Static and Statistical Bending of DNA Evaluated by Monte Carlo Simulations

To investigate the influence of thermal fluctuations on DNA curvature the Metropolis procedure at 300 K was applied to B-DNA decamers containing A5·T5and A4·T4blocks. Monte Carlo simulations have confirmed the DNA bending anisotropy: B-DNA bends most easily in a groove direction (roll). The A5·T5blo...

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Veröffentlicht in:Proceedings of the National Academy of Sciences - PNAS 1991-08, Vol.88 (16), p.7046-7050
Hauptverfasser: Zhurkin, V. B., Ulyanov, N. B., Gorin, A. A., Jernigan, R. L.
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container_issue 16
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container_title Proceedings of the National Academy of Sciences - PNAS
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creator Zhurkin, V. B.
Ulyanov, N. B.
Gorin, A. A.
Jernigan, R. L.
description To investigate the influence of thermal fluctuations on DNA curvature the Metropolis procedure at 300 K was applied to B-DNA decamers containing A5·T5and A4·T4blocks. Monte Carlo simulations have confirmed the DNA bending anisotropy: B-DNA bends most easily in a groove direction (roll). The A5·T5block is more rigid than the other sequences; the pyrimidine-purine dimers are found to be the most flexible. For A5TCTCT, A5CTCTC, and A5GAGAG, the average bend angle per decamer is 20-25⚬in a direction toward the minor groove in the center of the A5·T5tract, which is consistent with both the "junction" and "wedge AA" models. However, in A5T5, A4T4CG, and T4A4GC, bending is directed into the grooves at the 5' and 3' ends of purine tracts. Thus, directionality of bending caused by An·Tnblocks strongly depends on their neighboring sequences. These calculations demonstrate that the sequence-dependent variation of the minor-groove width mimics the observed hydroxyl radical cleavage pattern. To estimate the effect of fluctuations on the overall shape of curved DNA fragments, longer pieces of DNA (up to 200 base pairs) were generated. For sequences with strong curvature (A5X5and A4T4CG), the static model and Monte Carlo ensemble give similar results but, for moderately and slightly curved sequences (A5T5or T4A4GC), the static model predicts a much smaller degree of bending than does the statistical representation. Considering fluctuations is important for quantitative interpretation of the gel electrophoresis measurements of DNA curvature, where both the static and statistical bends are operative.
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For A5TCTCT, A5CTCTC, and A5GAGAG, the average bend angle per decamer is 20-25⚬in a direction toward the minor groove in the center of the A5·T5tract, which is consistent with both the "junction" and "wedge AA" models. However, in A5T5, A4T4CG, and T4A4GC, bending is directed into the grooves at the 5' and 3' ends of purine tracts. Thus, directionality of bending caused by An·Tnblocks strongly depends on their neighboring sequences. These calculations demonstrate that the sequence-dependent variation of the minor-groove width mimics the observed hydroxyl radical cleavage pattern. To estimate the effect of fluctuations on the overall shape of curved DNA fragments, longer pieces of DNA (up to 200 base pairs) were generated. For sequences with strong curvature (A5X5and A4T4CG), the static model and Monte Carlo ensemble give similar results but, for moderately and slightly curved sequences (A5T5or T4A4GC), the static model predicts a much smaller degree of bending than does the statistical representation. Considering fluctuations is important for quantitative interpretation of the gel electrophoresis measurements of DNA curvature, where both the static and statistical bends are operative.