Characteristics of equipartition for RNA structure.
BACKGROUND
With the continuous discovery of novel RNA molecules with key cellular functions and of novel pathways and interaction networks, the need for structural information of RNA is still increasing. In order to predict structure of long RNA and understand its natural folding mechanism, exploring the characteristic of RNA structure is an important issue.


METHODS
The real RNA secondary structures of all 480 sequences from the database of RNA strand, validated by nuclear magnetic resonance or x-ray are selected. For one sequence with multiple domains, the length ratios of these domains to the sequence are computed. For one sequence with one domain and multiple sub-domains, the length ratios of these sub-domains to the domain are computed. Then the ratios are compared and analyzed to seek the partition characteristic of domains and subdomains.


RESULTS
For most RNAs, the length ratios of multiple domains to its sequence are close to equal, and those of sub-domains to its domain are also nearly identical. Most RNAs with multiple domains have two domains, so the length ratios of the domains to its sequence are close to 0.5. For sequence with one domain and no sub-domain or one sub-domain, the centre of domain and sub-domain is close to that of the sequence.


CONCLUSIONS
A novel finding is given that RNA folding accords with the characteristic of equipartition based on statistical analysis. The characteristic reflects the folding rules of RNA from a new angle, which maybe more close to natural folding.
School of Computer Science and Technology, and Shandong Provincial Key Laboratory of Digital Media Technology, Shandong University of Finance and Economics, Jinan 250014, China ; School of Computer Science and Technology, and Shandong Provincial Key Laboratory of Software Engineering, Shandong University, Jinan 250014, China.
Hengwu
H
Li
School of Computer Science and Technology, and Shandong Provincial Key Laboratory of Software Engineering, Shandong University, Jinan 250014, China.
Daming
D
Zhu
School of Computer Science and Technology, and Shandong Provincial Key Laboratory of Software Engineering, Shandong University, Jinan 250014, China.
Caiming
C
Zhang
School of Computer Science and Technology, and Shandong Provincial Key Laboratory of Digital Media Technology, Shandong University of Finance and Economics, Jinan 250014, China.
Huijian
H
Han
Computational Biology Institute, George Washington University, Ashburn, Virginia 20147, USA.
Keith A
KA
Crandall