Dr. Syed Arshad Hussain Wellcomes You

Immobilization of single strand DNA on solid support

Recently we have demonstrated the immobilization of single strand DNA onto a solid support by electrostatic interaction with a polycation poly(allylamine hydrochloride) (PAH). The films were analyzed by UV–vis spectroscopy. We have shown that single stranded DNA gets immobilized on the PAH backbone of Layer-by-Layer (LbL) films when the films are fabricated above the melting temperature of DNA. Singly stranded DNA immobilized in the LbL films is not restored into double stranded DNA at room temperature.

Read the article here at Chemical Physics Letters

SEM image of 10 layer RB-PAH LbL films

SEM image of RB-PAH LbL films

AFM image of hectorite assembled onto quartz slide by Langmuir-Blodgett Technique



Can we see the atom or something of nano dimension?

            Twenty five years ago, this question was often met with amazement by common people and with scepticism by the teaching community. The answer may be ‘atom is something which is not really visible’. But nowadays, it’s a common phenomenon to visualize the atom, even seeing them moving. Its not really a challenge to see the atom but to know and visualize how they are arranged within matter. This is because it’s the arrangement of that determines the properties of materials- their hardness, ductility, brittleness, strength and the catalytic properties.

             With our eyes we can see a fraction of a millimeter, let’s say one tenth of a millimeter or one hundred micrometers which is a little more than the diameter of a single hair. If we want to see at smaller scales than this, we use a lens. The lens bends the light rays or refracts and the object appears larger. Optical microscopes work on this principle. Lenses work well as long as we do not have to work at scales smaller than the wavelength of light which is about half a micrometer. This is because the smallest object that can be seen with waves of wavelength  is about  in dimension (the Rayleigh criterion). At this scale, we have to take into account the wave nature of light, so things are different. Optical microscopes help us to image about hundred times smaller than what we can see with our naked eyes. If we want to track a molecule or a particle that is still smaller, we can improve the resolution by labeling it with a fluorescent molecule. The fluorescence can be detected and we can follow the movement of the molecule or particles in liquids for example. If we need higher resolution, we can use electrons instead. Modern electron microscopes can let us see the arrangement of atom within the matter.  Thinking of electrons one might be puzzled as to how electrons, which are particles, can be used to image things at very small scales. At small scales things are different, drastically different. It’s the realm of quantum physics. Quantum particles propagate like waves and interact like particles. When the sample is thin enough and the electron comes in at high speed it can go through the sample. The path of the electron can be influenced by magnetic and electric fields and this effect is used in producing lenses for electrons. The advantage of electrons is that their wavelength is several orders of magnitude smaller than optical wavelengths and the microscope resolution is not limited by the wavelength but by the performance of the lenses. The wavelength of an electron is related to its velocity by  (de Broglie’s equation non-relativistic),  is the Planck’s constant,  and  are the mass and the velocity of the electron respectively. Now if  is greater than 80% of the speed of light, then  is less than  of the atomic dimension. With electron microscopes we can increase the resolution by more than a factor of thousand when compared to optical microscopes. We can see one tenth of a nanometer with a high resolution electron microscope, the length scale of the atom world. We can see planes of atoms. Electrons are also reflected off and in fact there is a type of electron microscope that works in reflection mode (SEM). SEM’s have about ten fold smaller resolution than TEMs. The drawback of electron microscopes is that electrons are charged and we need vacuum environment in order for the electrons to propagate freely. There are SEMs available today that do not need high vacuum and can function in a partial nitrogen or argon atmosphere with reduced resolution. This makes it particularly interesting to observe growth processes at the nanometer scale. Non conducting samples are more difficult to observe with electrons and often need to be coated with a conducting metal layer. The electron microscope also needs a high voltage generator (10kV to several 100kV) to accelerate the electrons. All together electron microscopes are rather large instruments.

For example, in silicon nitride ceramics the arrangement of lanthanum ( ) atoms (arrowed in figure 1) at the interface between a glassy film (top) and a silicon nitride crystal (bottom) is shown. The  atoms play a role in controlling the path of cracks as they pass through the silicon nitride ceramic.


Figure 1: The interface between a silicon nitride crystal (bottom) and a glass (top) in a silicon nitride ceramic. The bright atoms at the interface are La, used to engineer the strength of the interface.

            However it is the Atomic Force Microscope (AFM) (Nobel prize in 1986 for Binning and Rohrer for the fundamental Scanning Tunnelling Microscope) made revolutionary advancement towards the visualization of nanometer order and atomic dimension. The AFM works in the same way as our fingers which touch and probe the environment when we cannot see it. By using a finger to “visualize” an object, our brain is able to deduce its topography while touching it. The resolution we can get by this method is determined by the radius of the fingertip. To achieve atomic scale resolution, a sharp tip (radius ~1-2 nm) attached to a cantilever is used in the AFM to scan an object point by point and contouring it while a constant small force is applied to the tip. With the AFM the role of the brain is taken over by a computer, while scanning the tip is accomplished by a piezoelectric tube.

 Figure 2: The principle of Atomic Force Microscopy


The atomic force microscope got its name from the interactions between probe and sample on the atomic level The attractive Van-der-Waals-forces and repellent equal electric charges are described by the Lennard- Jones- potential. The AFM is based on a relatively simple mechanical principle: if you drag a very fine and flexible pointed needle (called a cantilever) over uneven surface, then the forces acting on the cantilever will be directly related to the displacements (deflections) of the cantilever. These deflections can be measured by shining an ultra sensitive laser on the tip of the cantilever and looking for changes in the reflected beam as the cantilever changes its position slightly. Under ideal conditions, this technique allows lateral resolution on the atomic level. The vertical resolution is below 0,1 nm.