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Volume 1, December 2016, pages 35-42

Entanglement of wide variety of biomolecules as molecular switches in Bioelectronics

Ashish Katyal1*, Manjeet Singh2

1*Department of Biotechnology, Meerut Institute of Engineering and Technology, Meerut, Uttar Pradesh, India
2Department of Computer Science & Engineering, Galgotias University, Greater Noida, Uttar Pradesh, India


* Corresponding Author Email: aashishkatyal@gmail.com  | Tel: +919997031901

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Abstract

Molecular electronics (ME) is the branch of nanotechnology used to study molecules that act as primary building block for electronic circuitry. It is a molecular based approach that enables us to construct very small circuits as compared to conventional semiconductors such as silicon. The movement of the electrons in such circuit is inherently governed by quantum mechanics. There are different types of molecules; such as organic compounds which has shown promising entity for ME. These are a new class of small biomolecules which are non-protein coding such as microRNAs (miRNAs) responsible for controlling gene expression post-transcriptionally by binding to  various mRNA targets and acting as molecular switches in the regulatory pathways which involves thousands of transcripts. Now a day's organic molecules are considered as a potential candidate for ME because of their ease of access and great structural flexibility and diversity along with possession of suitable electronic and mechanical properties. Due to these reasons organic molecules are majorly used for the fabrication of electronic devices at the nano-scale In  this paper, we are presenting the various strategies that are involved for the development and application of organic switches towards Molecular electronics.

Keywords

Molecular switches, Nanotechnology, mRNA targets, Molecular electronics, Biomolecules, Gene expression

Introduction

Nanotechnology consists of various branches which include Molecular electronics (ME) that act as building blocks in electronic fabrication of biological or organic materials (Divigalpitiya et al. 1989). Sometimes, mimicking of macroscopic devices are done for instance in conventional computing and digital information storage is the condition of having clearly different state, but it only deals with 0 and 1 bit values (Figure 1).
When structure of Molecular switches changes it results into changes in physical and chemical properties of the switch due to this reason conformational, configurational and/or oxidation-state changes are strictly observed in molecular switches (Dickson et al. 1997). There are certain physical (mechanical stress, temperature,  electromagnetic radiation, electric fields) and chemical parameters (pH, redox reagents, coordination processes.) that are kept in mind for designing these molecular switches, any transition of these parameter from initial to final states results into changes  in overall properties of molecular switch.
In general, Molecular switches are linked to the surface of corresponding  device,  independent  of  switching  properties of molecule in the solution(known as intrinsic switching) which is helpful in controlling   of behavior of    the system  while on the other hand switching properties are not   maintained while attached to the surface (known      as extrinsic switching).
In case of electron transport (ET) via organic molecules, two limiting situations can be considered: (a) superexchange and (b) charge carriers hopping processes (Figure   3)
There is a wide range of methodology available for organic based compound which involves change in structural conformations (due to flexibility) in molecular electronics. A range of organic molecules are used in hybrid organic switches (organometallic structures) whose properties lies  in  between  organic  and  metallic  structures.  In  this  study, our work is focused on pure organic materials (mainly single molecule) that are used in switching  process.  When a molecule undergoes geometrical change (which involves rotations through single bond) at low energy it controls the electron  transport through molecules (Morise et al.   1974).
There are four types of Molecular switches based on
1.1. Conformational change
These switches are used to control the conductivity in  a molecular  device  by inducing  change  in  the  geometry of  the molecule (Figure  4).
1.2. Configurational change
It involves changes of a molecule that are related to bond breaking and forming reactions, and therefore higher interconversion  barriers  are  required  compared  with  conformational changes.  These includes:
1.2.1. Optoelectronic switching
These are the molecules that are able to change reversibly their configuration by exposure to light of specific frequencies  are  known  as  photochromic molecules.
1.2.2. Azobenzenes
Azobenzenes have been widely studied due to their simple  structure  and  their  reversible  cis–trans photoisomerization. Irradiation with ultraviolet (350 nm) and blue (440 nm)  light  induces  isomerization  to  metastable cis  (off  state)  and stable  trans (on state) configurations  respectively (Figure   5).
1.2.3. Dithienylethenes and related compounds
These are compounds that  are able to switch between an open and a closed isomer upon photoexposure with    light at 300–400 nm, and from closed to open form at 500–700 nm (Irie et al. 2002). These compounds have exceptional thermal stability and fatigue resistance, finding applications in solid-state devices (Figure 6).
1.3. Red–Ox processes
It involves oxidation or reduction of an organic switch that usually related to substantial changes in the corresponding HOMO–LUMO gaps, and with the electron transport (ET) transparency through them. These includes:
1.3.1. Off/on reversible voltage-driven  switches
The bipyridinium derivatives, called viologens, are good candidates for redox-based switches. A viologen-based device is then able to change from the off to the on state depending on the charge or discharge of its organic framework (Figure 7).
1.3.2. On/off reversible voltage-driven switches. NDR devices
When a voltage is applied between two electrodes an electric  field  is  generated  affecting  the  molecule  energy levels. At high voltages, a misalignment of the originally aligned molecular levels  takes  place  with  a consequent  drop in conductivity for the global system (Figure  8).
1.3.3. On/off irreversible voltage-driven switches.  molecular  fuses
Voltage dependent irreversible molecular systems working exclusively in the on/off sense could emulate a macroscopic fuse, and they could be potentially useful in many applications such as binary components of Read Only Memories (ROMs) (Figure 9).
1.4. Mechanically induced switching
These involves molecules that can respond to mechanical stress which resulted in to change in geometry, conformation, configuration or sometimes connectivity. When they are connected to a metallic surface such changes can also be translated to the electronic states of the surface (Figure   10).
1.5. Miscellaneous category
It includes:
1.5.1. Switches based on tautomerization reaction
These switches are associated with ME and it involve a change in original molecular backbone (which involve geometrical distortion in length, shape or volume) which turned out to be its major drawback (Figure 11).
1.5.2. Built-on molecular wires. Off–on irreversible  switches
These are Complex molecular switches having suitable anchoring groups which allow the chemisorption onto conducting  substrates  (Figure 12).
1.6. Application of Molecular Switches in Bioinformatics
In recent study miRNAs have  been  found  to  play an  important  role  in  cancer.  Bioinformatics  search algorithms and  databases  are mostly  used  for  the  identification  of  a  large  number  of  novel  miRNAs. These  miRNA  act as molecular switches  also known as ‘‘miRNA switches’’ which control signaling pathways by switching them  in on   and off mode. In case of metabolic pathways  analysis miRNA is included to complete protein-protein or protein-   small molecule interaction for example A genetic interactome of the let-7 microRNA in C. elegans (Rausch et al. 2015).These networks help us in understanding of the roles of miRNAs in normal physiology, pathophysiology and cancer chemotherapy in similar fashion to pharmacogenomics. Bioinformatics play an  important  role  in  designing of miRNA microarrays which is helpful for cancer prognosis and selection of chemotherapy (Figure 13).

