Skip to main content
Log in

Molecular modeling of B-DNA site recognition by Ru intercalators: molecular shape selection

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript


In this work, molecular modeling methods have been applied to the interaction characterization of polypyridyl transitional-metal complexes with the oligonucleotide (B-DNA fragment). In order to explore the factors governing the groove recognition and intercalative depth, we establish a simple and practical docking method (step-by-step docking operation) to obtain potential curves while making complexes inset into B-DNA along an assigned path. Energy values in the potential curve are obtained from energy minimization of binding geometries. Modeling results clearly show that the optimum binding conformation corresponding to the global minimum in the potential curve for each complex is found to correlate well with the experimental results. Our results also confirm that minor changes of the ligand structure can lead to profound influences on binding geometries, so the molecular shape of the complexes is a predominant factor in governing the binding mode. Moreover, we find that the vdW force and “water molecular effect” are strongly associated with molecular-shape selection in our model. These results complement and extend the knowledge of the nature of these complexes binding to B-DNA.

Figure Schematic illustration of metal complexes bound to B-DNA. The complexes are intercalated into the A5T6/T6A5 base step via a “head-on” fashion

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

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Scheme 1
Fig. 2
Fig. 3
Scheme 2
Fig. 4
Fig. 5
Scheme 3
Fig. 6

Similar content being viewed by others


  1. Sitlani A, Long EC, Pyle AM, Barton JK (1992) J Am Chem Soc 114:2303-2312

    CAS  Google Scholar 

  2. Arounaguiri S, Maiya BG (1996) Inorg Chem 35:4267–4270

    Article  CAS  PubMed  Google Scholar 

  3. Lincoln P, Norden B (1998) J Phys Chem B 102:9583-9594

    Article  CAS  Google Scholar 

  4. Terbrueggen RH, Johann TW, Barton JK (1998) Inorg Chem 37:6874-6883

    Article  CAS  PubMed  Google Scholar 

  5. Holmlin RE, Yao JA, Barton JK (1999) Inorg Chem 38:174-189

    Article  CAS  Google Scholar 

  6. Patterson BT, Collins JG, Foley FM, Keene FR (2002) J Chem Soc Dalton Trans 4343–4350

  7. Wilhelmsson LM, Esbjo1rner EK, Westerlund F, Norden B, Lincoln P (2003) J Phys Chem B 107:11784–11793

    Article  CAS  Google Scholar 

  8. Holmlin RE, Steamp EDA, Barton JK (1998) Inorg Chem 37:29-34

    CAS  PubMed  Google Scholar 

  9. Tuite E, Lincoln P, Norden B (1997) J Am Chem Soc 119:239-240

    Article  CAS  Google Scholar 

  10. Han DX, Yang P (2000) Sci Chin B 43:516–523

    Google Scholar 

  11. Yang P, Han DX, Xiong ZH (2001) J Mol Struct (Theochem) 540:211–219

    Google Scholar 

  12. HyperChem, Release 6.0 (2000) Hypercube Inc

  13. Lane AN, Jenkins TC, Brown T, Neidle S (1991) Biochemistry 30:1372–1385

    CAS  PubMed  Google Scholar 

  14. Watts CR, Kerwin SM, Kenyon GL, Kuntz ID, Kallick DA (1995) J Am Chem Soc 117:9941-9950

    CAS  Google Scholar 

  15. Frankjin CA, Fry JV, Collins JG (1996) Inorg Chem 35:7541-7545

    Article  Google Scholar 

  16. Dupureur CM, Barton JK (1997) Inorg Chem 36:33-43

    Article  CAS  Google Scholar 

  17. Marques HM, Warden C, Monye M, Shongwe MS, Brown KL (1998) Inorg Chem 37:2578-2581

    Article  CAS  Google Scholar 

  18. Collins JG, Sleeman AD, Janice RAW, Greguric I, Hambley TW (1998) Inorg Chem 37:3133-3141

    Article  CAS  Google Scholar 

  19. Erkkila KE, Odom DT, Barton JK (1999) Chem Rev 99:2777-2795

    Article  CAS  PubMed  Google Scholar 

  20. Ihtshamul H, Lincoln P, Suh D, Norden B, Chaires JB (1995) J Am Chem Soc 117:4788-4796

    CAS  Google Scholar 

  21. Linclon P, Broo A, Norden B (1996) J Am Chem Soc 118:2644-2653

    Article  Google Scholar 

  22. Greguric I, Aldrich-Wright JR, Collins JG (1997) J Am Chem Soc 119:3621-3622

    Article  CAS  Google Scholar 

  23. Campisi D, Marii T, Barton JK (1994) Biochemistry 33:4130-4139

    CAS  PubMed  Google Scholar 

  24. Hudson BP, Barton JK (1998) J Am Chem Soc 120:6877–6888

    Article  CAS  Google Scholar 

  25. Brandt P, Norrby T, Akermark B (1998) Inorg Chem 37:4120-4127

    Article  CAS  PubMed  Google Scholar 

Download references


The authors acknowledge the support of Provincial Education Science Foundation of GuangDong (Series Number: 0164).

Author information

Authors and Affiliations


Corresponding author

Correspondence to Nailin Ren.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Han, D., Wang, H. & Ren, N. Molecular modeling of B-DNA site recognition by Ru intercalators: molecular shape selection. J Mol Model 10, 216–222 (2004).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: