Atomistic insight into sequence-directed DNA bending and minicircle formation propensity in the absence and presence of phased A-tracts

Abstract

Bending of double-stranded (ds) DNA plays a crucial role in many important biological processes and is relevant for nanotechnological applications. Among all the elements that have been studied in relation to dsDNA bending, A-tracts stand out as one of the most controversial. The “ApA wedge” theory was disproved when a series of linear polynucleotides containing phased 5′-A4T4-3′ or 5′-T4A4-3′ runs were shown to be bent or straight, respectively, and crystallographic evidence revealed that A-tracts are unbent. Furthermore, some of the smallest dsDNA minicircles described to date (~ 100 bp in size) lack A-tracts and are subjected to varying levels of torsional stress. Representative DNA sequences from this experimental background were modeled in atomic detail and their dynamic behavior was simulated over hundreds of nanoseconds using the AMBER force field ParmBSC1. Subsequent analysis of the resulting trajectories allowed us to (i) unambiguously establish the location of the bends in all cases; (ii) identify the structural elements that are directly responsible for the macroscopically detected curvature; and (iii) reveal the importance not only of coherently summing the effects of the bending elements when they are in synchrony with the natural repeat of the helix (i.e. separated by an integral number of helical turns) but also when alternated with a half-integral separation of opposite effects. We conclude that the major determinant of the macroscopically observed bending is the proper grouping and phasing of the positive roll imposed by pyrimidine-purine (YR) steps and the negative or null roll characteristic of RY steps and A-tracts, respectively. This conclusion is in very good agreement with the structural parameters experimentally derived for much smaller DNA molecules either alone or as found in DNA–protein complexes. We expect that this work will pave the way for future studies on drug-induced DNA bending, DNA shape readout by transcription factors, structure of circular extrachromosomal DNA, and custom design of curved DNA origami scaffolds.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

References

  1. 1.

    Travers A, Hiriart E, Churcher M, Caserta M, Di Mauro E (2010) The DNA sequence-dependence of nucleosome positioning in vivo and in vitro. J Biomol Struct Dyn 27(6):713–724. https://doi.org/10.1080/073911010010524942

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  2. 2.

    Gorin AA, Zhurkin VB, Olson WK (1995) B-DNA twisting correlates with base-pair morphology. J Mol Biol 247(1):34–48

    CAS  Article  Google Scholar 

  3. 3.

    Olson WK, Gorin AA, Lu XJ, Hock LM, Zhurkin VB (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci USA 95(19):11163–11168. https://doi.org/10.1073/pnas.95.19.11163

    CAS  Article  PubMed  Google Scholar 

  4. 4.

    Balaceanu A, Buitrago D, Walther J, Hospital A, Dans PD, Orozco M (2019) Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond. Nucleic Acids Res 47(9):4418–4430. https://doi.org/10.1093/nar/gkz255

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  5. 5.

    Pasi M, Maddocks JH, Beveridge D, Bishop TC, Case DA, Cheatham T, Dans PD, Jayaram B, Lankas F, Laughton C, Mitchell J, Osman R, Orozco M, Perez A, Petkeviciute D, Spackova N, Sponer J, Zakrzewska K, Lavery R (2014) μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Res 42(19):12272–12283. https://doi.org/10.1093/nar/gku855

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  6. 6.

    Tomky LA, Strauss-Soukup JK, Maher LJ (1998) Effects of phosphate neutralization on the shape of the AP-1 transcription factor binding site in duplex DNA. Nucleic Acids Res 26(10):2298–2305. https://doi.org/10.1093/nar/26.10.2298

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  7. 7.

    Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS (2010) Origins of specificity in protein-DNA recognition. Annu Rev Biochem 79:233–269. https://doi.org/10.1146/annurev-biochem-060408-091030

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Abe N, Dror I, Yang L, Slattery M, Zhou T, Bussemaker HJ, Rohs R, Mann RS (2015) Deconvolving the recognition of DNA shape from sequence. Cell 161(2):307–318. https://doi.org/10.1016/j.cell.2015.02.008

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  9. 9.

    Rube HT, Rastogi C, Kribelbauer JF, Bussemaker HJ (2018) A unified approach for quantifying and interpreting DNA shape readout by transcription factors. Mol Syst Biol 14(2):e7902. https://doi.org/10.15252/msb.20177902

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  10. 10.

    Bates AD, Noy A, Piperakis MM, Harris SA, Maxwell A (2013) Small DNA circles as probes of DNA topology. Biochem Soc Trans 41(2):565–570. https://doi.org/10.1042/BST20120320

    CAS  Article  PubMed  Google Scholar 

  11. 11.