Conclusion

Current research on molecular switches has shown fruitful results in terms of applications and proof of principle. Sometimes ambiguities come during management of nanometric objects which further involves integration into functional devices. The development of molecular switches will replace silicon based technology due to  their  structural flexibility and different electronic properties (Castro et al. 2007). In this paper  we have studied various  types of molecular switches based  on  conformation,  configuration,  redox  properties,  mechanical  stress  and  voltage dependence. After identification and validation of human miRNAs it has become obvious that these tiny molecules can play a vital role as molecular switches that will turn on and off the expression of specific proteins.

Acknowledgement

Authors are thankful to the Department of Biotechnology, MIET, Meerut for providing infrastructure and financial support for the project.

References

  1. Castro E, Novoselov K, Morozov S, Peres N, dos Santos J, Nilsson J, Guinea F, Geim   A, Neto  A.2007. Biased bilayer graphene: semiconductor with a gap tunable by the electric field effect. Phys Rev Lett. 99.
  2. Dickson RM, Cubitt AB , Tsien RY, Moerner WE.1997.On/off blinking and switching behaviour of single molecules of green fluorescent protein. Nature. 388, 355-358.
  3. Divigalpitiya W, Frindt R, Morrison S.1989.Inclusion systems of organic molecules in restacked single-layer molybdenum Disulfide. Science. 246:369-371.
  4. Irie M, Fukaminato T, Sasaki T, Tamai N, Kawai T.2002.Organic chemistry: A digital fluorescent  molecular  photoswitch. Nature. 420:759-760.
  5. Morise H, Shimomura O, Johnson F, Winant J.1974.Intermolecular energy transfer in the bioluminescent system of Aequorea. Biochemistry. 13:2656-2662.
  6. Rausch M, Ecsedi M, Bartake H, Müllner A, Grosshans H.2015. A genetic interactome of the let-7 microRNA in C. elegans. Developmental Biology. 401:276-286.