e DE-627 ger DE-627 rakwb eng 670 ASE Long, Hai verfasserin aut Molecular Dynamics Studies of Ion Distributions around DNA Duplexes and Duplex Dimers: Salt Effects and the Connection to Cooperative DNA Melting 2002 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract We present extensive molecular dynamics simulations of DNA duplexes and duplex dimers based on the Amber force field to determine the distribution of ions as a function of salt (NaCl) concentration over the range 0.2–1.0M. Periodic boundary conditions are used to model an infinite DNA chain, and particle mesh Ewald summation is used to describe long range electrostatic interactions. We have used these simulations to determine the ion distributions associated with a 10 base pair duplex, and we find that the positive and negative ion distributions are identical for distances greater than a radius $ R_{counter} $ which is on the order of 25 Å from the DNA axis, and which decreases as the bulk salt concentration is varied. Based on the calculated $ R_{counter} $, we determine the local counterion concentration as a function of bulk salt concentration. Similar studies of DNA duplex dimers separated by 30–40 Å leads to a determination of the local counterion concentration around these dimers. Here we find that dimerization leads to greatly enhanced counterion concentrations. If this information is combined with the measured results concerning the dependence of DNA melting temperature on bulk salt concentration, we find that dimerization leads to a several degree increase in melting temperature, with the increase being 10°C for a dimer separation of 30 Å. This result provides justification for a recently developed cooperative melting model of DNA duplex aggregates. Schatz, George C. verfasserin aut Enthalten in MRS online proceedings library Warrendale, Pa. : MRS, 1998 735(2002), 1 vom: Dez. (DE-627)57782046X (DE-600)2451008-7 1946-4274 nnns volume:735 year:2002 number:1 month:12 https://dx.doi.org/10.1557/PROC-735-C10.1 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_2005 AR 735 2002 1 12 |
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10.1557/PROC-735-C10.1 doi (DE-627)SPR042513375 (DE-599)SPRPROC-735-C10.1-e (SPR)PROC-735-C10.1-e DE-627 ger DE-627 rakwb eng 670 ASE Long, Hai verfasserin aut Molecular Dynamics Studies of Ion Distributions around DNA Duplexes and Duplex Dimers: Salt Effects and the Connection to Cooperative DNA Melting 2002 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract We present extensive molecular dynamics simulations of DNA duplexes and duplex dimers based on the Amber force field to determine the distribution of ions as a function of salt (NaCl) concentration over the range 0.2–1.0M. Periodic boundary conditions are used to model an infinite DNA chain, and particle mesh Ewald summation is used to describe long range electrostatic interactions. We have used these simulations to determine the ion distributions associated with a 10 base pair duplex, and we find that the positive and negative ion distributions are identical for distances greater than a radius $ R_{counter} $ which is on the order of 25 Å from the DNA axis, and which decreases as the bulk salt concentration is varied. Based on the calculated $ R_{counter} $, we determine the local counterion concentration as a function of bulk salt concentration. Similar studies of DNA duplex dimers separated by 30–40 Å leads to a determination of the local counterion concentration around these dimers. Here we find that dimerization leads to greatly enhanced counterion concentrations. If this information is combined with the measured results concerning the dependence of DNA melting temperature on bulk salt concentration, we find that dimerization leads to a several degree increase in melting temperature, with the increase being 10°C for a dimer separation of 30 Å. This result provides justification for a recently developed cooperative melting model of DNA duplex aggregates. Schatz, George C. verfasserin aut Enthalten in MRS online proceedings library Warrendale, Pa. : MRS, 1998 735(2002), 1 vom: Dez. (DE-627)57782046X (DE-600)2451008-7 1946-4274 nnns volume:735 year:2002 number:1 month:12 https://dx.doi.org/10.1557/PROC-735-C10.1 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_2005 AR 735 2002 1 12 |
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10.1557/PROC-735-C10.1 doi (DE-627)SPR042513375 (DE-599)SPRPROC-735-C10.1-e (SPR)PROC-735-C10.1-e DE-627 ger DE-627 rakwb eng 670 ASE Long, Hai verfasserin aut Molecular Dynamics Studies of Ion Distributions around DNA Duplexes and Duplex Dimers: Salt Effects and the Connection to Cooperative DNA Melting 2002 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract We present extensive molecular dynamics simulations of DNA duplexes and duplex dimers based on the Amber force field to determine the distribution of ions as a function of salt (NaCl) concentration over the range 0.2–1.0M. Periodic boundary conditions are used to model an infinite DNA chain, and particle mesh Ewald summation is used to describe long range electrostatic interactions. We have used these simulations to determine the ion distributions associated