    Vafabakhsh R, Ha T (2012) Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization. Science 337(6098):1097–1101. https://doi.org/10.1126/science.1224139

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  12. 12.

    Vologodskii A, Frank-Kamenetskii DM (2013) Strong bending of the DNA double helix. Nucleic Acids Res 41(14):6785–6792. https://doi.org/10.1093/nar/gkt396

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  13. 13.

    Crothers DM, Haran TE, Nadeau JG (7096s) Intrinsically bent DNA. J Biol Chem 265(13):7093–7096s

    CAS  PubMed  Google Scholar 

  14. 14.

    Barbic A, Zimmer DP, Crothers DM (2003) Structural origins of adenine-tract bending. Proc Natl Acad Sci USA 100(5):2369–2373. https://doi.org/10.1073/pnas.0437877100

    CAS  Article  PubMed  Google Scholar 

  15. 15.

    Nelson HC, Finch JT, Luisi BF, Klug A (1987) The structure of an oligo(dA)·oligo(dT) tract and its biological implications. Nature 330(6145):221–226. https://doi.org/10.1038/330221a0

    CAS  Article  PubMed  Google Scholar 

  16. 16.

    Stefl R, Wu H, Ravindranathan S, Sklenar V, Feigon J (2004) DNA A-tract bending in three dimensions: solving the dA4T4 vs. dT4A4 conundrum. Proc Natl Acad Sci USA 101(5):1177–1182. https://doi.org/10.1073/pnas.0308143100

    CAS  Article  PubMed  Google Scholar 

  17. 17.

    Haran TE, Mohanty U (2009) The unique structure of A-tracts and intrinsic DNA bending. Q Rev Biophys 42(1):41–81. https://doi.org/10.1017/S0033583509004752

    CAS  Article  PubMed  Google Scholar 

  18. 18.

    McAteer K, Aceves-Gaona A, Michalczyk R, Buchko GW, Isern NG, Silks LA, Miller JH, Kennedy MA (2004) Compensating bends in a 16-base-pair DNA oligomer containing a T3A3 segment: a NMR study of global DNA curvature. Biopolymers 75(6):497–511. https://doi.org/10.1002/bip.20168

    CAS  Article  PubMed  Google Scholar 

  19. 19.

    Calladine CR, Drew HR, McCall MJ (1988) The intrinsic curvature of DNA in solution. J Mol Biol 201(1):127–137

    CAS  Article  Google Scholar 

  20. 20.

    Marini JC, Levene SD, Crothers DM, Englund PT (1982) Bent helical structure in kinetoplast DNA. Proc Natl Acad Sci USA 79(24):7664–7668

    CAS  Article  Google Scholar 

  21. 21.

    Ulanovsky L, Bodner M, Trifonov EN, Choder M (1986) Curved DNA: design, synthesis, and circularization. Proc Natl Acad Sci USA 83(4):862–866

    CAS  Article  Google Scholar 

  22. 22.

    Hagerman PJ (1986) Sequence-directed curvature of DNA. Nature 321(6068):449–450. https://doi.org/10.1038/321449a0

    CAS  Article  PubMed  Google Scholar 

  23. 23.

    Lionberger TA, Meyhofer E (2010) Bending the rules of transcriptional repression: tightly looped DNA directly represses T7 RNA polymerase. Biophys J 99(4):1139–1148. https://doi.org/10.1016/j.bpj.2010.04.074

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  24. 24.

    Du Q, Kotlyar A, Vologodskii A (2008) Kinking the double helix by bending deformation. Nucleic Acids Res 36(4):1120–1128. https://doi.org/10.1093/nar/gkm1125

    CAS  Article  PubMed  Google Scholar 

  25. 25.

    Lionberger TA, Demurtas D, Witz G, Dorier J, Lillian T, Meyhofer E, Stasiak A (2011) Cooperative kinking at distant sites in mechanically stressed DNA. Nucleic Acids Res 39(22):9820–9832. https://doi.org/10.1093/nar/gkr666

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  26. 26.

    Rauch CA, Perez-Morga D, Cozzarelli NR, Englund PT (1993) The absence of supercoiling in kinetoplast DNA minicircles. EMBO J 12(2):403–411

    CAS  Article  Google Scholar 

  27. 27.

    Snodin BEK, Schreck JS, Romano F, Louis AA, Doye JPK (2019) Coarse-grained modelling of the structural properties of DNA origami. Nucleic Acids Res. https://doi.org/10.1093/nar/gky1304

    Article  PubMed  PubMed Central  Google Scholar 

  28. 28.

    Beveridge DL, Barreiro G, Byun KS, Case DA, Cheatham TE, 3rd, Dixit SB, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Seibert E, Sklenar H, Stoll G, Thayer KM, Varnai P, Young MA (2004) Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps. Biophys J 87(6):3799–3813. https://doi.org/10.1529/biophysj.104.045252

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  29. 29.

