The Solution Structure of [d(CGC)r(aaa)d(TTTGCG)]2:Hybrid Junctions Flanked by DNA Duplexes
碩士 === 國立清華大學 === 生命科學系 === 87 === The solution structure of the chimeric duplex [d(CGC)r(aaa) d(TTTGCG)]2, in which the central hybrid segment is flanked by DNA duplexes at both ends, was determined using two-dimensional NMR, restrained molecular dynamics, and NOE back-calculation refine...
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| Format: | Others |
| Language: | zh-TW |
| Published: |
1999
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| Online Access: | http://ndltd.ncl.edu.tw/handle/99244360121606206401 |
| Summary: | 碩士 === 國立清華大學 === 生命科學系 === 87 === The solution structure of the chimeric duplex [d(CGC)r(aaa) d(TTTGCG)]2, in which the central hybrid segment is flanked by DNA duplexes at both ends, was determined using two-dimensional NMR, restrained molecular dynamics, and NOE back-calculation refinement. The solution structure of this chimeric duplex differs from the previously determined X-ray structure of the analogous B-DNA duplex [d(CGCAAATITGCG)]2 as well as NMR structure of the analogous A-RNA duplex [r(cgcaaauuugcg)]2. The global conformation of this chimeric duplex is closer to its A-RNA analog (rmsd = 3.07A) than to its B-DNA analog (rmsd = 4.77 A). The structural parameters of DNA residue at 5'-end of the DNA-hybrid junction are not affected by the A-type RNA at 3'-end. However, changes in structural parameters are observed for the DNA residue at 3'- end of hybrid junction. This influence is involved in only one step. The width of minor groove for [d(CGC)r(aaa)d(TTTGCG)]2 is close to the value of 7.5 A found for classical B-form DNA duplex but differs from that of the A-RNA analog (9-11A).It is further confirmed by titrating the minor groove binding drug distamycin to [d(CGC)r(aaa)d(TITGCG)]2 . A possible 2:1 binding mode was found by the titration experiments, suggesting that this chimeric duplex contains a wider minor groove but still narrow enough to hold two distamycin molecules.
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