RNA SECONDARY STRUCTURE PREDICTION TOOLS

RNA consists of a long chain of nucleotide units. RNA is transcribed from

DNA by enzymes called RNA polymerases . RNA is central to protein

synthesis via a type of RNA called messenger RNA carries information from

DNA to structures called ribosomes.

CONTENT

INTRODUCTIONSYNTHESISTYPES OF RNA

RNA SECONDARY STRUCTURETOOLS

MFOLDVIENNA RNA PACKAGE

•RNAFOLDSFOLD

SYNTHESIS

TYPES OF RNA1. Messenger RNAs (mRNAs): The genetic coding templates used by the

translation machinery to determine the order of amino acids in the process

of translation.

2. Transfer RNAs (tRNAs): They form covalent attachments to individual amino

acids and recognize the encoded sequences of the mRNAs

3. Ribosomal RNAs (rRNAs): They assembled, together with numerous ribosomal

proteins, to form the ribosome. The proteins of the ribosomes catalyze all of the

functions of polypeptide synthesis.

RNA is made of 4 nucleotides

A, G, C, U

RNA molecule are single-stranded but they can interact with themselves to

form secondary structures

The most typical RNA secondary structure is the hairpin

Hairpins are usually mad of a stem and a loop as shown here

RNA secondary structures

TOOLS

•It is possible to predict the secondary structure of an RNA sequence

•The accuracy is ~70%

•Predictions are easier and more accurate on small molecules (fewer

than 500 nucleotides)

•More accurate predictions can be made using multiple-sequence

alignments

•RNA secondary structure is often predicted from sequence by free

energy minimization.

TOOLS USED

•MFOLD

•Vienna (RNA) package

rna fold

•SFold

Single-Sequence Structure

Prediction for RNA

Mfold is an RNA and DNA folding package developed by Dr. Michael Zuker..

mfold package for RNA and DNA secondary structure prediction using nearest

neighbor thermodynamic rules

The server predicts the most stable secondary structure (with the lowest

potential energy)

Mfold can also return suboptimal structures (indicate good accuracy)

Detailed output, in the form of structure plots with or without reliability

information, single strand frequency plots and 'energy dot plots', are available for

the folding of single sequences.

PSEUDOKNOTS ARE NOT CONSIDERED BY MFOLD SERVER

Searching Databases

for tRNAs

Transfer RNAs are small RNA molecules

used to build proteins

Each protein has 64 tRNAs

One for each triplet of the genetic

code

All tRNAs have the same structure

MFOLD HOME PAGE

Link: DNA sec.str.prediction

INPUT: sequence of Human phe-tRNA

Linear sequence of RNA to be fold

Is maxi. energy diff. from optimal structure

Maxi. No. of suboptimal structure

Maxi no. of unpaired

nucleotide

To be filled for BATCH

JOB

Click it for structure prediction

OUTPUT

MULTIBRANCH LOOP

STEM

HAIRPIN LOOPINTERIOR

LOOP

Optimal &Suboptimal str. having:dG(GIBBS FREE ENERGY)=-151.52dG=-150.30

Suboptimal str.dG=-150.30

Conclusion

We have described several new computer programs that have been designed to enable the user to determine the reliability of predicted RNA secondary structuresrelatively easily.

Colored dots are used to provide a simple overview of how well determined an entire predicted structure and/or a predicted structural domain within a larger folding is.

Although the same information can be obtained from dot plot

Representations of optimal and suboptimal foldings that is created both by mfold and by the Vienna package, the dot plot representation of RNA secondary structures is relatively difficult to understand.