</description><subject>Arithmetic mean</subject><subject>Base Sequence</subject><subject>Bending</subject><subject>Biological and medical sciences</subject><subject>Boundary conditions</subject><subject>Conformational dynamics in molecular biology</subject><subject>Curvature</subject><subject>Dimers</subject><subject>DNA</subject><subject>DNA - chemistry</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genetic vectors</subject><subject>Hydrogen Bonding</subject><subject>Models, Molecular</subject><subject>Molecular biophysics</subject><subject>Molecular Sequence Data</subject><subject>Monte Carlo Method</subject><subject>Nucleic Acid Conformation</subject><subject>Nucleic acids</subject><subject>Nucleotides</subject><subject>Oligodeoxyribonucleotides - chemistry</subject><subject>Static modeling</subject><subject>Structure-Activity Relationship</subject><issn>0027-8424</issn><issn>1091-6490</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1991</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkc1v1DAQxS0EKkvhzAWQDwhO2Y7txIklLmVbvlTgUDhbE8cuqbzxNnaq9r_HYZeFXuA0Hr3fm_HoEfKUwZJBLY42A8Zl0yyZXNZQyntkwUCxQpYK7pMFAK-LpuTlQ_IoxksAUFUDB-SANTVjTC3Ip_OEqTcUh47-esbcoadv7dD1wwUNjp58Oaan1-gnTLaj7S39HIZk6QpHH-h5v558toUhPiYPHPpon-zqIfn-7vTb6kNx9vX9x9XxWWEqzlPBpG1bBC5VV7rWVa5GrpQBkI472woUiA6NMKWtOlZLBgKkAdc2UIkWhDgkb7ZzN1O7tp2xQxrR683Yr3G81QF7fVcZ-h_6IlzrvF5Atr_a2cdwNdmY9LqPxnqPgw1T1DUHoRgv_wsyOR9RqQwebUEzhhhH6_Z_YaDnlPSckm6abNFzStnx_O8T_vDbWLL-cqdjzGm4EQfTxz1WKimFrDL2YofN83-rd_a8_ieg3eR9sjcpk8-25GVMYdyjXFQ5gUb8BMbQvNE</recordid><startdate>19910815</startdate><enddate>19910815</enddate><creator>Zhurkin, V. 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Psychology</topic><topic>Genetic vectors</topic><topic>Hydrogen Bonding</topic><topic>Models, Molecular</topic><topic>Molecular biophysics</topic><topic>Molecular Sequence Data</topic><topic>Monte Carlo Method</topic><topic>Nucleic Acid Conformation</topic><topic>Nucleic acids</topic><topic>Nucleotides</topic><topic>Oligodeoxyribonucleotides - chemistry</topic><topic>Static modeling</topic><topic>Structure-Activity Relationship</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhurkin, V. B.</creatorcontrib><creatorcontrib>Ulyanov, N. B.</creatorcontrib><creatorcontrib>Gorin, A. A.</creatorcontrib><creatorcontrib>Jernigan, R. 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L.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Static and Statistical Bending of DNA Evaluated by Monte Carlo Simulations</atitle><jtitle>Proceedings of the National Academy of Sciences - PNAS</jtitle><addtitle>Proc Natl Acad Sci U S A</addtitle><date>1991-08-15</date><risdate>1991</risdate><volume>88</volume><issue>16</issue><spage>7046</spage><epage>7050</epage><pages>7046-7050</pages><issn>0027-8424</issn><eissn>1091-6490</eissn><coden>PNASA6</coden><abstract>To investigate the influence of thermal fluctuations on DNA curvature the Metropolis procedure at 300 K was applied to B-DNA decamers containing A5·T5and A4·T4blocks. Monte Carlo simulations have confirmed the DNA bending anisotropy: B-DNA bends most easily in a groove direction (roll). The A5·T5block is more rigid than the other sequences; the pyrimidine-purine dimers are found to be the most flexible. For A5TCTCT, A5CTCTC, and A5GAGAG, the average bend angle per decamer is 20-25⚬in a direction toward the minor groove in the center of the A5·T5tract, which is consistent with both the "junction" and "wedge AA" models. However, in A5T5, A4T4CG, and T4A4GC, bending is directed into the grooves at the 5' and 3' ends of purine tracts. Thus, directionality of bending caused by An·Tnblocks strongly depends on their neighboring sequences. These calculations demonstrate that the sequence-dependent variation of the minor-groove width mimics the observed hydroxyl radical cleavage pattern. To estimate the effect of fluctuations on the overall shape of curved DNA fragments, longer pieces of DNA (up to 200 base pairs) were generated. 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source MEDLINE; Jstor Complete Legacy; PubMed Central; Alma/SFX Local Collection; Free Full-Text Journals in Chemistry
subjects Arithmetic mean
Base Sequence
Bending
Biological and medical sciences
Boundary conditions
Conformational dynamics in molecular biology
Curvature
Dimers
DNA
DNA - chemistry
Fundamental and applied biological sciences. Psychology
Genetic vectors
Hydrogen Bonding
Models, Molecular
Molecular biophysics
Molecular Sequence Data
Monte Carlo Method
Nucleic Acid Conformation
Nucleic acids
Nucleotides
Oligodeoxyribonucleotides - chemistry
Static modeling
Structure-Activity Relationship
title Static and Statistical Bending of DNA Evaluated by Monte Carlo Simulations
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