A duplex DNA model with regular inter-base-pair hydrogen bonds

作者：Li, Xu-Qing^*; Fan, Ping

来源：Journal of Theoretical Biology, 2010, 266(3): 374-379.

DOI：10.1016/j.jtbi.2010.07.002

• Non-planar amino groups
• Base-pair stacking
• Dinucleotide step
• Sequence-dependent properties
• DNA flexibility and thermal stability

It is well known that base-pair stacking is the main factor in stabilizing DNA duplex and plays an important role in determining DNA sequence-dependence. What is the dominant force in base-pair stacking? This fundamental biological question remains a challenging problem. Here, based on recent studies about the non-planarity of amino groups on DNA bases, we propose a new duplex DNA model, in which all base amino groups are non-planar and participate in forming regular inter-base-pair hydrogen bonds (IBP H-bonds). This model implies that IBP H-bonds are the dominant force stabilizing base-pair stacking and play a crucial role in determining the geometry and physical properties of sequence-dependent twisted stacking between adjacent base pairs. The model presents a new insight into the link, through regular IBP H-bonds, between base-sequence, fine structure and physical properties at dinucleotide step level, and provides an attractively concise, uniform and quantitative interpretation for various experimentally observed DNA sequence-dependent properties in terms of regular IBP H-bonds. It would provide a new approach to understanding the dynamics and underlying mechanisms of DNA sequence-dependent biological processes, sequence-structure-property relationships, DNA strand separation during replication and transcriptions, etc.

• 出版日期2010-10-7
• 单位昆明理工大学