with a 10 base pair duplex, and we find that the positive and negative ion distributions are identical for distances greater than a radius $ R_{counter} $ which is on the order of 25 Å from the DNA axis, and which decreases as the bulk salt concentration is varied. Based on the calculated $ R_{counter} $, we determine the local counterion concentration as a function of bulk salt concentration. Similar studies of DNA duplex dimers separated by 30–40 Å leads to a determination of the local counterion concentration around these dimers. Here we find that dimerization leads to greatly enhanced counterion concentrations. If this information is combined with the measured results concerning the dependence of DNA melting temperature on bulk salt concentration, we find that dimerization leads to a several degree increase in melting temperature, with the increase being 10°C for a dimer separation of 30 Å. This result provides justification for a recently developed cooperative melting model of DNA duplex aggregates. Schatz, George C. verfasserin aut Enthalten in MRS online proceedings library Warrendale, Pa. : MRS, 1998 735(2002), 1 vom: Dez. (DE-627)57782046X (DE-600)2451008-7 1946-4274 nnns volume:735 year:2002 number:1 month:12 https://dx.doi.org/10.1557/PROC-735-C10.1 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_2005 AR 735 2002 1 12 |
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10.1557/PROC-735-C10.1 doi (DE-627)SPR042513375 (DE-599)SPRPROC-735-C10.1-e (SPR)PROC-735-C10.1-e DE-627 ger DE-627 rakwb eng 670 ASE Long, Hai verfasserin aut Molecular Dynamics Studies of Ion Distributions around DNA Duplexes and Duplex Dimers: Salt Effects and the Connection to Cooperative DNA Melting 2002 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract We present extensive molecular dynamics simulations of DNA duplexes and duplex dimers based on the Amber force field to determine the distribution of ions as a function of salt (NaCl) concentration over the range 0.2–1.0M. Periodic boundary conditions are used to model an infinite DNA chain, and particle mesh Ewald summation is used to describe long range electrostatic interactions. We have used these simulations to determine the ion distributions associated with a 10 base pair duplex, and we find that the positive and negative ion distributions are identical for distances greater than a radius $ R_{counter} $ which is on the order of 25 Å from the DNA axis, and which decreases as the bulk salt concentration is varied. Based on the calculated $ R_{counter} $, we determine the local counterion concentration as a function of bulk salt concentration. Similar studies of DNA duplex dimers separated by 30–40 Å leads to a determination of the local counterion concentration around these dimers. Here we find that dimerization leads to greatly enhanced counterion concentrations. If this information is combined with the measured results concerning the dependence of DNA melting temperature on bulk salt concentration, we find that dimerization leads to a several degree increase in melting temperature, with the increase being 10°C for a dimer separation of 30 Å. This result provides justification for a recently developed cooperative melting model of DNA duplex aggregates. Schatz, George C. verfasserin aut Enthalten in MRS online proceedings library Warrendale, Pa. : MRS, 1998 735(2002), 1 vom: Dez. (DE-627)57782046X (DE-600)2451008-7 1946-4274 nnns volume:735 year:2002 number:1 month:12 https://dx.doi.org/10.1557/PROC-735-C10.1 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_2005 AR 735 2002 1 12 |
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10.1557/PROC-735-C10.1 doi (DE-627)SPR042513375 (DE-599)SPRPROC-735-C10.1-e (SPR)PROC-735-C10.1-e DE-627 ger DE-627 rakwb eng 670 ASE Long, Hai verfasserin aut Molecular Dynamics Studies of Ion Distributions around DNA Duplexes and Duplex Dimers: Salt Effects and the Connection to Cooperative DNA Melting 2002 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract We present extensive molecular dynamics simulations of DNA duplexes and duplex dimers based on the Amber force field to determine the distribution of ions as a function of salt (NaCl) concentration over the range 0.2–1.0M. Periodic boundary conditions are used to model an infinite DNA chain, and particle mesh Ewald summation is used to describe long range electrostatic interactions. We have used these simulations to determine the ion distributions associated with a 10 base pair duplex, and we find that the positive and negative ion distributions are identical for distances greater than a radius $ R_{counter} $ which is on the order of 25 Å from the DNA axis, and which decreases as the bulk salt concentration is varied. Based on the calculated $ R_{counter} $, we determine the local counterion concentration as a function of bulk salt concentration. Similar studies of DNA duplex dimers separated by 30–40 Å leads to a determination of the local counterion concentration around these dimers. Here we find that dimerization leads to greatly enhanced counterion concentrations. If this information is combined with the measured results concerning the dependence of DNA melting temperature on bulk salt concentration, we find that dimerization leads to a several degree increase in melting temperature, with the increase being 10°C for a dimer separation of 30 Å. This result provides justification for a recently developed cooperative melting model of DNA duplex aggregates. Schatz, George C. verfasserin aut Enthalten in MRS online proceedings library Warrendale, Pa. : MRS, 1998 735(2002), 1 vom: Dez. (DE-627)57782046X (DE-600)2451008-7 1946-4274 nnns volume:735 year:2002 number:1 month:12 https://dx.doi.org/10.1557/PROC-735-C10.1 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_2005 AR 735 2002 1 12 |
