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
Famous quotes containing the words structure and/or prediction:
“... the structure of our public morality crashed to earth. Above its grave a tombstone read, “Be tolerant—even of evil.” Logically the next step would be to say to our commonwealth’s criminals, “I disagree that it’s all right to rob and murder, but naturally I respect your opinion.” Tolerance is only complacence when it makes no distinction between right and wrong.”
—Sarah Patton Boyle, U.S. civil rights activist and author. The Desegregated Heart, part 2, ch. 2 (1962)
“Recent studies that have investigated maternal satisfaction have found this to be a better prediction of mother-child interaction than work status alone. More important for the overall quality of interaction with their children than simply whether the mother works or not, these studies suggest, is how satisfied the mother is with her role as worker or homemaker. Satisfied women are consistently more warm, involved, playful, stimulating and effective with their children than unsatisfied women.”
—Alison Clarke-Stewart (20th century)