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Journal of Biomolecular NMR

, Volume 70, Issue 4, pp 229–244 | Cite as

Atomic structures of excited state A–T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations

  • Honglue Shi
  • Mary C. Clay
  • Atul Rangadurai
  • Bharathwaj Sathyamoorthy
  • David A. Case
  • Hashim M. Al-HashimiEmail author
Article

Abstract

NMR relaxation dispersion studies indicate that in canonical duplex DNA, Watson–Crick base pairs (bps) exist in dynamic equilibrium with short-lived low abundance excited state Hoogsteen bps. N1-methylated adenine (m1A) and guanine (m1G) are naturally occurring forms of damage that stabilize Hoogsteen bps in duplex DNA. NMR dynamic ensembles of DNA duplexes with m1A–T Hoogsteen bps reveal significant changes in sugar pucker and backbone angles in and around the Hoogsteen bp, as well as kinking of the duplex towards the major groove. Whether these structural changes also occur upon forming excited state Hoogsteen bps in unmodified duplexes remains to be established because prior relaxation dispersion probes provided limited information regarding the sugar-backbone conformation. Here, we demonstrate measurements of C3′ and C4′ spin relaxation in the rotating frame (R1ρ) in uniformly 13C/15N labeled DNA as sensitive probes of the sugar-backbone conformation in DNA excited states. The chemical shifts, combined with structure-based predictions using an automated fragmentation quantum mechanics/molecular mechanics method, show that the dynamic ensemble of DNA duplexes containing m1A–T Hoogsteen bps accurately model the excited state Hoogsteen conformation in two different sequence contexts. Formation of excited state A–T Hoogsteen bps is accompanied by changes in sugar-backbone conformation that allow the flipped syn adenine to form hydrogen-bonds with its partner thymine and this in turn results in overall kinking of the DNA toward the major groove. Results support the assignment of Hoogsteen bps as the excited state observed in canonical duplex DNA, provide an atomic view of DNA dynamics linked to formation of Hoogsteen bps, and lay the groundwork for a potentially general strategy for solving structures of nucleic acid excited states.

Keywords

DNA dynamics Rotating frame spin relaxation Nucleic acids Sugar pucker Major groove kinking DNA bending 

Notes

Acknowledgements

We thank all Al-Hashimi lab members for critical comments on the manuscript. We acknowledge the technical support and resources from the Duke Magnetic Resonance Spectroscopy Center. This work was supported by US National Institute for General Medical Sciences (5P50GM103297 to H.M.A. and D.A.C and R01GM089846 to H.M.A.). The authors declare no conflict of interest.

Supplementary material

10858_2018_177_MOESM1_ESM.docx (7.6 mb)
Supplementary material 1 (DOCX 7741 KB)

References

  1. Aeschbacher T, Schubert M, Allain FH (2012) A procedure to validate and correct the 13C chemical shift calibration of RNA datasets. J Biomol NMR 52:179–190CrossRefGoogle Scholar
  2. Alvey HS, Gottardo FL, Nikolova EN, Al-Hashimi HM (2014) Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics. Nat Commun 5:4786ADSCrossRefGoogle Scholar
  3. Barette J, Velyvis A, Religa TL, Korzhnev DM, Kay LE (2012) Cross-validation of the structure of a transiently formed and low populated FF domain folding intermediate determined by relaxation dispersion NMR and CS-Rosetta. J Phys Chem B 116:6637–6644CrossRefGoogle Scholar
  4. Bhabha G et al (2011) A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Science 332:234–238ADSCrossRefGoogle Scholar
  5. Bouvignies G, Kay LE (2012) A 2D C-13-CEST experiment for studying slowly exchanging protein systems using methyl probes: an application to protein folding. J Biomol NMR 53:303–310CrossRefGoogle Scholar
  6. Bouvignies G et al (2011) Solution structure of a minor and transiently formed state of a T4 lysozyme mutant. Nature 477:111–114ADSCrossRefGoogle Scholar
  7. Brown JD, Summers MF, Johnson BA (2015) Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression. J Biomol NMR 63:39–52CrossRefGoogle Scholar
  8. Case DA (2013) Chemical shifts in biomolecules. Curr Opin Struct Biol 23:172–176CrossRefGoogle Scholar
  9. Cavanagh J, Fairbrother WJ, Palmer AG III, Rance M, Skelton NJ (2007) Protein NMR spectroscopy, 2nd edn. Elsevier, New YorkGoogle Scholar
  10. Chen B, LeBlanc R, Dayie TK (2016) SAM-II riboswitch samples at least two conformations in solution in the absence of ligand: implications for recognition. Angew Chem Int Ed Engl 55:2724–2727CrossRefGoogle Scholar
  11. Clay MC, Ganser LR, Merriman DK, Al-Hashimi HM (2017) Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics. Nucleic Acids Res.  https://doi.org/10.1093/nar/gkx525 Google Scholar
  12. Clore GM, Tang C, Iwahara J (2007) Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement. Curr Opin Struct Biol 17:603–616CrossRefGoogle Scholar
  13. Dallmann A et al (2011) Structure and dynamics of triazole-linked DNA: biocompatibility explained. Chemistry 17:14714–14717CrossRefGoogle Scholar
  14. Dejaegere AP, Case DA (1998) Density functional study of ribose and deoxyribose chemical shifts. J Phys Chem A 102:5280–5289CrossRefGoogle Scholar
  15. Delaglio F et al (1995) Nmrpipe—a multidimensional spectral processing system based on unix pipes. J Biomol NMR 6:277–293CrossRefGoogle Scholar
  16. Dethoff EA, Petzold K, Chugh J, Casiano-Negroni A, Al-Hashimi HM (2012) Visualizing transient low-populated structures of RNA. Nature 491:724–728ADSCrossRefGoogle Scholar
  17. Fonville JM et al (2012) Chemical shifts in nucleic acids studied by density functional theory calculations and comparison with experiment. Chemistry-a European Journal 18:12372–12387CrossRefGoogle Scholar
  18. Handy NC, Cohen AJ (2001) Left-right correlation energy. Mol Phys 99:403–412ADSCrossRefGoogle Scholar
  19. Hansen DF, Vallurupalli P, Kay LE (2008) Quantifying two-bond 1HN-13CO and one-bond 1H(alpha)-13C(alpha) dipolar couplings of invisible protein states by spin-state selective relaxation dispersion NMR spectroscopy. J Am Chem Soc 130:8397–8405CrossRefGoogle Scholar
  20. Hansen AL, Nikolova EN, Casiano-Negroni A, Al-Hashimi HM (2009) Extending the range of microsecond-to-millisecond chemical exchange detected in labeled and unlabeled nucleic acids by selective carbon R(1rho) NMR spectroscopy. J Am Chem Soc 131:3818–3819CrossRefGoogle Scholar
  21. Hoogsteen K (1963) Crystal and molecular structure of a hydrogen-bonded complex between 1-methylthymine and 9-methyladenine. Acta Crystallogr A 16:907-+CrossRefGoogle Scholar
  22. Igumenova TI, Brath U, Akke M, Palmer AG (2007) Characterization of chemical exchange using residual dipolar coupling. J Am Chem Soc 129:13396-+CrossRefGoogle Scholar
  23. Kay LE (2016) New views of functionally dynamic proteins by solution NMR spectroscopy. J Mol Biol 428:323–331CrossRefGoogle Scholar
  24. Kimsey IJ, Petzold K, Sathyamoorthy B, Stein ZW, Al-Hashimi HM (2015) Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes. Nature 519:315–320ADSCrossRefGoogle Scholar
  25. Kitayner M et al (2010) Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs. Nat Struct Mol Biol 17:423–429CrossRefGoogle Scholar
  26. Kladwang W, VanLang CC, Cordero P, Das R (2011) A two-dimensional mutate-and-map strategy for non-coding RNA structure. Nat Chem 3:954–962CrossRefGoogle Scholar
  27. Korzhnev DM, Orekhov VY, Kay LE (2005) Off-resonance R1(p) NMR studies of exchange dynamics in proteins with low spin-lock fields: an application to a fyn SH3 domain. J Am Chem Soc 127:713–721CrossRefGoogle Scholar
  28. Korzhnev DM, Religa TL, Banachewicz W, Fersht AR, Kay LE (2010) A transient and low-populated protein-folding intermediate at atomic resolution. Science 329:1312–1316ADSCrossRefGoogle Scholar
  29. Korzhnev DM et al (2011) Nonnative interactions in the FF domain folding pathway from an atomic resolution structure of a sparsely populated intermediate: an NMR relaxation dispersion study. J Am Chem Soc 133:10974–10982CrossRefGoogle Scholar
  30. Koster AM, Geudtner G, Calaminici P, Casida ME, Dominguez VD, Flores-Moreno R, Gamboa GU, Goursot A, Heine T, Ipatov A, Janetzko F, del Campo JM, Reveles JU, Vela A, Zuniga-Gutierrez B, Salahub DR (2011) deMon2k, version 3. The deMon developers, Cinvestav, Mexico CityGoogle Scholar
  31. Lee J, Dethoff EA, Al-Hashimi HM (2014) Invisible RNA state dynamically couples distant motifs. Proc Natl Acad Sci USA 111:9485–9490ADSCrossRefGoogle Scholar
  32. Long D, Bouvignies G, Kay LE (2014) Measuring hydrogen exchange rates in invisible protein excited states. Proc Natl Acad Sci USA 111:8820–8825ADSCrossRefGoogle Scholar
  33. Lorieau JL, Louis JM, Bax A (2010) The complete influenza hemagglutinin fusion domain adopts a tight helical hairpin arrangement at the lipid:water interface. Proc Natl Acad Sci USA 107:11341–11346ADSCrossRefGoogle Scholar
  34. Lu XJ, Olson WK (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 31:5108–5121CrossRefGoogle Scholar
  35. Lu XJ, Olson WK (2008) 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nat Protoc 3:1213–1227CrossRefGoogle Scholar
  36. Lu L, Yi C, Jian X, Zheng G, He C (2010) Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system. Nucleic Acids Res 38:4415–4425CrossRefGoogle Scholar
  37. Macon JB, Wolfenden R (1968) 1-Methyladenosine. Dimroth rearrangement and reversible reduction. Biochemistry 7:3453–3458CrossRefGoogle Scholar
  38. Merriman DK et al (2016) Shortening the HIV-1 TAR RNA bulge by a single nucleotide preserves motional modes over a broad range of timescales. Biochemistry.  https://doi.org/10.1021/acs.biochem.6b00285 Google Scholar
  39. Mulder FA, Mittermaier A, Hon B, Dahlquist FW, Kay LE (2001) Studying excited states of proteins by NMR spectroscopy. Nat Struct Biol 8:932–935CrossRefGoogle Scholar
  40. Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2005) Human DNA polymerase iota incorporates dCTP opposite template G via a G.C + Hoogsteen base pair. Structure 13:1569–1577CrossRefGoogle Scholar
  41. Nikolova EN et al (2011) Transient Hoogsteen base pairs in canonical duplex DNA. Nature 470:498–502ADSCrossRefGoogle Scholar
  42. Nikolova EN, Gottardo FL, Al-Hashimi HM (2012) Probing transient Hoogsteen hydrogen bonds in canonical duplex DNA using NMR relaxation dispersion and single-atom substitution. J Am Chem Soc 134:3667–3670CrossRefGoogle Scholar
  43. Nikolova EN, Goh GB, Brooks CL 3rd, Al-Hashimi HM (2013a) Characterizing the protonation state of cytosine in transient G.C Hoogsteen base pairs in duplex DNA. J Am Chem Soc 135, 6766–6769CrossRefGoogle Scholar
  44. Nikolova EN et al (2013b) A historical account of Hoogsteen base-pairs in duplex DNA. Biopolymers 99:955–968Google Scholar
  45. Nikolova EN, Stull F, Al-Hashimi HM (2014) Guanine to inosine substitution leads to large increases in the population of a transient G.C Hoogsteen base pair. Biochemistry 53:7145–7147CrossRefGoogle Scholar
  46. Palmer AG 3rd (2004) NMR characterization of the dynamics of biomacromolecules. Chem Rev 104:3623–3640CrossRefGoogle Scholar
  47. Palmer AG 3rd, Massi F (2006) Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem Rev 106:1700–1719CrossRefGoogle Scholar
  48. Richardson WH, Peng C, Bashford D, Noodleman L, Case DA (1997) Incorporating solvation effects into density functional theory: calculation of absolute acidities. Int J Quantum Chem 61:207–217CrossRefGoogle Scholar
  49. Rossi P, Harbison GS (2001) Calculation of 13C chemical shifts in RNA nucleosides: structure-13C chemical shift relationships. J Magn Reson 151:1–8ADSCrossRefGoogle Scholar
  50. Santos RA, Tang P, Harbison GS (1989) Determination of the DNA sugar pucker using C-13 NMR-spectroscopy. Biochemistry 28:9372–9378CrossRefGoogle Scholar
  51. Sathyamoorthy B et al (2017) Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A. Nucleic Acids Res.  https://doi.org/10.1093/nar/gkx186 Google Scholar
  52. Sekhar A, Kay LE (2013) NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers. Proc Natl Acad Sci USA 110:12867–12874ADSCrossRefGoogle Scholar
  53. Sekhar A, Rosenzweig R, Bouvignies G, Kay LE (2016) Hsp70 biases the folding pathways of client proteins. Proc Natl Acad Sci USA 113:E2794–E2801ADSCrossRefGoogle Scholar
  54. Swails J, Zhu T, He X, Case DA (2015) AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. J Biomol NMR 63:125–139CrossRefGoogle Scholar
  55. Topal MD, Fresco JR (1976) Complementary base pairing and the origin of substitution mutations. Nature 263:285–289ADSCrossRefGoogle Scholar
  56. Trewick SC, Henshaw TF, Hausinger RP, Lindahl T, Sedgwick B (2002) Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage. Nature 419:174–178ADSCrossRefGoogle Scholar
  57. Ulrich EL et al (2008) BioMagResBank. Nucleic Acids Res 36:D402–D408CrossRefGoogle Scholar
  58. Vallurupalli P, Hansen DF, Stollar E, Meirovitch E, Kay LE (2007) Measurement of bond vector orientations in invisible excited states of proteins. Proc Natl Acad Sci USA 104:18473–18477ADSCrossRefGoogle Scholar
  59. Vallurupalli P, Hansen DF, Kay LE (2008a) Probing structure in invisible protein states with anisotropic NMR chemical shifts. J Am Chem Soc 130:2734-+CrossRefGoogle Scholar
  60. Vallurupalli P, Hansen DF, Kay LE (2008b) Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy. Proc Natl Acad Sci USA 105:11766–11771ADSCrossRefGoogle Scholar
  61. Vallurupalli P, Bouvignies G, Kay LE (2012) Studying “invisible” excited protein states in slow exchange with a major state conformation. J Am Chem Soc 134:8148–8161CrossRefGoogle Scholar
  62. van Wijk J, Huckriede BD, Ippel JH, Altona C (1992) Furanose sugar conformations in DNA from NMR coupling constants. Methods Enzymol 211:286–306CrossRefGoogle Scholar
  63. Whittier SK, Hengge AC, Loria JP (2013) Conformational motions regulate phosphoryl transfer in related protein tyrosine phosphatases. Science 341:899–903ADSCrossRefGoogle Scholar
  64. Xu XP, Au-Yeung SCF (2000) Investigation of chemical shift and structure relationships in nucleic acids using NMR and density functional theory methods. J Phys Chem B 104:5641–5650CrossRefGoogle Scholar
  65. Xu XP, Chiu WLAK, Au-Yeung SCF (1998) Chemical shift and structure relationship in nucleic acids: correlation of backbone torsion angles gamma and alpha with C-13 chemical shifts. J Am Chem Soc 120, 4230–4231CrossRefGoogle Scholar
  66. Xue Y et al (2015) Characterizing RNA excited states using NMR relaxation dispersion. Methods Enzymol 558:39–73CrossRefGoogle Scholar
  67. Xue Y, Gracia B, Herschlag D, Russell R, Al-Hashimi HM Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch. Nat Commun 7(2016)Google Scholar
  68. Yang H, Lam SL (2009) Effect of 1-methyladenine on thermodynamic stabilities of double-helical DNA structures. FEBS Lett 583:1548–1553CrossRefGoogle Scholar
  69. Yang CG et al (2008a) Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature 452:961–965ADSCrossRefGoogle Scholar
  70. Yang H, Zhan Y, Fenn D, Chi LM, Lam SL (2008b) Effect of 1-methyladenine on double-helical DNA structures. FEBS Lett 582:1629–1633CrossRefGoogle Scholar
  71. Yang CG, Garcia K, He C (2009) Damage detection and base flipping in direct DNA alkylation repair. Chembiochem 10:417–423CrossRefGoogle Scholar
  72. Zhao B, Zhang Q (2015) Measuring residual dipolar couplings in excited conformational states of nucleic acids by CEST NMR spectroscopy. J Am Chem Soc 137:13480–13483CrossRefGoogle Scholar
  73. Zhao B, Hansen AL, Zhang Q (2014) Characterizing slow chemical exchange in nucleic acids by carbon CEST and low spin-lock field R(1rho) NMR spectroscopy. J Am Chem Soc 136:20–23CrossRefGoogle Scholar
  74. Zhao B, Guffy SL, Williams B, Zhang Q (2017) An excited state underlies gene regulation of a transcriptional riboswitch. Nat Chem Biol 13:968–974CrossRefGoogle Scholar
  75. Zhou H et al (2015) New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey. Nucleic Acids Res 43:3420–3433CrossRefGoogle Scholar
  76. Zhou H et al (2016) m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs. Nat Struct Mol Biol 23:803–810CrossRefGoogle Scholar
  77. Zimmer DP, Crothers DM (1995) NMR of enzymatically synthesized uniformly 13C15N-labeled DNA oligonucleotides. Proc Natl Acad Sci USA 92:3091–3095ADSCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  • Honglue Shi
    • 1
  • Mary C. Clay
    • 2
  • Atul Rangadurai
    • 2
  • Bharathwaj Sathyamoorthy
    • 1
    • 2
    • 4
  • David A. Case
    • 3
  • Hashim M. Al-Hashimi
    • 1
    • 2
    Email author
  1. 1.Department of ChemistryDuke UniversityDurhamUSA
  2. 2.Department of BiochemistryDuke University School of MedicineDurhamUSA
  3. 3.Department of Chemistry and Chemical BiologyRutgers UniversityPiscatawayUSA
  4. 4.Department of ChemistryIndian Institute of Science Education and Research BhopalBhopalIndia

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