    Pérez A, Luque FJ, Orozco M (2012) Frontiers in molecular dynamics simulations of DNA. Acc Chem Res 45(2):196–205. https://doi.org/10.1021/ar2001217

    CAS  Article  PubMed  Google Scholar 

  30. 30.

    Salomon-Ferrer R, Götz AW, Poole D, Le Grand S, Walker RC (2013) Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle Mesh Ewald. J Chem Theory Comput 9(9):3878–3888. https://doi.org/10.1021/ct400314y

    CAS  Article  Google Scholar 

  31. 31.

    Galindo-Murillo R, Robertson JC, Zgarbova M, Sponer J, Otyepka M, Jurecka P, Cheatham TE (2016) Assessing the current state of AMBER force filed modifications for DNA. J Chem Theory Comput 12(8):4114–4127. https://doi.org/10.1021/acs.jctc.6b00186

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  32. 32.

    Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117(19):5179–5197. https://doi.org/10.1021/ja00124a002

    CAS  Article  Google Scholar 

  33. 33.

    Sprous D, Young MA, Beveridge DL (1999) Molecular dynamics studies of axis bending in d(G5-(GA4T4C)2–C5) and d(G5-(GT4A4C)2–C5): effects of sequence polarity on DNA curvature. J Mol Biol 285(4):1623–1632. https://doi.org/10.1006/jmbi.1998.2241

    CAS  Article  PubMed  Google Scholar 

  34. 34.

    Harris SA, Laughton CA, Liverpool TB (2008) Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations. Nucleic Acids Res 36(1):21–29. https://doi.org/10.1093/nar/gkm891

    CAS  Article  PubMed  Google Scholar 

  35. 35.

    Wang J, Cieplak P, Kollman PA (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21(12):1049–1074. https://doi.org/10.1002/1096-987X(200009)21:12%3c1049:AID-JCC3%3e3.0.CO;2-F

    CAS  Article  Google Scholar 

  36. 36.

    Pérez A, Marchan I, Svozil D, Sponer J, Cheatham TE, 3rd, Laughton CA, Orozco M (2007) Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers. Biophys J 92(11):3817–3829. https://doi.org/10.1529/biophysj.106.097782

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  37. 37.

    Mitchell JS, Laughton CA, Harris SA (2011) Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA. Nucleic Acids Res 39(9):3928–3938. https://doi.org/10.1093/nar/gkq1312

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  38. 38.

    Joung IS, Cheatham TE (2008) Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J Phys Chem B 112(30):9020–9041. https://doi.org/10.1021/jp8001614

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  39. 39.

    Pasi M, Zakrzewska K, Maddocks JH, Lavery R (2017) Analyzing DNA curvature and its impact on the ionic environment: application to molecular dynamics simulations of minicircles. Nucleic Acids Res 45(7):4269–4277. https://doi.org/10.1093/nar/gkx092

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  40. 40.

    Ivani I, Dans PD, Noy A, Perez A, Faustino I, Hospital A, Walther J, Andrio P, Goni R, Balaceanu A, Portella G, Battistini F, Gelpi JL, Gonzalez C, Vendruscolo M, Laughton CA, Harris SA, Case DA, Orozco M (2016) Parmbsc1: a refined force field for DNA simulations. Nat Methods 13(1):55–58. https://doi.org/10.1038/nmeth.3658

    CAS  Article  PubMed  Google Scholar 

  41. 41.

    Macke T, Case DA (1998) Modeling unusual nucleic acid structures. In: Santa-Lucia J (ed) Leontes NB, J. Molecular s. American Chemical Society, Washington, DC, pp 379–393

    Google Scholar 

  42. 42.

    Case DA, Ben-Shalom IY, Brozell SR, Cerutti DS, Cheatham TE, Cruzeiro VWD, Darden TA, Duke RE, Ghoreishi D, Gilson MK, Gohlke H, Goetz AW, Greene D, Harris R, Homeyer N, Izadi S, Kovalenko A, Kurtzman T, Lee TS, LeGrand S, Li P, Lin C, Liu J, Luchko T, Luo R, Mermelstein DJ, Merz KM, Miao Y, Monard G, Nguyen C, Nguyen H, Omelyan I, Onufriev A, Pan F, Qi R, Roe DR, Roitberg A, Sagui C, Schott-Verdugo S, Shen J, Simmerling CL, Smith J, Salomon-Ferrer R, Swails J, Walker RC, Wang J, Wei H, Wolf RM, Wu X, Xiao L, York DM, Kollman PA (2018) AmberTools18, 18th edn. UCSF, San Francisco

    Google Scholar 

  43. 43.

