Intramolecular folding in human ILPR fragment with three C-rich repeats.
Enrichment of four tandem repeats of guanine (G) rich and cytosine (C) rich sequences in functionally important regions of human genome forebodes the biological implications of four-stranded DNA structures, such as G-quadruplex and i-motif, that can form in these sequences. However, there have been...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3382603?pdf=render |
| _version_ | 1818021129246212096 |
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| author | Soma Dhakal Javonne L Lafontaine Zhongbo Yu Deepak Koirala Hanbin Mao |
| author_facet | Soma Dhakal Javonne L Lafontaine Zhongbo Yu Deepak Koirala Hanbin Mao |
| author_sort | Soma Dhakal |
| collection | DOAJ |
| description | Enrichment of four tandem repeats of guanine (G) rich and cytosine (C) rich sequences in functionally important regions of human genome forebodes the biological implications of four-stranded DNA structures, such as G-quadruplex and i-motif, that can form in these sequences. However, there have been few reports on the intramolecular formation of non-B DNA structures in less than four tandem repeats of G or C rich sequences. Here, using mechanical unfolding at the single-molecule level, electrophoretic mobility shift assay (EMSA), circular dichroism (CD), and ultraviolet (UV) spectroscopy, we report an intramolecularly folded non-B DNA structure in three tandem cytosine rich repeats, 5'-TGTC4ACAC4TGTC4ACA (ILPR-I3), in the human insulin linked polymorphic region (ILPR). The thermal denaturation analyses of the sequences with systematic C to T mutations have suggested that the structure is linchpinned by a stack of hemiprotonated cytosine pairs between two terminal C4 tracts. Mechanical unfolding and Br(2) footprinting experiments on a mixture of the ILPR-I3 and a 5'-C4TGT fragment have further indicated that the structure serves as a building block for intermolecular i-motif formation. The existence of such a conformation under acidic or neutral pH complies with the strand-by-strand folding pathway of ILPR i-motif structures. |
| first_indexed | 2024-04-14T08:14:33Z |
| format | Article |
| id | doaj.art-b14ed94a916641639ac9784683a56f14 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-14T08:14:33Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-b14ed94a916641639ac9784683a56f142022-12-22T02:04:26ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0176e3927110.1371/journal.pone.0039271Intramolecular folding in human ILPR fragment with three C-rich repeats.Soma DhakalJavonne L LafontaineZhongbo YuDeepak KoiralaHanbin MaoEnrichment of four tandem repeats of guanine (G) rich and cytosine (C) rich sequences in functionally important regions of human genome forebodes the biological implications of four-stranded DNA structures, such as G-quadruplex and i-motif, that can form in these sequences. However, there have been few reports on the intramolecular formation of non-B DNA structures in less than four tandem repeats of G or C rich sequences. Here, using mechanical unfolding at the single-molecule level, electrophoretic mobility shift assay (EMSA), circular dichroism (CD), and ultraviolet (UV) spectroscopy, we report an intramolecularly folded non-B DNA structure in three tandem cytosine rich repeats, 5'-TGTC4ACAC4TGTC4ACA (ILPR-I3), in the human insulin linked polymorphic region (ILPR). The thermal denaturation analyses of the sequences with systematic C to T mutations have suggested that the structure is linchpinned by a stack of hemiprotonated cytosine pairs between two terminal C4 tracts. Mechanical unfolding and Br(2) footprinting experiments on a mixture of the ILPR-I3 and a 5'-C4TGT fragment have further indicated that the structure serves as a building block for intermolecular i-motif formation. The existence of such a conformation under acidic or neutral pH complies with the strand-by-strand folding pathway of ILPR i-motif structures.http://europepmc.org/articles/PMC3382603?pdf=render |
| spellingShingle | Soma Dhakal Javonne L Lafontaine Zhongbo Yu Deepak Koirala Hanbin Mao Intramolecular folding in human ILPR fragment with three C-rich repeats. PLoS ONE |
| title | Intramolecular folding in human ILPR fragment with three C-rich repeats. |
| title_full | Intramolecular folding in human ILPR fragment with three C-rich repeats. |
| title_fullStr | Intramolecular folding in human ILPR fragment with three C-rich repeats. |
| title_full_unstemmed | Intramolecular folding in human ILPR fragment with three C-rich repeats. |
| title_short | Intramolecular folding in human ILPR fragment with three C-rich repeats. |
| title_sort | intramolecular folding in human ilpr fragment with three c rich repeats |
| url | http://europepmc.org/articles/PMC3382603?pdf=render |
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