Secondary structure of rna and its predicting elements
- 1. V I N A K H A N Secondary Structure Of RNA And Its Predicting Elements
- 2. CONTENTS INTRODUCTION STRUCTURE OF RNA Primary structure Secondary structure Tertiary structure Importance of prediction Secondary structure elements Predicting method
- 3. INTRODUCTION Like protein, nucleic acid and DNA(deoxyribonucleic acid), RNA(ribonucleic acid) play an important role in reproducing and maintaining life. RNA molecules are used for the synthesis of proteins, they act as messengers. RNA are composed of subunits, the so-called nucleotides or bases. The nucleotides are linked together by phosphodiester linkages through the hydroxyl group on the sugar on one nucleotide and the phosphate on the next one. As a result one can observe a strand with the so-called 5'-end, where a free phosphate group can be found, and the 3'-end with a free hydroxyl group.
- 4. Structure Of RNA In RNA nucleotides the sugar which is used is ribose and therefore they are also called ribonucleotides. The purine bases are also adenosine (A) and guanine (G), but the pyrimidine bases are cytosine (C) and uracil (U) RNA molecules are much smaller than DNA molecules, but they are also linear polymers. Moreover they do not seem to have a regular three- dimensional structure and are mostly single stranded. This makes them more flexible than DNA and they can also act also as enzymes
- 5. CONTINUE…
- 6. Primary and Secondary structure The primary structure of a molecule describes only the one- dimensional sequence of it components. The primary structure of RNA is almost identical to the primary structure of DNA, besides the components being A,C,G and U instead of T. The secondary structure of molecules is more complex than the primary structure and can be drawn in two- dimensional space . RNA secondary structure is mainly composed of double stranded RNA regions formed by folding the single stranded RNA molecule back on itself.
- 8. Tertiary Structure The tertiary structure is the overall three-dimensional structure of molecules. It is built on the interactions of the lower-order secondary structures. Helices are examples of RNA and DNA tertiary structures. pseudoknot is a tertiary structure of RNA.
- 10. Importance of Prediction of RNA Secondary structure Important aspect of the prediction of RNA secondary structure is that there are many sequences whose structures have not yet been experimentally determined and ; for which there are no homologues in the databases from which the structure could be derived; Hence it is a good idea to predict the structure. Moreover it has been shown that RNA secondary structure prediction has applications to the design of nucleic acid probes .
- 11. Continue.. It is also used by molecular biologists to help predict conserved structural elements in non- coding regions of gene transcripts. Finally there is also an application in predicting structures that are conserved during evolution
- 12. Different secondary structure elements 1. Stem Loops: (Hairpin Loops) is a lollipop shaped structure formed when a single stranded nucleic acid molecule loops back on itself to form a complementary double helix (stem) topped by a loop.
- 13. Bulge loop Bulge loops are commonly found in helical segments of cellular RNAs. Bulge loops occur when bases on one side of the structure cannot form base pairs and they cause bends in the helix.
- 14. 3.Interior loop: Interior loops occur when bases on both sides of the structure cannot form base pairs. 4. Junctions or Mltiloops: Junctions include two or more double stranded regions converging to form a closed structure.
- 15. 5. Pseudoknot A pseudoknot is a tertiary structural element of RNA. It is formed by base-pairing between an already existing secondary structure loop and a free ending. Nucleotides within a hairpin loop form base pairs with nucleotides outside the stem Hence basepairs occur that overlap each other in their sequence position .
- 16. Pseudoknot
- 17. RNA structure prediction methods Base Pair Maximization Energy Minimization The most commonly used method is free energy minimization. The accuracy of structure prediction is improved either by using experimental mapping data or by predicting a structure conserved in a set of homologous sequences
- 18. CONTINUE… Energy minimization method is thermodynamic Stable Estimated using experimental techniques Theory : Most Stable is the Most likely No Pseudoknots due to algorithm limitations Uses Dynamic Programming alignment technique Attempts to maximize the score taking into account thermodynamics Gaps represent some form of a loop The most widely used software that incorporates this minimum free energy algorithm is MFOLD/RNAfold/ViennaRNA
- 19. References https://pubmed.ncbi.nlm.nih.gov/22736001/ https://bmcbioinformatics.biomedcentral.com/articles/10.1186/14 71-2105-11-129 https://www.slideshare.net/sadiqpa/rna-secondary-structure- prediction-35444501