What Is a Mutation?Genetic information is encoded by the sequence of the nucleotide bases in DNA of the gene. The four nucleotides are: adenine (A), thymine (T), guanine (G), and cytosine (C), a mutation is a change in the order of these nucleotides.A change in the order can cause the gene to encode for wrong proteins and inhibit the function of the gene or cause the gene to be virtually inactive.

What Is a Mutation?Genetic information is encoded by the sequence of the nucleotide bases in DNA of the gene. The four nucleotides are: adenine (A), thymine (T), guanine (G), and cytosine (C), a mutation is a change in the order of these nucleotides.A change in the order can cause the gene to encode for wrong proteins and inhibit the function of the gene or cause the gene to be virtually inactive.

What Is a Mutation?Genetic information is encoded by the sequence of the nucleotide bases in DNA of the gene. The four nucleotides are: adenine (A), thymine (T), guanine (G), and cytosine (C), a mutation is a change in the order of these nucleotides.A change in the order can cause the gene to encode for wrong proteins and inhibit the function of the gene or cause the gene to be virtually inactive.

Random mutagenesis-> based on the process of natural

evolution

- NO structural information required

-NO understanding of the mechanism required

General Procedure:Generation of genetic diversity

Random mutagenesis

Identification of successful variants Screening and seletion

Site-directed Mutagenesis

Site Directed Mutagenesis is a molecular biology technique in which a mutation is created at a defined site in a DNA molecule known as a plasmid. Wild-type gene sequence must be known. Or Site Directed Mutagenesis is a powerful technique where site specific changes in DNA sequence are produced in vitro-for instance to change an amino acid residue into another by changing the codon sequence within the gene sequence.

CAG

GTC

CAG

+ primer

CAG

primer GCC

+ polymerase

CAG

GCCreplication

CAG

GTC

Wild type

translation

Val

MutantWild type protein

CGGGCC

translation

Thr

Mutant protein

Only one amino acid changed

Val → Thr

(1)

(2)

(3)

(4)

(5)

(6)

Smith (1993)

GeneticsGenetics Mutant phenotype

Mutant allele

DNA sequence

Protein sequence

Why Site directed mutagenesis -> site-directed mutagenesis

-> point mutations in particular known area

result -> library of wild-type and mutated DNA (site-specific)

not really a library -> just 2 species

-> random mutagenesis -> point mutations in all areas within DNA of

interest

result -> library of wild-type and mutated DNA (random)

a real library -> many variants -> screening !!!

if methods efficient -> mostly mutated DNA

INVENTIONSite Directed Mutagenesis using oligonucleotide was first described in 1978 by Michael Smith & shared Nobel Prize in chemistry in October 1993 with Kary B. Mullis who developed the PCR technique.

Site –directed mutagenesis Requirements: -> Knowledge of sequence and preferable Structure (active site,….)

-> Understanding of mechanism (knowledge about structure – function relationship)

Site Directed Mutagenesis1. Cassette mutagenesis

2. Oligonucleotide directed mutagenesis Using M13 DNA OR Using Plasmid DNA

3. PCR amplified Oligonucleotide directed mutagenesis

4. Random mutagenesis With Degenerate Oligonucleotide primers

or Using Nucleotide Analogues

CASSETTE MUTAGENESIS

Cleavage by a Restriction Enzyme (RE) at a particular site in the plasmid.Ligation of an Oligonucleotide containing Mutation in the gene of interest to the plasmid.RE that cuts at the plasmid and Oligonucleotide is same, permitting sticky ends of the plasmid & inserts to ligate to one another.

Site-directed mutagenesis methods – Oligonucleotide - directed method

Synthetic single-stranded fragments of DNA used for priming the mutated clones.

In order to work, the primers must meet the following criteria:

-must contain desired mutation. -mutation should be in the middle of

the primer. -the GC content should be at a

minimum of 40% and should terminate in one or more of C or G bases.

