8. Bionanoscience - Helsinki

8. Bionanoscience

[Poole-Owens 12; Niemeyer, Mirkin: Nanobiotechnology]

The controlled design of biological molecules on the nanometer scale to achieve desired structures

or functionalities can be called bionanoscience or nanobioscience.

- But conventional biochemistry of course deals with the same kind of size scale, so defining bionano

is quite difficult...

- In addition to the actual control of biological molecules themselves, also for instance:

- Human Implant coatings (e.g. DLC on hip coatings)

- Modifying inner surface of stents to change blood adhesion

- Lab-on-a-chips for analysis of biological substances

- Interactions between living organisms and nanostructures

are at least in some sources considered nanobioscience.

Introduction to Nanoscience, 2005 JJ J � I II × 1

Since nature is in some respects (most dramatically in replication) ahead of human nanoscience, it

is also natural to think whether humans can learn from nature.

- Materials which somehow mimic natural materials are called biomimetic.

- In this section we will first present the basic structure of the two main building blocks of

nanomatter, proteins and DNA

- Then in this and the next section I will give a couple of examples of bionanoscience topics.

8.0.1. Size range of biological objects

It is of immediate nanoscience interest to consider what size and mass range biological nanoparticles

have.

Here is a list of several possibilities. The masses are given in units of Daltons (Da), which is just

g/mol i.e. the same as one atomic mass unit (u).


- The basic building blocks of proteins are the amino acid molecules, which are quite small, sub-nm

(see Table).

- Proteins can come in a wide variety of sizes and shapes, here is four examples:

- Viruses are small containers of genetic information RNA or DNA), not really alive

- Example: polymyelitis virus, one of the smallest ones: about 30 nm diameter i.e. exactly nanoscale

object:


- Bacteriophages are somewhat larger viruses.

- E.g. bacteriophage of size 40 nm head and tail that is 100nm × 13 nm.

can not reproduce independently, but has moving parts: it injects its DNA into a the cell


Actual living cells and their main parts are already much larger in size scale (and hence can not be

considered nanostructures):


8.1. Proteins

[Poole-Owens 12, http://www.people.virginia.edu/ rjh9u/]

Proteins which make the basic building block of most of a cell and thus living organisms are quite

complex objects.

The basic so called primary structure is simple. Proteins are composed of 20 amino acids.

Each of these has the following basic structure:

where for the neutral form the NH2 is the amino group, and the COOH is the acid group. R1 is

the characteristic group which changes from one amino acid to the next.

Note that placement of one of the H’s is a bit arbitrary, either as COOH + NH2 or COO + NH3


Here is a list of all of them:

[http://www.people.virginia.edu/~rjh9u/aminacid.html

The eight amino acids in the orange area are nonpolar and hydrophobic. The other amino acids are polar and hydrophilic (”water


loving”). The two amino acids in the magenta box are acidic (”carboxy” group in the side chain). The three amino acids in the

light blue box are basic (”amine” group in the side chain)

These are joint together in the following kind of reaction:

=⇒ =⇒ =⇒

=⇒ =⇒ =⇒

- The C-N bond is called a peptide bond


- Repeating this reaction forms a polypeptide chain.

- The polypeptide chain without consideration of the R groups is called the (protein) backbone.This is often plotted as a band-like structure.

- This chain does not stay linear, though.

- Reason: ionic and hydrogen bonds between adjacent and non-adjacent amino acids make it

energetically preferential to find a denser shape.

- The secondary structure is either a so called alpha helix or a so called beta sheet (backbone

plotted as band):


- In both of these hydrogen bonds between the NH in one amino acid and the O in the C=0 part

of another are formed which keep the structure stable.

- These are then curved up into a tertiary structure whose stability is maintained via disulfide


bonds formed between two cysteine amino acids (this is the only one with sulfur S in the end, most

other contain only H, C, O and N, and in methionine the sulfur is not at the end).

Finally in the largest proteins the tertiary structure forms an even larger overall quaternary structure.

Apparently in modern usage protein complex is often preferred over quaternary structure


8.2. DNA

DNA is of course the encoder of genetic information.

It consists of a sugar-phosphate backbone consisting of alternating groups of deoxyribose sugar

and phosphate molecules.

The genetic information is coded into four nucleotides


These can bond to each other with hydrogen bonds such that A always bonds to T and C always

bonds to G.