    Anzaldi LJ, Muñoz-Fernández D, Erill I (2012) BioWord: a sequence manipulation suite for Microsoft Word. BMC Bioinform 13:124. https://doi.org/10.1186/1471-2105-13-124

    Article  Google Scholar 

  44. 44.

    Li P, Merz KM Jr (2014) Taking into account the ion-induced dipole interaction in the nonbonded model of ions. J Chem Theory Comput 10(1):289–297. https://doi.org/10.1021/ct400751u

    CAS  Article  PubMed  Google Scholar 

  45. 45.

    Wang H, Laughton CA (2010) Molecular modelling methods to quantitate drug-DNA interactions. Methods Mol Biol 613:119–131. https://doi.org/10.1007/978-1-60327-418-0_8

    CAS  Article  PubMed  Google Scholar 

  46. 46.

    Lavery R, Moakher M, Maddocks JH, Petkeviciute D, Zakrzewska K (2009) Conformational analysis of nucleic acids revisited: curves+. Nucleic Acids Res 37(17):5917–5929. https://doi.org/10.1093/nar/gkp608

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  47. 47.

    DeLano WL (2015) The PyMOL molecular graphics system. 1.8.2.0. edn. Schrödinger, LLC

  48. 48.

    Zhou T, Yang L, Lu Y, Dror I, Dantas Machado AC, Ghane T, Di Felice R, Rohs R (2013) DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale. Nucleic Acids Res 41:W56–W62. https://doi.org/10.1093/nar/gkt437

    Article  PubMed  PubMed Central  Google Scholar 

  49. 49.

    Widlund HR, Cao H, Simonsson S, Magnusson E, Simonsson T, Nielsen PE, Kahn JD, Crothers DM, Kubista M (1997) Identification and characterization of genomic nucleosome-positioning sequences. J Mol Biol 267(4):807–817. https://doi.org/10.1006/jmbi.1997.0916

    CAS  Article  PubMed  Google Scholar 

  50. 50.

    Zewail-Foote M, Hurley LH (1999) Ecteinascidin 743: a minor groove alkylator that bends DNA toward the major groove. J Med Chem 42(14):2493–2497. https://doi.org/10.1021/jm990241l

    CAS  Article  PubMed  Google Scholar 

  51. 51.

    Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, Luebeck J, Rajkumar U, Diao Y, Li B, Zhang W, Jameson N, Corces MR, Granja JM, Chen X, Coruh C, Abnousi A, Houston J, Ye Z, Hu R, Yu M, Kim H, Law JA, Verhaak RGW, Hu M, Furnari FB, Chang HY, Ren B, Bafna V, Mischel PS (2019) Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature 575(7784):699–703. https://doi.org/10.1038/s41586-019-1763-5

    CAS  Article  PubMed  Google Scholar 

  52. 52.

    Franquelim HG, Khmelinskaia A, Sobczak JP, Dietz H, Schwille P (2018) Membrane sculpting by curved DNA origami scaffolds. Nat Commun 9(1):811. https://doi.org/10.1038/s41467-018-03198-9

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  53. 53.

    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(7):1213–1227. https://doi.org/10.1038/nprot.2008.104

    CAS  Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

A.M. gratefully acknowledges being the recipient of a predoctoral fellowship from the University of Alcalá. We are indebted to Jason Swails for help provided in the AMBER reflector regarding circular DNA molecules, Jürgen Walther for assistance at the MCDNA server, and the anonymous reviewers for helpful suggestions. We thankfully acknowledge the GPU time granted on Minotauro (BCV-2019-2-0016) and the technical support provided by staff at the Barcelona Supercomputing Center.

Funding

Financial support from the Spanish Ministerio de Economía y Competitividad (SAF2015-64629-C2-2-R) and PharmaMar S.A.U. (Colmenar Viejo, Madrid, Spain) is gratefully acknowledged.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Federico Gago.

Ethics declarations

Conflict of interest

There are no conflicts to declare.

Additional information

This work is dedicated to the memory of Prof. Michael Waring (University of Cambridge, UK).

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

10822_2020_288_MOESM2_ESM.mov

Supplementary file2 (MOV 26204 kb)

Supplementary file3 (MOV 23381 kb)

Supplementary file4 (MOV 29594 kb)

Supplementary file1 (DOCX 2176 kb)

Supplementary file2 (MOV 26204 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Mills, A., Gago, F. Atomistic insight into sequence-directed DNA bending and minicircle formation propensity in the absence and presence of phased A-tracts. J Comput Aided Mol Des 34, 253–265 (2020). https://doi.org/10.1007/s10822-020-00288-z

Download citation

Keywords

  • DNA structure
  • Molecular dynamics simulations
  • Circular DNA