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How sequence defines structure: a crystallographic map of DNA structure and conformation.

Hays FA, Teegarden A, Jones ZJ, Harms M, Raup D, Watson J, Cavaliere E, Ho PS
Proc Natl Acad Sci U S A 102 7157-62 (2005)
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Cited: 75 times
EuropePMC logo PMID: 15870206

Abstract

The fundamental question of how sequence defines conformation is explicitly answered if the structures of all possible sequences of a macromolecule are determined. We present here a crystallographic screen of all permutations of the inverted repeat DNA sequence d(CCnnnN6N7N8GG), where N6, N7, and N8 are any of the four naturally occurring nucleotides. At this point, 63 of the 64 possible permutations have been crystallized from a defined set of solutions. When combined with previous work, we have assembled a data set of 37 single-crystal structures from 29 of the sequences in this motif, representing three structural classes of DNA (B-DNA, A-DNA, and four-stranded Holliday junctions). This data set includes a unique set of amphimorphic sequence, those that crystallize in two different conformations and serve to bridge the three structural phases. We have thus constructed a map of DNA structures that can be walked through in single nucleotide steps. Finally, the resulting data set allows us to dissect in detail the stabilization of and conformational variations within structural classes and identify significant conformational deviations within a particular structural class that result from sequence rather than crystal or crystallization effects.

Articles - 1zf9 mentioned but not cited (7)

  1. Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. Zgarbová M, Luque FJ, Sponer J, Cheatham TE, Otyepka M, Jurečka P. J Chem Theory Comput 9 2339-2354 (2013)
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  3. How sequence defines structure: a crystallographic map of DNA structure and conformation. Hays FA, Teegarden A, Jones ZJ, Harms M, Raup D, Watson J, Cavaliere E, Ho PS. Proc Natl Acad Sci U S A 102 7157-7162 (2005)
  4. Conformational preferences of DNA in reduced dielectric environments. Yildirim A, Sharma M, Varner BM, Fang L, Feig M. J Phys Chem B 118 10874-10881 (2014)
  5. Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps. Kailasam S, Bhattacharyya D, Bansal M. BMC Res Notes 7 83 (2014)
  6. Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments. Yildirim A, Brenner N, Sutherland R, Feig M. BMC Biophys 11 8 (2018)
  7. DNA Sequence and Structure under the Prism of Group Theory and Algebraic Surfaces. Planat M, Amaral MM, Fang F, Chester D, Aschheim R, Irwin K. Int J Mol Sci 23 13290 (2022)


Reviews citing this publication (13)

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  6. Crystal structures of Λ-[Ru(phen)₂dppz]²⁺ with oligonucleotides containing TA/TA and AT/AT steps show two intercalation modes. Niyazi H, Hall JP, O'Sullivan K, Winter G, Sorensen T, Kelly JM, Cardin CJ. Nat Chem 4 621-628 (2012)
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  16. Overexpression of high mobility group (HMG) B1 and B2 proteins directly correlates with the progression of squamous cell carcinoma in skin. Sharma A, Ray R, Rajeswari MR. Cancer Invest 26 843-851 (2008)
  17. Programmable oligomers for minor groove DNA recognition. Doss RM, Marques MA, Foister S, Chenoweth DM, Dervan PB. J Am Chem Soc 128 9074-9079 (2006)
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  19. Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs. Marathe A, Karandur D, Bansal M. BMC Struct Biol 9 24 (2009)
  20. Cheminformatics methods for novel nanopore analysis of HIV DNA termini. Winters-Hilt S, Landry M, Akeson M, Tanase M, Amin I, Coombs A, Morales E, Millet J, Baribault C, Sendamangalam S. BMC Bioinformatics 7 Suppl 2 S22 (2006)
  21. Programmable oligomers targeting 5'-GGGG-3' in the minor groove of DNA and NF-kappaB binding inhibition. Chenoweth DM, Poposki JA, Marques MA, Dervan PB. Bioorg Med Chem 15 759-770 (2007)
  22. Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations. Singhal P, Jayaram B, Dixit SB, Beveridge DL. Biophys J 94 4173-4183 (2008)
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  27. Hot-spot consensus of fluoroquinolone-mediated DNA cleavage by Gram-negative and Gram-positive type II DNA topoisomerases. Richter SN, Giaretta G, Comuzzi V, Leo E, Mitchenall LA, Fisher LM, Maxwell A, Palumbo M. Nucleic Acids Res 35 6075-6085 (2007)
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  34. Carboxylate-functionalized foldamer inhibitors of HIV-1 integrase and Topoisomerase 1: artificial analogues of DNA mimic proteins. Corvaglia V, Carbajo D, Prabhakaran P, Ziach K, Mandal PK, Santos VD, Legeay C, Vogel R, Parissi V, Pourquier P, Huc I. Nucleic Acids Res 47 5511-5521 (2019)
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  45. In silico profiling and structural insights of zinc metal ion on O6-methylguanine methyl transferase and its interactions using molecular dynamics approach. Gharouni M, Mosaddeghi H, Mehrzad J, Es-Haghi A, Motavalizadehkakhky A. J Mol Model 27 40 (2021)
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