RPA subunit arrangement near the 3′-end of the primer is modulated by the length of the template strand and cooperative protein interactions
To analyze the interaction of human replication protein A (RPA) and its subunits with the DNA template-primer junction in the DNA replication fork, we designed several template-primer systems differing in the size of the single-stranded template tail (4, 9, 13, 14,19 and 31 nt). Base substituted pho...
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| Veröffentlicht in: | Nucleic acids research 1999-11, Vol.27 (21), p.4235-4240 |
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| creator | Lavrik, Olga I. Kolpashchikov, Dmitry M. Weisshart, Klaus Nasheuer, Heinz-Peter Khodyreva, Svetlana N. Favre, Alain |
| description | To analyze the interaction of human replication protein A (RPA) and its subunits with the DNA template-primer junction in the DNA replication fork, we designed several template-primer systems differing in the size of the single-stranded template tail (4, 9, 13, 14,19 and 31 nt). Base substituted photoreactive dNTP analogs—5-[N-(2-nitro-5-azidobenzoyl)-frans-3-amino-propenyl-1]-2′-deoxyuridine-5′-triphosphate (NAB-4-dUTP) and 5-[N-[N-(2-nitro-5-azidobenzoyl)glycyl]-trans-3-aminopropenyl-1]-2′-deoxyuridine-5′-triphos-phate (NAB-7-dUTP)—were used as substrates for elongation of radiolabeled primer-template by DNA polymerases in the presence or absence of RPA. Subsequent UV crosslinking showed that the pattern of p32 and p70 RPA subunit labeling, and consequently their interaction with the template-primer junction, is strongly dependent on the template extension length at a particular RPA concentration, as well as on the ratio of RPA to template concentration. Our results suggest a model of changes in the RPA configuration modulating by the length of the template extension in the course of nascent DNA synthesis. |
| doi_str_mv | 10.1093/nar/27.21.4235 |
| format | Article |
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Base substituted photoreactive dNTP analogs—5-[N-(2-nitro-5-azidobenzoyl)-frans-3-amino-propenyl-1]-2′-deoxyuridine-5′-triphosphate (NAB-4-dUTP) and 5-[N-[N-(2-nitro-5-azidobenzoyl)glycyl]-trans-3-aminopropenyl-1]-2′-deoxyuridine-5′-triphos-phate (NAB-7-dUTP)—were used as substrates for elongation of radiolabeled primer-template by DNA polymerases in the presence or absence of RPA. Subsequent UV crosslinking showed that the pattern of p32 and p70 RPA subunit labeling, and consequently their interaction with the template-primer junction, is strongly dependent on the template extension length at a particular RPA concentration, as well as on the ratio of RPA to template concentration. Our results suggest a model of changes in the RPA configuration modulating by the length of the template extension in the course of nascent DNA synthesis.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/27.21.4235</identifier><identifier>PMID: 10518616</identifier><identifier>CODEN: NARHAD</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Azides - chemistry ; Azides - metabolism ; Cross-Linking Reagents - chemistry ; Cross-Linking Reagents - metabolism ; DNA - biosynthesis ; DNA Helicases - chemistry ; DNA Helicases - metabolism ; DNA Polymerase beta - metabolism ; DNA Polymerase I - metabolism ; DNA Primers - genetics ; DNA Primers - metabolism ; DNA Replication - genetics ; DNA, Single-Stranded - chemistry ; DNA, Single-Stranded - genetics ; DNA, Single-Stranded - metabolism ; DNA-Binding Proteins - chemistry ; DNA-Binding Proteins - metabolism ; Escherichia coli - enzymology ; Humans ; Models, Biological ; Molecular Weight ; p32 protein ; p70 protein ; Protein Binding ; Protein Conformation ; Replication Protein A ; Templates, Genetic ; Ultraviolet Rays ; Uridine Triphosphate - analogs & derivatives ; Uridine Triphosphate - chemistry ; Uridine Triphosphate - metabolism</subject><ispartof>Nucleic acids research, 1999-11, Vol.27 (21), p.4235-4240</ispartof><rights>Copyright Oxford University Press(England) Nov 1, 1999</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c547t-6b99fa3bfce55a7ef2cdb40bb0f113305b43c571e205408135b62b3c24d5079b3</citedby><cites>FETCH-LOGICAL-c547t-6b99fa3bfce55a7ef2cdb40bb0f113305b43c571e205408135b62b3c24d5079b3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC148699/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC148699/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/10518616$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lavrik, Olga I.</creatorcontrib><creatorcontrib>Kolpashchikov, Dmitry M.</creatorcontrib><creatorcontrib>Weisshart, Klaus</creatorcontrib><creatorcontrib>Nasheuer, Heinz-Peter</creatorcontrib><creatorcontrib>Khodyreva, Svetlana N.</creatorcontrib><creatorcontrib>Favre, Alain</creatorcontrib><title>RPA subunit arrangement near the 3′-end of the primer is modulated by the length of the template strand and cooperative protein interactions</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Research</addtitle><description>To analyze the interaction of human replication protein A (RPA) and its subunits with the DNA template-primer junction in the DNA replication fork, we designed several template-primer systems differing in the size of the single-stranded template tail (4, 9, 13, 14,19 and 31 nt). Base substituted photoreactive dNTP analogs—5-[N-(2-nitro-5-azidobenzoyl)-frans-3-amino-propenyl-1]-2′-deoxyuridine-5′-triphosphate (NAB-4-dUTP) and 5-[N-[N-(2-nitro-5-azidobenzoyl)glycyl]-trans-3-aminopropenyl-1]-2′-deoxyuridine-5′-triphos-phate (NAB-7-dUTP)—were used as substrates for elongation of radiolabeled primer-template by DNA polymerases in the presence or absence of RPA. Subsequent UV crosslinking showed that the pattern of p32 and p70 RPA subunit labeling, and consequently their interaction with the template-primer junction, is strongly dependent on the template extension length at a particular RPA concentration, as well as on the ratio of RPA to template concentration. Our results suggest a model of changes in the RPA configuration modulating by the length of the template extension in the course of nascent DNA synthesis.</description><subject>Azides - chemistry</subject><subject>Azides - metabolism</subject><subject>Cross-Linking Reagents - chemistry</subject><subject>Cross-Linking Reagents - metabolism</subject><subject>DNA - biosynthesis</subject><subject>DNA Helicases - chemistry</subject><subject>DNA Helicases - metabolism</subject><subject>DNA Polymerase beta - metabolism</subject><subject>DNA Polymerase I - metabolism</subject><subject>DNA Primers - genetics</subject><subject>DNA Primers - metabolism</subject><subject>DNA Replication - genetics</subject><subject>DNA, Single-Stranded - chemistry</subject><subject>DNA, Single-Stranded - genetics</subject><subject>DNA, Single-Stranded - metabolism</subject><subject>DNA-Binding Proteins - chemistry</subject><subject>DNA-Binding Proteins - metabolism</subject><subject>Escherichia coli - enzymology</subject><subject>Humans</subject><subject>Models, Biological</subject><subject>Molecular Weight</subject><subject>p32 protein</subject><subject>p70 protein</subject><subject>Protein Binding</subject><subject>Protein Conformation</subject><subject>Replication Protein A</subject><subject>Templates, Genetic</subject><subject>Ultraviolet Rays</subject><subject>Uridine Triphosphate - analogs & derivatives</subject><subject>Uridine Triphosphate - chemistry</subject><subject>Uridine Triphosphate - metabolism</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1999</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFks1u1DAUhSMEokNhyxJZLNhl6t84WbCoKmCQBoEqfio2lp3czLgk9mA7Fd3xBDwMj8ST4HRKVdiwsCz7fPfIxzpF8ZjgJcENO3I6HFG5pGTJKRN3igVhFS15U9G7xQIzLEqCeX1QPIjxHGPCieD3iwOCBakrUi2KH6fvjlGczORsQjoE7TYwgkvIgQ4obQGxX99_luA65Pur8y7YEQKyEY2-mwadoEPm8koawG3S9g-YYNzNMoop23ZoXq33Owg62YvZyCewDlmX8lWbrHfxYXGv10OER9f7YfHh5Yv3J6ty_fbV65PjddkKLlNZmabpNTN9C0JoCT1tO8OxMbgnhOXUhrNWSAIUC45rwoSpqGEt5Z3AsjHssHi-991NZoSuzYmDHtScTYdL5bVVfyvObtXGXyjC66pp8vyz6_ngv04QkxptbGEYtAM_RSVxzWsm5H9BIjmuGkoy-PQf8NxPweVPUBRjkWPXLEPLPdQGH2OA_ubFBKu5Dyr3QVGpKFFzH_LAk9s5b-H7AmSg3AM2Jvh2o-vwRVWSSaFWZ5_VWfNx_WZVf1Kn7Dc-OMQ6</recordid><startdate>199911</startdate><enddate>199911</enddate><creator>Lavrik, Olga I.</creator><creator>Kolpashchikov, Dmitry M.</creator><creator>Weisshart, Klaus</creator><creator>Nasheuer, Heinz-Peter</creator><creator>Khodyreva, Svetlana N.</creator><creator>Favre, Alain</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>199911</creationdate><title>RPA subunit arrangement near the 3′-end of the primer is modulated by the length of the template strand and cooperative protein interactions</title><author>Lavrik, Olga I. ; 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Base substituted photoreactive dNTP analogs—5-[N-(2-nitro-5-azidobenzoyl)-frans-3-amino-propenyl-1]-2′-deoxyuridine-5′-triphosphate (NAB-4-dUTP) and 5-[N-[N-(2-nitro-5-azidobenzoyl)glycyl]-trans-3-aminopropenyl-1]-2′-deoxyuridine-5′-triphos-phate (NAB-7-dUTP)—were used as substrates for elongation of radiolabeled primer-template by DNA polymerases in the presence or absence of RPA. Subsequent UV crosslinking showed that the pattern of p32 and p70 RPA subunit labeling, and consequently their interaction with the template-primer junction, is strongly dependent on the template extension length at a particular RPA concentration, as well as on the ratio of RPA to template concentration. Our results suggest a model of changes in the RPA configuration modulating by the length of the template extension in the course of nascent DNA synthesis.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>10518616</pmid><doi>10.1093/nar/27.21.4235</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Azides - chemistry Azides - metabolism Cross-Linking Reagents - chemistry Cross-Linking Reagents - metabolism DNA - biosynthesis DNA Helicases - chemistry DNA Helicases - metabolism DNA Polymerase beta - metabolism DNA Polymerase I - metabolism DNA Primers - genetics DNA Primers - metabolism DNA Replication - genetics DNA, Single-Stranded - chemistry DNA, Single-Stranded - genetics DNA, Single-Stranded - metabolism DNA-Binding Proteins - chemistry DNA-Binding Proteins - metabolism Escherichia coli - enzymology Humans Models, Biological Molecular Weight p32 protein p70 protein Protein Binding Protein Conformation Replication Protein A Templates, Genetic Ultraviolet Rays Uridine Triphosphate - analogs & derivatives Uridine Triphosphate - chemistry Uridine Triphosphate - metabolism |
| title | RPA subunit arrangement near the 3′-end of the primer is modulated by the length of the template strand and cooperative protein interactions |
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