Dna based nanobioelectronics

DNA based Nanobioelectronics

PRESENTED BY

ROOPAVATH UDAY KIRANM.Tech 1st year

Outline

• Introduction

• DNA based Nanoelectronics

• DNA mediated assembly of Metal nanoparticles

• Sequence specific Molecular Lithography

• DNA detection with Metallic nanoparticles

• The combination of biological elements withelectronics is of great interest for manyresearch areas.

• Inspired by biological signal processes

• To explore ways of manipulating, assembling,and applying biomolecules and cells onintegrated circuits, joining biology withelectronic devices.

INTRODUCTION

The overall goal

• To create bioelectronic devices for biosensing

• Drug discovery

• Curing diseases

• To build new electronic systems based onbiologically inspired concepts

• Having tools similar in size to biomoleculesenables us to manipulate, measure, and (in thefuture) control them with electronics, ultimatelyconnecting their unique functions.

Recent advances in the field

• Electrical contacting of redox proteins withelectrodes.

• The use of DNA or proteins as templates toassemble nanoparticles .

• Use of nanoelectrodes, nano-objects, andnanotools in living cells and tissue, for bothfundamental biophysical studies and cellularsignaling detection and nanowires.

• Functional connection of neuronal signalprocessing elements and electronics in order tobuild brain–machine interfaces and futureinformation systems.

Deoxyribonucleic acid (DNA)• Deoxyribonucleic acid (DNA) is a nucleic acid that

contains the genetic instructions for thedevelopment and function of living organisms.

• DNA is a long polymer made from repeating unitscalled nucleotides. The DNA chain is 22 to 24 Åwide and one nucleotide unit is 3.3 Å long.

• DNA polymers can be enormous moleculescontaining millions of nucleotides. For instance,the largest human chromosome is 220 millionbase pairs long.

DNA Based Nanoelectronics

DNA FOR MOLECULAR DEVICES

• The two- and three-dimensional assembly of complex objects(cubes, octahedral, etc.) made with DNA (Seeman 1998, 2003) ontoorganized chips to recognize and position other biologicalmaterials, with applications in diagnostics and medicine.

• To explore the conductivity of DNA, Alternatively, if measurablecurrents cannot be sustained by DNA molecules, anotherinteresting strategy is to realize hybrid objects (metalnanoparticles/ wires, proteins/antibodies, etc.) in which electronsmove and carry current flows, templated by DNA helices atselected locations This route also allows to embed conductingobjects into the hybrid architectures, to realize, e.g., a carbonnanotube DNA-templated nanotransistor

Both of these ways could lead to the development of DNA based molecular electronics.

WHAT IS KNOWN ABOUT DNA’S ABILITYTO CONDUCT ELECTRICAL CURRENTS?

• We just point out here the salient results thatmotivated the pursuit of optimizedmeasurement setups on one hand, and ofDNA-derivatives and mimics beyond native-DNA on the other hand.

• The desired “mutants” should exhibitenhanced conductivity and/or otherexploitable functions, whereas maintainingthe inherent recognition and structuringtraits of native Watson-Crick DNA that aredemanded for self-assembling.

The molecules used for electronic applicationsneed to express three main features:

(a) Structuring, namely, the possibility to tailortheir structural properties (composition,length, etc.) “on demand”.

(b) Recognition, namely, the ability to attachthem to specific sites or to other targetmolecules.

(c) Electrical functionality, namely, suitableconductivity and control of their electricalcharacteristics.

• One of the main challenges with such molecules,however, is the control of their electrical conductivity.

• Early work in this field has yielded seeminglycontroversial results for native-DNA, showing electricalbehaviours from insulating through semiconducting toconducting, with even a single report of proximity-induced superconductivity.

• Indeed, recent reviews of the experimental literaturehighlighted that the variety of available experimentscannot be analyzed in a unique way; for instance,electrical measurements conducted on single molecules,bundles, and networks, are not able to reveal a uniforminterpretation scheme for the conductivity of DNA,because they refer to different materials or at leastaggregation states.

DNA mediated Assembly of Metal Nanoparticles

DNA - templated electronics

• Sequence-specific molecular lithography.