Oligonucleotides are…

Oligonucleotide directed mutagenesis

Basic Methods1. Base pair substitution: Change of one nucleotide (A-> C)

2. Insertion: Gaining one additional nucleotide

3. Deletion: Loss of one nucleotide

Deletion Mutagenesis

1. Synthesize an Oligonucleotide containing the changed sequence.Ex.---ATT---Wild type sequence (Codon for ILe)---CTT---Desired Change (Leu)---GAA---Mutagenic Oligonucleotide (MO)2.Hybridize MO ss form of gene cloned into M13.3.Synthesize second strand of DNA with KLENOW fragment &dNTPs.4.Seal nick in new strand with T4 DNA ligase.5.Introduce into E. Coli.6.ss + phage isolated from plaques & screened by hybridization.

Oligonucleotide directed mutagenesis with M13 DNA:

Oligonucleotide Directed Mutagenesis Using Plasmids

Increases the chances of obtaining the desired mutation in the target geneCo selection technique

Antibiotic resistance gene restored and a second one eliminated

Approx 90% of Ampr and Tets clones have target mutated in directed fashion

Primer design for PCR-Amplified Oligonucleotide-directed

mutagenesis

Site-directed mutagenesis methods -PCR based

Perform two separate PCR rx. With two sets of primers.Each primer set introduces the desired nucleotide change but produces linear PCR products with different ends.Denaturation, mixing & ligation of PCR products produces mutated circular DNA that can be introduced into E. Coli by transformation.

Random Mutagenesis Using Degenerate Oligonucleotide

PrimersMake primers at sites to be mutated which are degenerate at one or more sitesRandom changes in nucleotide sequences of the primer are introduced during chemical synthesis of a pool of degenerate oligonucleotides.Must express mutant genes & screen gene products to find the improved version of the PROTEIN.

Random Mutagenesis With

Nucleotide AnalogueCut clone to side of target geneDigest with ExoIIISynthesize with DNAP I, dNTPs and a dNTP analog.Ex.N4-hydroxy cytosine is an analog of cytosine.Presence in DNA causes an A-T base pair transition mutation when the DNA is replicated by the host. Ex.---AAA---(Lys) to ---GAA---(Glu)---TTT---…………---CTT---Analog causes replication errors when transformed into E. coli

Uses of Site Directed Mutagenesis

1.Site Directed Mutagenesis is also used to ‘engineer’ commercially important Proteins for many different purposes, for example•Improve stability•Change specificity•Reduce toxicity 2.It can be used to produce proteins which can ‘improve’ laundry detergentsSUBTILISIN, a bacterial serine-protease that can breakdown most proteins which soil clothing & a major additive to modern ‘BIO’ detergents. Before it became commercially useful, the recombinant protein was improved in order that it remained active in the presence of Bleach. Bleach caused the oxidation of a methionine residue (position 22) & the enzyme lost 90% of its activity. By replacing this amino acid with alanine, the enzyme was no longer sensitive to oxidation & found best in terms of ACTIVITY &STABILITY.

3. Site Directed Mutagenesis enabled new approaches to drug designing – particularly in order to improve FUNCTION.

4.Random Mutagenesisis is used to construct large &diverse clone libraries of mutated DNA fragments.

FUTURE ASPECTSAttempts are being made to produce biotechnically a mutated haemoglobin which may give us a new means of replacing blood.By mutating proteins in the immune system researchers have come a long way towards constructing antibodies that can neutralize cancer cells.Future also holds possibilities of gene therapy, curing hereditary diseases by specifically correcting mutated code words in the genetic material.Site directed mutagenesis of plant proteins is opening up the possibility of producing of producing crops that can make more efficient use of atmospheric carbon dioxide during photosynthesis.

Conclusion:• any amino acid in a protein can be selectively replaced with another amino acid

• the replacements are made at the genetic level by modifying the Codon to incorporate the new amino acid

• characterizing the mutant enzyme that is obtained will provide information on the role of the amino acid that has been replaced

REFERENCES:Old R.W. and Primrose S.B. (2001), Principles Of

Gene Manipulation, Blackwell Scientific Publications, Page (132-138)

Brown T.A. (2001) Gene cloning and DNA analysis – An Introduction Blackwell Publication Page – (236 – 241)

Watson J.D., Gilman M, Zoller M and Witkowski(1992) Recombinant DNA, Scientific American Books, Page (191-207)

En. Wikipedia. Org/wiki /site directed mutagenesis 32K

WWW. Che.Utoledo. Edu / nadarajah / WebPages / mutagene. Htm.14K

Glick, Molecular Biotechnology Page (171 – 183)