The overall structure is the familiar double helix:


- Note the scale: diameter 2 nm, one pair 0.34 nm, one full turn of the helix 3.4 nm. I.e. this is

very small.

The pairings AT and CG means all the information is doubly coded into the double helix. Hence if

the helices are opened up into the two subhelices no information is lost.

- This enables the DNA info to be recoded into RNA (except that T is replaced by U (uracil)), and

replicated.

- RNA in its different varieties takes transfers the information in DNA into information on how to

build up proteins

- Groups of 3 nucleotides form a codon which tells which is the next amino acid to build up into a

protein polypeptide primary structure.

Like for the proteins, the basic structure described above is only the starting point for the whole

structure of DNA. Here is a figure of the structural hierarchy:


8.2.1. DNA as a building block

- As already alluded to before, DNA is a useful building block for nanostructures.

- One particular reason is that because the nucleotides can only pair with the exact opposite variety,

one sequence of DNA is highly selective in which other DNA it can be attached to; in effect it can

select which other strand to bind to.


- The DNA chains can also be joint with other molecules in the end. This has allowed e.g. for

making a branched DNA structure:

[http://www.hanadisleiman.com/BranchedDNAStructures.php]

Yellow atom is Ru

- Such a branched structure and the connectivity allows for using DNA to build up nanostructures:


- In a different approach, several DNA double helices can be assembled together into DNA bundles

of different shapes. Here is an example of how six helices are joint to produce an altogether sixfold

symmetric bundle:


[Nano Letters 5 (2005) 661]

The ends are sticky, and can join into the opposite end of the same kind of bundle. Thus long, in

principle straight, 1D arrays of these things can be formed:


Note that these are almost but not quite straight; but the lengths are impressive, microns

Thexe can also be assembled into regular 2D arrays:

Right-hand slide shows vacancies in array!


8.2.2. Self-assembly of RNA

[http://news.uns.purdue.edu/html4ever/2004/040811.Guo.scaffold.html, Nano Letters 4 (2004) 1717]

- Also RNA is of nanoscience interest

- Small basic RNA blocks can with suitable chemicals be made to self-assemble into various shapes:


- Here the basic building blocks are so called pRNA with ends which match each others in certain

ways:


8.3. Biomimetic polypeptides

[PO 12-4, Nature 403 (2000) 6767]

- It is also possible to design structures by mimicing proteins. Instead of using just the standard 20

amino acids, it is possible to use other molecules with similar properties and assemble these into

chains.

- The manufacturing can utilize self-assembly techniques similar to those making up conventional

polymers; the RNA or DNA codons can be changed to correspond to other molecules than the

standard 20 ones!

- E.g. Tirrell et al. have gotten bacteria to make a protein with the nonstick properties of

Teflon by having the microbes substitute an unnatural amino acid for one of the 20 natural ones.

[[http://online.sfsu.edu/~rone/GEessays/DNAaltlife.html]

- By suitable choice of the molecules the shape of the particles can be controlled

- The materials need not even be limited to H, C, O, N:


- E.g. Deming et al have manufactured different ordered silica shapes; below is a figure of two

kinds of shapes originating in the same silica shape, one synthesized under nitrogen (left), the other

under air (right):


8.4. Au nanoparticles and DNA

[Niemeyer, Mirkin sect. 19]

- We have already mention¡ed that nanoparticles can be coated with organic molecules

- These organics can be DNA

- There are several reasons why this is interesting. We will here describe a couple of so called

DNA-gold-nanoparticle conjugates

- Monodisperse Au nanoparticles alone are red (due to a surface plasmon resonance)

- Au nanoparticles in solution with DNA can form aggregates, and then are no longer red but purple

in color!

- The DNA strands a′b′ (matching the ab molecules on the surface of the nanoparticles) linked to

them shifts the plasmon resonance upwards in wavelength: 520 to 574 nm.


- This can be used in DNA detection systems

- The nanoparticles can also be bound to surfaces with DNA:


When the suitable DNA strands a′c′ or b′d′ (which selectively match the ac or bd molecules) are

present, the nanoparticles will be bound to the surface

- The DNA-Au system is also electrically conductive. Thus it may be used for electrical detection

systems of DNA!


8. Bionanoscience - Helsinki

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