• The protein RecA, which is normally responsible forhomologous recombination in Escherichia colibacteria, is utilized as a sequence-specific resist,analogous to photoresist in conventionalphotolithography.

• The patterning information is encoded in theunderlying DNA substrate rather than in glass masks.

• Facilitates precise localization of molecular deviceson the DNA substrate and formation of molecularlyaccurate junctions.

A possible scheme for the DNA templatedassembly of molecular-scale electronics

• Homologous recombination• Addresses three major challenges on the way to

molecular electronics.I. Precise localization of a large number of

devices at molecularly accurate addresses onthe substrate.

II. Construction, inter-device wiring.III. It wires the molecular network to the

macroscopic world, thus bridging between thenanometer and macroscopic scales.

There are four major obstacles to the realization of this concept.

• Biological processes need to be adopted and modifiedto enable the in-vitro construction of stable DNAjunctions and networks with well-defined connectivity.

• The hybridization of electronic materials withbiological molecules needs to be advanced to the pointwhere precise localization of electronic devices on thenetwork is made possible.

• Appropriate nanometer-scale electronic devices need tobe developed. These devices should be compatiblewith the assembly and functionalization chemistry.

• Since DNA molecules are insulating, they need to beconverted into conductive wires.

• Homologous recombination is a protein-mediatedreaction by which two DNA molecules, possessing samesequence homology, crossover at equivalent sites.

• RecA is the major protein responsible for this process inEscherichia coli.

• RecA proteins are polymerized on a probe DNA moleculeto form a nucleoprotein filament, which is then mixedwith the substrate molecules.

• The nucleoprotein filament binds to the DNA substrate athomologous probe–substrate locations.

• Note that RecA polymerization on the probe DNA is notsensitive to sequence. The binding specificity of thenucleoprotein filament to the substrate DNA is dictated bythe probe’s sequence and its homology to the substratemolecule.

Sequence Specific Molecular Lithography

DNA molecules were first aldehyde-derivatized by reactingthem with glutaraldehyde.

Sample was incubated in an AgNO3 solution.

The reduction of silver ions by the DNA-bound aldehyde inthe unprotected segments of the substrate molecule resultedin tiny silver aggregates along the DNA skeleton.

The aggregates catalyzed subsequent electroless gold deposition.

Continuous highly conductive gold wire

• RecA-mediated recombination can be harnessed togenerate the molecularly accurate DNA junctionsrequired for the realization of elaborate DNA scaffolds.

• Two types of DNA molecules which were 15 kbp and4.3 kbp long respectively, were prepared.

• The short molecule was homologous to a 4.3 kbpsegment at one end of the long molecule.

• The RecA was first polymerized on the shortmolecules and then reacted with the long molecules.

• The recombination reaction led to the formation of astable, three-armed junction with two 4.3 kbp-longarms and an 11 kbp-long third arm.

DNA Detection

• Through the fast increasing knowledge aboutbiomolecules and their interaction with otherbiomolecules, the study of thosebiorecognition events has become more andmore important.

• One of the most remarkable technologies thathad a strong impact on DNA detection isprobably the DNA chip (or gene chip)technology.

• This allows researchers to conduct thousandsor even millions of different DNA sequencetests simultaneously on a single chip or array.

The DNA chip technology also comes with some limitations.

• The miniaturized probe spots on a DNA chip needexpensive fabrication procedures, which are alsoused in microfabrication.

• The readout of the DNA arrays must beminiaturized. Finally, the detection scheme must besensitive enough to detect just a few copies oftarget and selective enough to discriminate betweentarget DNAs with slightly different compositions.

Solution to the above demerit - DNA Labelling :

• DNA labeled with fluorescent dyes in combinationwith confocal fluorescence imaging of DNA chips hasprovided the high sensitivity needed

• For instance, nowadays many hundreds of diseasesare diagnosable by the molecular analysis of DNA.

• Mainly the DNA hybridization reaction is used forthe detection of unknown DNA, where the target(unknown single-stranded DNA; ssDNA) isidentified, when it forms a double-stranded(dsDNA) helix structure with it complementaryprobe (known ssDNA).

• By labeling of either the target DNA or the probeDNA, the hybridization reaction can be detected byradiochemical, fluorescence, electrochemical,microgravimetric, enzymatic, andelectroluminescence methods

• Fluorescence labeling also allows multicolorlabeling, making possible the multiplexeddetection of differently labeled single-strandedDNA targets on one array.

• However, fluorescent dyes have significantdrawbacks;

• Expensive• Susceptible to photobleaching• Broad emission and absorption bands, which

limit the number of dyes.

These disadvantages have limited the use of DNAchips mainly to specialized laboratories

DNA Detection using Metal Nanoparticles

• These new detection schemes are based on theunique properties of metal nanoparticles, such as

Large optical extinction and scattering coefficients.

Catalytic activity, and surface electronics.

metal nanoparticles have approached as alternativelabels in a variety of DNA detection schemes.

• Most notably, gold nanoparticles have been used for the DNA detection, because they can be easily modified with biomolecules.

• However, other metal nanoparticles, such as Ag, Pt, and Pd, have also been used for DNA detection

Label-Free, Fully Electronic Detection of DNA with aField-Effect Transistor Array

• Field-effect sensors, especially FETs, offer an alternativeapproach for the label-free detection of DNA with a directelectrical readout .

• Recently, the detection limit of potentiometric field-effect sensors was enhanced such that single nucleotidepolymorphisms (SNPs) were successfully detected.

• The sensors used the field-effect at the electrolyte-oxide-semiconductor (EOS) interface, which was firstlydescribed for ion-selective field-effect transistors (ISFET).

• Typically, the response of such devices is interpreted asshift of the flat-band voltage of the field effect structure

• Most of these sensor chips were operated aspotentiometric ISFETs and used the ion-selectivity of thesolid–liquid interface or artificial molecular membranes,which were attached to the FET gate structure.

• In this context, the dc as well as the ac readout of theFETs has been reported and the influence of abiomembrane attached to the transistor gate structurehas been described.

The ISFET structure can be highly integrated to multichannelsensors by using standard industrial processes.

• A miniaturized, low-cost, fast readout, highly integrated,and addressable multichannel sensor with sensitivity highenough to detect SNPs, would be the ideal device forgenetic testing and medical diagnostics.

Last but not least

• the other way to pursue DNA-basednanoelectronics is by looking at derivatives thatmay exhibit intrinsic conductivity better than thedouble helix. One of the most appealingcandidates in the guanine quadruple helix G4-DNA.

• Other viable candidates are DNA hybrids withmetal ions and double helices in which the nativebases are substituted with more aromatic basesthat may improve the longitudinal π-overlap

Applications of Hybrid Nanobioelectronic systems

• Nanoelectronics for the future. The fascinatingworld of the bio–self-assembly provides newopportunities and directions for future electronics,opening the way to a new generation ofcomputational systems based on biomolecules andbiostructures at the nanoscale.

• Life sciences. Rapid pharmaceutical discovery andtoxicity screening using arrays of receptors on anintegrated circuit, with the potential to developtargeted “smart drugs.”

• Medical diagnostics. Rapid, inexpensive, andbroad-spectrum point-of-use human and animalscreening for antibodies specific to infections

• Environmental quality. Distinguishing dioxin isomers forcleaning up polluted sites, improving productionefficiency of naturally derived polysaccharides such aspectin and cellulose, and measuring indoor air qualityfor “sick” buildings.

• Food safety. Array sensors for quality control and forsensing bacterial toxins.

• Crop protection. High-throughput screening of pesticideand herbicide candidates.

• Military and civilian defense. Ultrasensitive, broad-spectrum detection of biological warfare agents andchemical detection of antipersonnel land mines,screening passengers and baggage at airports, andproviding early warning for toxins from virulent bacterialstrains.

References:

• Nanobioelectronics - for Electronics,Biology, and Medicine – Edited by Andreas Offenhausser and Ross Rinaldi.

• Nanobiotechnology Concepts, Applications and Perspectives Edited by Christof M. Niemeyer and Chad A. Mirkin.

• Yubing Xie - The nanobiotechnologyhandbook-CRC Press – Taylor - Francis (2013)