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iPARTS: an improved tool of pairwise alignment of RNA tertiary structures

Chih-Wei Wang1, Kun-Tze Chen, Chin Lung Lu

  • 1Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan, R.O.C.

Nucleic Acids Research
|May 29, 2010
PubMed

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The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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