Mukund's Brief Overview on Synthetic Biology Basics

'''Q1-''' What will you see if you add mud to water?

'''A-''' Sedimentation and floating particles of mud; Darkish-colored water

'''Q2-'''What will you see if DNA if added to water?

'''A-'''Clear water.

How does the phenomenon of 'seeing' the particles of mud and not the DNA take place?
This is because the particles of mud scatter light that results in the eye being able to view them.
DNA, however,allows light to pass right through it, due to which it becomes invisible to the eye.

[[File:DSC01403.JPG|200px|thumb|right|The discussion with Mukund]]
[[File:DSC01405.JPG|200px|thumb|right|Scattering of light (sketch)]]
[[File:DSC01406.JPG|200px|thumb|right|Flourescence of light (sketch)]]


'''There are three main ways by which light passes through an object:'''

a) '''Scattering :'''

A phenomenon in which light is forced to deviate from a straight path due to some non-uniformities present in the medium through which they pass.

b) '''Absorption:'''

In absorption, the frequency of the incoming light wave is at or near the energy levels of the electrons in the matter. The electrons will absorb the energy of the light wave and change their energy state.
The absorption of light makes an object dark or opaque to the wavelengths or colours of the incoming wave.

Another manner that the absorption of light is apparent is by color. If a material 
absorbs light of certain wavelengths or colors of the spectrum, an observer will not see these colors in the reflected light.

On the other hand if certain wavelengths of colors are reflected from the material, an observer will see them and see the material in those colours.

c) '''Flouresence:'''

A phenomenon in which the absorption of a photon leads to the emission of a photon with a longer (less energetic) wavelength.

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*There is one major problem with DNA, that is, its too small to see - even with high levels of  of magnification.Some of the ways of attempting to see them are through:

a) Addition of dyes

b) Increasing the quantity of the sample observed
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== '''Some basics of DNA Cloning:''' ==

'''Recombinant DNA:'''

Recombinant DNA is the general name for taking a piece of one DNA, and 
and combining it with another strand of DNA.

'''Plasmid:'''

A DNA molecule that is separate from the chromosomal DNA and is capable of replicating independently.This is a small, circular piece of DNA (usually a few thousand base pairs long) and can be found in bacteria.

'''Palindrome:'''

A sequence that reads the same in the forward and backward direction.

The Sequence:   ATGCAT

Its complement :TACGTA

It is due to this characteristic of the DNA sequences that they can bind to other sequences.

'''Restriction enzymes:'''

Enzymes responsible for cuting DNA strands.They recognize a specific, short sequence of DNA and cut the DNA at that point. Different restriction enzymes recognize and cut different sequences.

'''Sticky end:'''

When certain restriction enzymes cut DNA, they don't cut through both strands of DNA at the same point.The end that is left is called a sticky end. One strand is left with unpaired bases, which can later pair up with another sticky end created by the same enzyme.

'''Ligase:'''

Any of a group of enzymes that catalyze the binding of two molecules.

'''DNA Ligase:'''

A special type of ligase that can link together two DNA strands that have a double-strand break (a break in both complementary strands of DNA)

'''Selectable Marker:'''

A gene whose expression allows the identification of a specific trait or gene in an organism.

'''An overview of Transformation:'''

Transformation is one of the three methods by which DNA cloning takes place today.

'''Method:'''

1)A a piece of DNA to be inserted  into a vector is selected.

2)The DNA piece is cut with a restriction enzyme

3) The DNA to be inserted is ligated into the vector with DNA Ligase. The DNA insert contains a selectable marker that identifies recombinant molecules.
 
[[File:Dna cloning.gif|centre]]