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Sequence-specific Solution Structures of the Four Isosequential Pairs of Single-stranded DNAs and RNAs

Subhrangsu Chatterjee¹, Wimal Pathmasiri¹ & Jyoti Chattopadhyaya¹

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1. Bioorganic Chemistry, Uppsala University

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Date:

Received 13 March 2008 13:35 UTC; Posted 13 March 2008

Subjects:

Biotechnology, Chemistry, Bioinformatics

Tags:

• single-stranded DNA
• single-stranded RNA
• NMR

Abstract:

The role of the sequence-context in the self-organization of four single-stranded (ss) isosequential pairs of DNAs (1 – 4) and RNAs (5 – 8), [d/r-(5’C¹A²X³G⁴Y⁵A⁶C⁷): X³ = A or C, Y⁵ = A or C; sequence variations: 2² = 4], has been elucidated by NMR-constrained Molecular Dynamics (MD) simulations (2 ns). Following sequence-specific observations have been made from the solution NMR and the NMR constrained MD simulation study: (i) Analysis of the NOESY footprints, mainly (H8/H6)_n to (H1’ and H3’)_n-1 contacts, of ssDNAs (1 – 4) and ssRNAs (5 – 8) in the aqueous medium have shown that all ssDNAs (1 – 4) and ssRNAs (5 – 8) adopt right handed stacked helical structures in the NMR time scale. (ii) Intra-residual cross-peak intensities for the H(8/6)_n- H(1’/2’/2’’/H3’)_n contacts in ssDNAs and ssRNAs are stronger at the 3’-ends in comparison with those at the 5’-ends, suggesting that the dynamics of the nucleobases at the 3’-end are more restricted, whereas those at the 5’-end are more flexible. (iii) This relative NMR found mobility is consistent with the final RMSd calculations of the final NMR-MD structures of ssDNAs and ssRNAs. They show that the 5’-end nucleobases have higher RMSd values compared to those at the 3’-end, except for the sequence d/r(5’C¹A²A³G⁴A⁵A⁶C⁷). (iv) Relative nOe intensities of inter-residual H(8/6)_n – H(1’)_n-1 and H(8/6)_n – H(3’)_n-1 contacts, as well as NMR observed fluctuations in the sugar conformations, for ssDNAs (1 – 4) and ssRNAs (5 – 8) show that no ssDNA or ssRNA adopts either a typical B-type DNA or A-type RNA form. (v) In the final NMR-MD structures all the [H8/6N_(n)—H1’N_(n-1)/ H3’N_(n-1), N = A, G, C] distances in different isosequential pairs of ssDNA (1 – 4) and ssRNA (5 – 8) change depending upon the sequence context of the single-stranded nucleic acids. Both in the deoxy and ribo series, it is the purine-rich sequences [d/r-(5’C¹A²A³G⁴A⁵A⁶C⁷) which form the most stable self-organized right-handed helical structures because of the favorable purine-purine stacking interactions. (vi) Stacking pattern at each of the dinucleotide steps show that the base-base nearest neighbor stacking interactions depend solely upon the sequence contexts of the respective ssDNAs (1 – 4) and ssRNAs (5 – 8). See pages 47 – 145 for Supplementary Information for detailed spectroscopic data.

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This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Chatterjee, Subhrangsu , Pathmasiri, Wimal , and Chattopadhyaya, Jyoti. Sequence-specific Solution Structures of the Four Isosequential Pairs of Single-stranded DNAs and RNAs. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2008.1685.1> (2008)

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