uu.seUppsala University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Sequence-specific Solution Structures of the Four Isosequential Pairs of Single-stranded DNAs and RNAs
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Bioorganic Chemistry.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Bioorganic Chemistry.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Bioorganic Chemistry.
2008 (English)In: Nature PrecedingsArticle in journal (Other academic) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2008.
National Category
Organic Chemistry
Identifiers
URN: urn:nbn:se:uu:diva-106717OAI: oai:DiVA.org:uu-106717DiVA: diva2:225937
Available from: 2009-06-29 Created: 2009-06-29 Last updated: 2009-07-09Bibliographically approved

Open Access in DiVA

No full text

Other links

Fulltext
By organisation
Bioorganic Chemistry
Organic Chemistry

Search outside of DiVA

GoogleGoogle Scholar

urn-nbn

Altmetric score

urn-nbn
Total: 411 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf