Molecular modeling and structural studies of 12-mer immobile four-way DNA junction in solution.

Ramesh Kumar Yadav,Umesh Yadava

doi:10.6026/97320630010394

Ramesh Kumar Yadav, Umesh Yadava

Open Access

https://doi.org/10.6026/97320630010394

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Journal: Bioinformation	Publication Date: Jul 22, 2014
Citations: 2	License type: cc-by

Affiliation: Deen Dayal Upadhyaya Gorakhpur University

Abstract

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.

Highlights

Molecular modelling and structural studies of 12-mer immobile four-way DNA junction model is reported here
Generation of coordinates The coordinates of DNA junction were generated according to the ideal geometry with the help of AMBER EDIT module, using following sequences 5’d(GGAAGGGGCTGG), 5’d(CCAGCCTGAGCC), 5’d(GGCTCAACTCGG), and 5’d(CCGAGTCCTTCC)
Results & Discussion: Dynamic structure of the DNA junction model A series of twelve snapshots taken from the MD trajectory at periodic intervals of 100 ps is shown in (Figure 2)

Summary

Introduction

Molecular modelling and structural studies of 12-mer immobile four-way DNA junction model is reported here. The first clue as to the problem, Seeman and Kallenbach [5] proposed the study of three dimensional shape of the junction came from the work of synthetic analogs of Holliday junctions in which the sequence is Cooper and Hagermann [8] who studied the relative designed in such a way that the branch point is immobile. These electrophoretic mobilities of a small synthetic junction to which synthetic immobile Holliday junctions consist of four stranded reporter arms had been ligated in various combinations. In order to understand the structural and biological functions of these biomolecules, molecular modeling has become an important tool in the design and construction of new nucleotide sequences

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Results

Conclusion