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Molecular Dynamics Studies of Ion Distributions around DNA Duplexes and Duplex Dimers: Salt Effects and the Connection to Cooperative DNA Melting |
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Abstract We present extensive molecular dynamics simulations of DNA duplexes and duplex dimers based on the Amber force field to determine the distribution of ions as a function of salt (NaCl) concentration over the range 0.2–1.0M. Periodic boundary conditions are used to model an infinite DNA chain, and particle mesh Ewald summation is used to describe long range electrostatic interactions. We have used these simulations to determine the ion distributions associated with a 10 base pair duplex, and we find that the positive and negative ion distributions are identical for distances greater than a radius $ R_{counter} $ which is on the order of 25 Å from the DNA axis, and which decreases as the bulk salt concentration is varied. Based on the calculated $ R_{counter} $, we determine the local counterion concentration as a function of bulk salt concentration. Similar studies of DNA duplex dimers separated by 30–40 Å leads to a determination of the local counterion concentration around these dimers. Here we find that dimerization leads to greatly enhanced counterion concentrations. If this information is combined with the measured results concerning the dependence of DNA melting temperature on bulk salt concentration, we find that dimerization leads to a several degree increase in melting temperature, with the increase being 10°C for a dimer separation of 30 Å. This result provides justification for a recently developed cooperative melting model of DNA duplex aggregates. |
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Abstract We present extensive molecular dynamics simulations of DNA duplexes and duplex dimers based on the Amber force field to determine the distribution of ions as a function of salt (NaCl) concentration over the range 0.2–1.0M. Periodic boundary conditions are used to model an infinite DNA chain, and particle mesh Ewald summation is used to describe long range electrostatic interactions. We have used these simulations to determine the ion distributions associated with a 10 base pair duplex, and we find that the positive and negative ion distributions are identical for distances greater than a radius $ R_{counter} $ which is on the order of 25 Å from the DNA axis, and which decreases as the bulk salt concentration is varied. Based on the calculated $ R_{counter} $, we determine the local counterion concentration as a function of bulk salt concentration. Similar studies of DNA duplex dimers separated by 30–40 Å leads to a determination of the local counterion concentration around these dimers. Here we find that dimerization leads to greatly enhanced counterion concentrations. If this information is combined with the measured results concerning the dependence of DNA melting temperature on bulk salt concentration, we find that dimerization leads to a several degree increase in melting temperature, with the increase being 10°C for a dimer separation of 30 Å. This result provides justification for a recently developed cooperative melting model of DNA duplex aggregates. |
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Abstract We present extensive molecular dynamics simulations of DNA duplexes and duplex dimers based on the Amber force field to determine the distribution of ions as a function of salt (NaCl) concentration over the range 0.2–1.0M. Periodic boundary conditions are used to model an infinite DNA chain, and particle mesh Ewald summation is used to describe long range electrostatic interactions. We have used these simulations to determine the ion distributions associated with a 10 base pair duplex, and we find that the positive and negative ion distributions are identical for distances greater than a radius $ R_{counter} $ which is on the order of 25 Å from the DNA axis, and which decreases as the bulk salt concentration is varied. Based on the calculated $ R_{counter} $, we determine the local counterion concentration as a function of bulk salt concentration. Similar studies of DNA duplex dimers separated by 30–40 Å leads to a determination of the local counterion concentration around these dimers. Here we find that dimerization leads to greatly enhanced counterion concentrations. If this information is combined with the measured results concerning the dependence of DNA melting temperature on bulk salt concentration, we find that dimerization leads to a several degree increase in melting temperature, with the increase being 10°C for a dimer separation of 30 Å. This result provides justification for a recently developed cooperative melting model of DNA duplex aggregates. |
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| up_date |
2024-07-04T02:14:59.513Z |
| _version_ |
1803612900047192064 |
| fullrecord_marcxml |
<?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>01000caa a22002652 4500</leader><controlfield tag="001">SPR042513375</controlfield><controlfield tag="003">DE-627</controlfield><controlfield tag="005">20220112053007.0</controlfield><controlfield tag="007">cr uuu---uuuuu</controlfield><controlfield tag="008">201227s2002 xx |||||o 00| ||eng c</controlfield><datafield tag="024" ind1="7" ind2=" "><subfield code="a">10.1557/PROC-735-C10.1</subfield><subfield code="2">doi</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-627)SPR042513375</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-599)SPRPROC-735-C10.1-e</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(SPR)PROC-735-C10.1-e</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-627</subfield><subfield code="b">ger</subfield><subfield code="c">DE-627</subfield><subfield code="e">rakwb</subfield></datafield><datafield tag="041" ind1=" " ind2=" "><subfield code="a">eng</subfield></datafield><datafield tag="082" ind1="0" ind2="4"><subfield code="a">670</subfield><subfield code="q">ASE</subfield></datafield><datafield tag="100" ind1="1" ind2=" "><subfield code="a">Long, Hai</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Molecular Dynamics Studies of Ion Distributions around DNA Duplexes and Duplex Dimers: Salt Effects and the Connection to Cooperative DNA Melting</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2002</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="a">Text</subfield><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">Computermedien</subfield><subfield code="b">c</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">Online-Ressource</subfield><subfield code="b">cr</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">Abstract We present extensive molecular dynamics simulations of DNA duplexes and duplex dimers based on the Amber force field to determine the distribution of ions as a function of salt (NaCl) concentration over the range 0.2–1.0M. Periodic boundary conditions are used to model an infinite DNA chain, and particle mesh Ewald summation is used to describe long range electrostatic interactions. We have used these simulations to determine the ion distributions associated with a 10 base pair duplex, and we find that the positive and negative ion distributions are identical for distances greater than a radius $ R_{counter} $ which is on the order of 25 Å from the DNA axis, and which decreases as the bulk salt concentration is varied. Based on the calculated $ R_{counter} $, we determine the local counterion concentration as a function of bulk salt concentration. Similar studies of DNA duplex dimers separated by 30–40 Å leads to a determination of the local counterion concentration around these dimers. Here we find that dimerization leads to greatly enhanced counterion concentrations. If this information is combined with the measured results concerning the dependence of DNA melting temperature on bulk salt concentration, we find that dimerization leads to a several degree increase in melting temperature, with the increase being 10°C for a dimer separation of 30 Å. This result provides justification for a recently developed cooperative melting model of DNA duplex aggregates.</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Schatz, George C.</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="773" ind1="0" ind2="8"><subfield code="i">Enthalten in</subfield><subfield code="t">MRS online proceedings library</subfield><subfield code="d">Warrendale, Pa. : MRS, 1998</subfield><subfield code="g">735(2002), 1 vom: Dez.</subfield><subfield code="w">(DE-627)57782046X</subfield><subfield code="w">(DE-600)2451008-7</subfield><subfield code="x">1946-4274</subfield><subfield code="7">nnns</subfield></datafield><datafield tag="773" ind1="1" ind2="8"><subfield code="g">volume:735</subfield><subfield code="g">year:2002</subfield><subfield code="g">number:1</subfield><subfield code="g">month:12</subfield></datafield><datafield tag="856" ind1="4" ind2="0"><subfield code="u">https://dx.doi.org/10.1557/PROC-735-C10.1</subfield><subfield code="z">lizenzpflichtig</subfield><subfield code="3">Volltext</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_USEFLAG_A</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">SYSFLAG_A</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_SPRINGER</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_2005</subfield></datafield><datafield tag="951" ind1=" " ind2=" "><subfield code="a">AR</subfield></datafield><datafield tag="952" ind1=" " ind2=" "><subfield code="d">735</subfield><subfield code="j">2002</subfield><subfield code="e">1</subfield><subfield code="c">12</subfield></datafield></record></collection>
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| score |
7.3999977 |