Title

Authors

Affiliation

¹Department of Physics, B.R.D. P.G. College, Deoria 274001, India; ²Department of Physics, DDU Gorakhpur University, Gorakhpur 273009, India

Email

u_yadava@yahoo.com; *Corresponding author

Article Type

Hypothesis

Date

Received May 22, 2014; Accepted May 26, 2014; Published July 22, 2014

Molecular modelling and structural studies of 12-mer immobile four-way DNA junction model is reported here. The DNA junction which was built and investigated, consisted of the following sequences 5'd(GGAAGGGGCTGG), 5'd(CCAGCCTGAGCC), 5'd(GGCTCAACTCGG) and 5'd(CCGAGTCCTTCC). The model was made in such a way that the junction may lack two-fold sequence symmetry at the crossover point. A new version of the AMBER force field has been used, in addition to the Particle Mesh Ewald (PME) method which deals with the refinement treatment of the long range interaction potentials, the well known limitation in MD protocol. After molecular dynamics simulation the backbone parameters and helical parameters of the DNA junction model is calculated and its dynamical pathway is discussed. A close observation near the junction point reveals the shifting in the orientation of some of the P-O bonds from the usual π3 turn for A- and B- DNA to either π1 or π2 type of turn in order to achieve conformational stability. With this study it seems possible to derivatize synthetic DNA molecules with special functional groups both on the bases and at the backbones as in the case of some natural processes by which drugs, particular proteins etc. recognizes and binds to the specific sites of DNA.

Keywords

DNA Junction, Molecular Modeling, AMBER, Dynamical pathway.

Citation

Yadav RK & Yadav U,   Bioinformation 10(7): 394-400 (2014)
 

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.