Nano-biotechnology

Cell biology and biomedicine primarily deal with functional entities such as DNA , proteins. Mimicking these structures and functions in the nanosize range offers exciting opportunities for the development of biosensors, biochips, and bioplatforms. Pathogenic agents including E. coli, S.aureus, S. typhimurium, T. Gondi as well as viral, fungal or parasitic organisms, being ubiquitous, microscopic living organisms lead to the pathogenesis of infectious as well as chronic diseases such as Meningitis, Gastro-instestinal tract disorders, Diarrhea in addition to certain forms of Cancer, Coronary Artery Diseases , Multiple Sclerosis and Chronic Pulmonary Infection and are accountable for a major single cause of estimated (50 million) annual worldwide deaths. [2],[3].

Recent trends in biological warfare involve the use of pathogens ,B. anthracis ,as potential bio-weapons, utilized with the intention to kill, incapacitate or impede an adversary and are of particular concern as they are highly resistant to environmental stress and are relatively easily produced into weapon-grade material outside the laboratory. Bioterrorism being difficult to predict or prevent, reliable platforms to rapidly detect and identify the biothreat agents are important to minimize the spread of these agents and to protect the public health and human safety. These platforms must not only be sensitive and specific, but must also be able to accurately detect a variety of pathogens, including modified or previously uncharacterized agents, directly from complex sample matrices. [4]. Thus the prophylactic measures to prevent the pathogenesis of the microbial infections is of paramount importance. the accurate identification and rapid detection of these pathogenic agents play a pivotal rule in regulation and control of caused as well as natural outbreaks of infectious diseases, clinical medicine, food safety and environmental monitoring. The modern antimicrobial arsenal consists of antibiotics (viral and microbial), disinfectants, sanitizers and various drugs. Despite the plethora of these existing measures, the viral and fungal diseases being more defiant to the treatment, it is the microbial infections that are treated commonly and often one encounters the appearance of multi-drug resistant bacteria due to improper use of the above treatment. The current detection, diagnosis and enumeration technology utilizing biochemical, immunological, nucleic acid, and bioluminescence procedures [6] being relatively inefficient , require millions of copies of virus/bacteria to be present in a milli-liter(ml) of blood for accurate results besides being time consuming and labor intensive. [6].This need for an efficient, rapid detection method can be fulfilled by the emerging nanobio sensors, an amalgamation of signal transducers and bio-components or biorecognition element which promise early detection of a single virus, bacteria, or pathogen in simple, inexpensive, and ubiquitous tests alongwith more effective prevention. Nanotechnology refers to research and technology development at the atomic, molecular, and macromolecular scale, leading to the controlled manipulation and study of structures and devices with length scales in the nanometers range. The nanoparticles possess novel properties and functions that differ markedly from those seen in the bulk scale. Miniaturization of biosensors enables the integration into Hazard Analysis and Critical Control Point programs, enabling critical microbial analysis of the entire food manufacturing process.[8]. The novel properties of nanomaterials such as the size, surface tailorability, improved solubility, and multifunctionality offer the ability to interact and operate with complex biological functions in new ways and enable fast or real-time detection, portability, and multipathogen detection for both field and laboratory analysis. [7]. Magnetic nanobiosensors exhibiting high specificity and biocompatibility have been synthesized for the in vitro and in vivo detection of molecular interactions. and could also be useful as generic biosensors in variety of applications such as immunogenecity assays, affinity ligand determination for rapid magnetic resonance of arrays, DNA analysis and target delivery of anti-cancerous drugs. [12], [9]. These biosensors have several potential advantages over other methods of analysis, including sensitivity in the range of ng/mL for microbial toxins and < 100 colony-forming units/mL for bacteria. Fast or real-time detection can provide almost immediate interactive information about the sample tested, enabling users to take corrective measures before consumption or further contamination can occur.[7]. Sensitive and cost-effective biosensors are important for high throughput pathogen detection in un-modified biological samples and in-vivo.[9]. The usage of magnetic nanoparticles as label in immunodiagnostic assays is based on the principle of specificity of binding and immunocomplex formation between the antigen and the antibody and is used to measure the analyte concentration indirectly. Controlled fabrication of functionalized nanostructures involve the development of assemblies of inorganic materials with biomolecules.[13]. The biocompatible magnetic nanosensors have been designed to detect molecular interactions in biological media. Upon target binding, these nanosensors cause changes in the spin-spin relaxation times of neighboring water molecules, which can be detected by magnetic resonance (NMR/MRI) techniques. These magnetic nanosensors have been designed to detect specific mRNA, proteins, enzymatic activity, and pathogens (e.g., virus) with sensitivity in the low femtomole range (0.5-30 fmol).[10].External magnetic fields can be used to manipulate and control the mnps. Gold and iron-oxide based Nanoparticles possessing native properties such as excellent biocompatibility, reduced size, ease of transport over large distances, stability , low toxicity combined with hitherto established synthesis , assembly, modification and attachment protocols prove promising in the biotechnological applications of highly sensitive and specific sensors for bacterial detection. [12]. The composite bifunctional nanomaterials inherit the attributes of robust surface chemistry, special optical properties, super paramagnetic properties thus enhancing the potential and broaden specific applications on coating the surface/ synthesis of magnetic nanoparticles with gold.[11]. The utility of the magnetic nano-biosensors for prophylactic, diagnostic and therapeutical applications in clinical assessment shows great promise.

Recent trends in biological warfare involve the use of pathogens ,B. anthracis ,as potential bio-weapons, utilized with the intention to kill, incapacitate or impede an adversary and are of particular concern as they are highly resistant to environmental stress and are relatively easily produced into weapon-grade material outside the laboratory. Bioterrorism being difficult to predict or prevent, reliable platforms to rapidly detect and identify biothreat agents are important to minimize the spread of these agents and to protect the public health and human safety. These platforms must not only be sensitive and specific, but must also be able to accurately detect a variety of pathogens, including modified or previously uncharacterized agents, directly from complex sample matrices. [4]. Thus the prophylactic measures to prevent the pathogenesis of the microbial infections is of paramount importance. the accurate identification and rapid detection of these pathogenic agents play a pivotal rule in regulation and control of caused as well as natural outbreaks of infectious diseases, clinical medicine, food safety and environmental monitoring. The modern antimicrobial arsenal consists of antibiotics (viral and microbial), disinfectants, sanitizers and various drugs. Despite the plethora of these existing measures, the viral and fungal diseases being more defiant to the treatment, it is the microbial infections that are treated commonly and often one encounters the appearance of multi-drug resistant bacteria due to improper use of the above treatment. The current detection, diagnosis and enumeration technology utilizing biochemical, immunological, nucleic acid, and bioluminescence procedures [6] being relatively inefficient , require millions of copies of virus/bacteria to be present in a milli-liter(ml) of blood for accurate results besides being time consuming and labor intensive. [6].This need for an efficient, rapid detection method can be fulfilled by the emerging nanobio sensors, an amalgamation of signal transducers and bio-components or biorecognition element which promise early detection of a single virus, bacteria, or pathogen in simple, inexpensive, and ubiquitous tests alongwith more effective prevention. Nanotechnology refers to research and technology development at the atomic, molecular, and macromolecular scale, leading to the controlled manipulation and study of structures and devices with length scales in the nanometers range. The nanoparticles possess novel properties and functions that differ markedly from those seen in the bulk scale. Miniaturization of biosensors enables the integration into Hazard Analysis and Critical Control Point programs, enabling critical microbial analysis of the entire food manufacturing process.[8]. The novel properties of nanomaterials such as the size, surface tailorability, improved solubility, and multifunctionality offer the ability to interact and operate with complex biological functions in new ways and enable fast or real-time detection, portability, and multipathogen detection for both field and laboratory analysis. [7]. Magnetic nanobiosensors exhibiting high specificity and biocompatibility have been synthesized for the in vitro and in vivo detection of molecular interactions. and could also be useful as generic biosensors in variety of applications such as immunogenecity assays, affinity ligand determination for rapid magnetic resonance of arrays, DNA analysis and target delivery of anti-cancerous drugs. [12], [9]. These biosensors have several potential advantages over other methods of analysis, including sensitivity in the range of ng/mL for microbial toxins and < 100 colony-forming units/mL for bacteria. Fast or real-time detection can provide almost immediate interactive information about the sample tested, enabling users to take corrective measures before consumption or further contamination can occur.[7]. Sensitive and cost-effective biosensors are important for high throughput pathogen detection in un-modified biological samples and in-vivo.[9]. The usage of magnetic nanoparticles as label in immunodiagnostic assays is based on the principle of specificity of binding and immunocomplex formation between the antigen and the antibody and is used to measure the analyte concentration indirectly. Controlled fabrication of functionalized nanostructures involve the development of assemblies of inorganic materials with biomolecules.[13]. The biocompatible magnetic nanosensors have been designed to detect molecular interactions in biological media. Upon target binding, these nanosensors cause changes in the spin-spin relaxation times of neighboring water molecules, which can be detected by magnetic resonance (NMR/MRI) techniques. These magnetic nanosensors have been designed to detect specific mRNA, proteins, enzymatic activity, and pathogens (e.g., virus) with sensitivity in the low femtomole range (0.5-30 fmol).[10].External magnetic fields can be used to manipulate and control the mnps. Gold and iron-oxide based Nanoparticles possessing native properties such as excellent biocompatibility, reduced size, ease of transport over large distances, stability , low toxicity combined with hitherto established synthesis , assembly, modification and attachment protocols prove promising in the biotechnological applications of highly sensitive and specific sensors for bacterial detection. [12]. The composite bifunctional nanomaterials inherit the attributes of robust surface chemistry, special optical properties, super paramagnetic properties thus enhancing the potential and broaden specific applications on coating the surface/ synthesis of magnetic nanoparticles with gold.[11]. The utility of the magnetic nano-biosensors for prophylactic, diagnostic and therapeutical applications in clinical assessment shows great promise.

Nano-biomaterials- An introduction

The rapidly burgeoning field of ‘nano-biotechnology’ reflects a growing opportunity for materials scientists and researchers ,to get the best of both worlds by forming novel combinations of biological and nonbiological molecules. Indeed, one implication seems to be that at such small scales, the biological and nonbiological materials are often indistinguishable. The hybrid nano-biomaterials are a specific class of materials that combine biological entities such as DNA, proteins with the artificially engineered nano scale particles.

The belief, supported by a wealth of evidence, is that nano-scaled inorganic materials can exhibit mechanical, electrical, and optical properties that are not manifested by their more macroscopic or smaller atomic counterparts. For example, nanocrystals or quantum dots are excellent candidates for novel optical devices as they exhibit highly efficient, size-tunable optical emission. Of special importance are the intrinsic properties such as the large surface-to-volume ratio of these nanostructured materials makes them particularly suitable as high-sensitivity sensors or as efficient new catalysts.

In addition, nanotechnological innovations in micro/nanofluidics show great promise in sensing applictions in environmental as well as clinical diagnosis.

Natural, nano-scaled building blocks being abundant in the biological world, exhibiting amazing specificity in recognition of other molecules combined with the commonality of scale and the rapid technological progress to integrate the organic & the inorganic materials promises to transform our ability to engineer novel nano-biomaterials possessing tremendous capability and utility.

Nanoparticles disambiguated

What exactly is a nanoparticle? what kind of research does that entail? ain’t nanoparticle not a chemical? and then should this not be classified under chemistry and not biology? how do you use nanoparticles? is this got applications in nanocomputing?

these are common qns that I pretty often (even during bar chats!)…anyways, a good answer to these and especially the applications part can be found on this great article/paper. A must read if you have questions related to the above. If you got any qns, feel free to email me. Happy to discuss and assist.

the microbe blog- an interesting read

As almost every other day, spent today general surfing the net for microbes and nanoparticles. And guess what I found today, a very interesting site on microbes..interstingly called the microbe blog and witting titled as ’small things considered’. Its got quite amazing posts with a neutral view of things, especially when it comes to phylosophy behind small things. Oh well, don’t want to get started on that- well worth a good write.

For the impatient (and that’s me later visiting my own pages), here are some of the goodies that look good on fist glance. Worth a read later:

Pathogens:http://schaechter.asmblog.org/schaechter/pathogens/index.html

Evolution:http://schaechter.asmblog.org/schaechter/evolution/index.html

Antibody-Nanoparticle Computational Modeling

The conjugation of antibodies and nanoparticles with high affinity & specificity through receptor-ligand recognition modes is of paramount importance in the development of vehicles which can be used for diagnosis, treatment of cancer and various other diseases, application of immudiagnostic nano-biosensors etc. The bio-nanocomplex formed by an artificial nanomaterial (nanoliposomes , nanoparticles ) and a biological entity such as an antibody is brought about by the formation of covalent bonds based on their specific chemical and structural properties such as water solubility, biocompatibility, and biodegradability. [5]. There is a requirement of a comprehensive understanding of the relationship of the thermodynamic & kinetic aspects of antibody-membrane association, translational , rotational mobilities of membrane bound antibodies, interactions with the diverse cell surface , circulating molecules and various artificial nanomolecules as well as the conformation. These details are of great importance in the development, application of various nanoscale immunodiagnostic devices. The association of antibodies with cell surfaces is a key molecular event in antibody-mediated immune mechanisms such as phagocytosis, antibody mediated immune dependent cell-mediated cytotoxicity.[6].

The interfacial properties,especially the dynamic, thermodynamic, and mechanical properties, at different spatial and temporal resolutions of these bio-nano systems can be readily investigated with the aid of computer simulations, which consist of studies of interactions of the proteins as well as those of various nanomaterials with organic biological molecules such as proteins, nucleic acids, membrane lipids, and water and of significance importance is the study of the interactions of nanoparticles in the protein binding sites and optimization of the same for improved bio-nano recognition. [4].

Recently it has been noted that there exists certain natural proteins, antibodies, that can recognize specific nanoparticles . For example, a specific antibody from the mouse immune system can specifically recognize derivatized C₆₀ fullerenes with a binding affinity of about 25 nM [5]. From the studies carried out by Noon et al, it is hypothized that the fullerene-binding site is formed at the interface of the light and heavy chains lined with a cluster of shape-complementary hydrophobic amino acid residues. As the covalent modifications of the functionalized fullerenes, occupy only a small fraction of the particle surface area , the largely unoccupied surface would be free to interact with the antibody.

Therefore, in order to gain in-depth understanding of the detailed interactions of the nps and the antibody, molecular dynamics simulation is carried out using molecular dynamics simulation; the purpose of our theoretical modeling studies is to be able to identify the energetically favorable binding modes. [4].

For the modeling study, the initial coordinates of the antibody can be made available from the Protein Data Bank (PDB). [5], [7]. The coordinates of the nanoparticle in this case , would be obtained from the AFM, TEM studies carried out at the AMERI and Nano-biotechnology laboratory, FIU, Miami. The CHARMm (Chemistry at HARvard Macromolecular Mechanics) an Unix-based commercialized software using Fortran 77 source codes uses set of force fields for molecular dynamics for simulation and analysis.[3].

The basic assumptions, as a first approximation, during the modeling study would be that the hydrophilic derivatizations do not play a critical role in the predominantly hydrophobic nanomaterial-antibody interactions and that the electronic structure remains undisturbed during the conjugation. The nanoparticle is docked into a suggested binding site from the previously done literature studies.[5]. Polar-hydrogen potential function (PARAM19) and a modified TIP3P water solvent model for the protein is used.[1].

The simulation involves approximately about 300 steps of minimization, using the Steepest Descent and the Newton Raphson method. To reduce the necessary simulation time, a highly efficient method for simulating the localized interactions in the active site of a protein, the stochastic boundary molecular dynamics (SBMD) is used. The reference point for partitioning the system in SBMD was chosen to be near the center of the nanomaterials, which is assumed to be an unifom sphere.The complex nano-bio system can be assumed to be separated into spherical reservoir and reaction zones; the latter is further sub-divided into a reaction region and a buffer region. The atoms in the reaction region are propagated by molecular dynamics, whereas those in the buffer region involve Langevin dynamics are retained using harmonic restoring forces .

References:

1. http://www.ocms.ox.ac.uk/mirrored/xplor/manual/htmlman/node65.html
2. Brunger et al. “Trypsinogen-Trypsin Transition: A Molecular Dynamics Study of Induced Conformational Change in the Activation Domain”
3. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983). “CHARMM: A program for macromolecular energy, minimization, and dynamics calculations“. J Comp Chem 4: 187–217.
4. Noon et al “Molecular dynamics analysis of a buckyball-antibody complex”
5. Braden et al . “X-ray crystal structure of an anti-Buckminsterfullerene antibody Fab fragment: Biomolecular recognition of C₆₀ “ (2000) Proc. Natl. Acad. Sci. USA 97, 12193-12197
6. Pisarchick et al. “Binding of a monoclonal antibody and its Fab fragment to supported phospholipid monolayers measured by total internal reflection fluorescence microscopy”.
7. http://www.rcsb.org/pdb/home/home.do

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