tailieunhanh - Báo cáo khoa học: Solution structure of 2¢,5¢ d(G4C4) Relevance to topological restrictions and nature’s choice of phosphodiester links

The NMR structure of 2¢,5¢ d(GGGGCCCC) was deter-mined togain insights into the structural differences between 2¢,5¢-and 3¢,5¢-linked DNA duplexes that may be relevant in elucidating nature’s choice of sugar-phosphate links to encode genetic information. The oligomer assumes a duplex with extended nucleotide repeats formed out of mostly N-type sugar puckers. With the exception of the 5¢-terminal guanine that assumes thesyn glycosyl conformation, all other bases prefer theantiglycosyl conformation. Base pairs in the duplex exhibit slide () A ˚ ) and intermediate values for X-displacement () A ˚ ), as in ADNA, while their inclination to the helical axis is not prominent. . | Eur. J. Biochem. 271 2956-2966 2004 FEBS 2004 doi Solution structure of 2 5 d G4C4 Relevance to topological restrictions and nature s choice of phosphodiester links Bernard J. Premraj1 Swaminathan Raja1 Neel S. Bhavesh2 Ke Shi3 Ramakrishna V. Hosur2 Muttaiya Sundaralingam3 and Narayanarao Yathindra1 1 Department of Crystallography and Biophysics University of Madras Guindy Campus Chennai India 2Department of Chemical Sciences TIFR Colaba Mumbai India 3Department of Chemistry The Ohio State University Columbus OH USA The NMR structure of 2 5 d GGGGCCCC was determined to gain insights into the structural differences between 2 5 - and 3 5 -linked DNA duplexes that may be relevant in elucidating nature s choice of sugar-phosphate links to encode genetic information. The oligomer assumes a duplex with extended nucleotide repeats formed out of mostly N-type sugar puckers. With the exception of the 5 -terminal guanine that assumes the syn glycosyl conformation all other bases prefer the anti glycosyl conformation. Base pairs in the duplex exhibit slide A and intermediate values for X-displacement A as in ADNA while their inclination to the helical axis is not prominent. Major and minor grooves display features intermediate to A and BDNA. The duplex structure of iso d GGGGCCCC may therefore be best characterized as a hybrid of A and BDNA. Importantly the results confirm that even 3 deoxy 2 5 DNA supports duplex formation only in the presence of distinct slide A and X-displacement A for base pairs and hence does not favor an ideal BDNA topology characterized by their near-zero values. Such restrictions on base pair movements in 2 5 DNA which are clearly absent in 3 5 DNA are expected to impose constraints on its ability for deformability of the kind observed in DNA during its compaction and interaction with proteins. It is therefore conceivable that selection pressure relating to the optimization of topological features