SNP (Single nucleotide polymorphism) & SSCP (Single-strand conformational polymorphism)

Studies on the solution structure dynamics of RNA/DNA now-a-days becoming crucially important for understanding various phenomena related to gene control reagents such as antisense RNA/DNA, RNAi, non-coding microRNAs and other newer families of functional RNA. A short single-stranded (ss) DNA or RNA molecule can be thought of conformationally not as short strings but rather as sequence dependent folded structure which adopts, with comparable probability, many different conformations in solution that distinguishes it from other biological macromolecules. What are typical conformations of short ss molecules and what factors govern their conformational space? To answer these and similar questions which concern the intimate behavior of ssDNA require the knowledge of accurate molecular conformations. For this purposes, we have studied a general nature of SSCP phenomenon at the oligodexynucleotide level by gel electrophoresis (J. Biochemistry, 2005). SSCP is the separation of single-stranded nucleic acids based on subtle differences in sequence (often a single base) which results in a different secondary structure and a measurable difference in mobility during electrophoresis.

However, the gel data (less informative) could be explored more in conjunction with computational tools such as molecular dynamics (MD) simulation; to create a graphical representation of the experimental structure, to generate hypothetical model and to predict new physical properties. Further, a cohesive approach, correlating the simulated results with the corresponding experimental data will undoubtedly serves a better platform for obtaining novel information and new insights. MD of d(G12) possessing a single-base substitution revealed that both the ends were sufficiently close to form a semi-stable hairpin-like folded structure which is depended on the type and position of substitution.

In this research, SSCP phenomenon at the oligodeoxyribonucleotide level was studied and interpreted as structures dynamics by employing a joint approach of gel electrophoresis and nanosecond MD. A high correlation between the electrophoretic mobility and the size-related parameters obtained from MD shows the significance of negligibly weak, intra-molecular interactions between adjacent nucleotides of a strand, which can and do contribute to the distribution of dynamic structures in solution representing SSCP phenomenon. The knowledge about solution structure dynamics of ssDNA appear to be beneficial to understand various phenomena to control gene networking.