Nucleic Acid Structure Prediction

Nucleic acid structure prediction is a computational method to determine nucleic acid secondary and tertiary structure from its sequence. Secondary structure can be predicted from a single or from several nucleic acid sequences. Tertiary structure can be predicted from the sequence, or by comparative modeling (when the structure of a homologous sequence is known).

The problem of predicting nucleic acid secondary structure is dependent mainly on base pairing and base stacking interactions; many molecules have several possible three-dimensional structures, so predicting these structures remains out of reach unless obvious sequence and functional similarity to a known class of nucleic acid molecules, such as transfer RNA or microRNA, is observed. Many secondary structure prediction methods rely on variations of dynamic programming and therefore are unable to efficiently identify pseudoknots.

While the methods are similar, there are slight differences in the approaches to RNA and DNA structure prediction. In vivo, DNA structures are more likely to be duplexes with full complementarity between two strands, while RNA structures are more likely to fold into complex secondary and tertiary structures such as in the ribosome, spliceosome, or tRNA. This is partially because the extra oxygen in RNA increases the propensity for hydrogen bonding in the nucleic acid backbone. The energy parameters are also different for the two nucleic acids.

Read more about Nucleic Acid Structure Prediction:  Single Sequence Structure Prediction, Comparative Secondary Structure Prediction, Tertiary Structure Prediction, See Also

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