FALLSEM2024-25_BST6009_ETH_VL2024250101135_2024-08-13_Reference-Material-I (1).pptx

Nanobiotechnology

1. Module – 2 Bio macro molecules in nano biology Lecture 1 DNA based nanostructures Dr. Vijayalakshmi Shankar

2. What are Biomacromolecules? made up of monomers linked Large biological polymers Nucleic acids Proteins Lipids Carbohydrates that are together.

3. Self- assembly

4. Self- assembly

5. Main noncovalent interactions useful in self-assembly

6. Electrostatic interactions Between materials and material to biomolecules Layer-by-layer assembly to form self-assembled monolayers, multilayers, synthetic polyelectrolytes, and high ordered hybrid bionanostructures such as DNA, proteins, peptides, enzymes, based biomaterials

7. Hydrogen Bonding Interaction between electronegative atoms and hydrogen atoms in materials or biomolecules Self-assembled-based long-chain 1D biomolecular-based biomaterials biomolecule-material hybrid biomaterials

8. Hydrophobic interaction Protein folding, enzyme-substrate bindings, and biomembrane organization interaction is weaker than hydrogen bonds Takes place between two hydrophobic regions of biomolecules such as protein or peptides Crucial noncovalent force that will cause the linear polypeptide to fold into a compact structure Aggregation of the hydrophobic surface gives the tightly packed core of the protein

9. π–π conjugation Vital interaction force - smart materials and smart biomaterials Aromatic motifs like proteins, peptides, DNAs, enzymes, and viruses Highly ordered suprastructures

10. Self- assembly

11. Self- assembly P rocess by which an organized structure spontaneously forms from individual components, as a result of specific, local interactions among the components. When the constitutive components are molecules, the process is termed molecular self-assembly. It combines Recognition and Self-organisation Recognition: Interaction between two molecularly matching complementary molecules and shapes recognize each other, thus initially forming a receptor- substrate supramolecule. Self- organization: formation of long range structural order via additional interactions, such as attractive forces.

12. Significance of Biomacromolecules in Nanotechnology

13. Structure of DNA Double helix structure Two helical strands wound together Monomer : Nucleotides Nucleotides within each strand are joined by covalent phosphodiester bonds (-O- P- O-) in a condensation reaction. Each nucleotide subunit is made of a deoxyribose joined to a phosphate group and one of four bases (adenine, A; guanine, G; cytosine, C; and thymine, T). Two strands are connected to one another by bonds ( hydrogen bonds )

14. Structure of DNA D ouble helix – each base pairs up wit h another base to form a base pair A always pairs with T and C with G F our bases are - ‘ letters ’ of the genetic code. L etters make up ‘words’ each o f which is three nucleotides (or 3 bases) lon g – a single ‘word’ code for one of about 20 different amino acids Each such 'word' is called a codon . ‘words’ are grouped into ‘sentences’ or genes, each of which encodes the sequence of amino acids that make up a single protein.

15. Structure of DNA One strand of the DNA molecule will contain the necessary code for the proteins the cell needs to make, this is the sense strand (coding strand), the other strand is complementary to the sense strand ( the antisense or non- coding strand ). Cytosine and thymine are single ring molecules, guanine and adenine are double- rings and these rings all contain nitrogen (N). Ribose and deoxyribose are 5C monosaccharide sugars. Thus, DNA contains the elements C, H, O, N and P (but NOT S).

16. DNA Nanotechnology Advantages to use DNA for nanoscale constructions B inding between two nucleic acid strands depends on simple base pairing rules which are highly specific and well understood , and thus form the specific nanoscale structure of the nucleic acid double helix. Easy to control the assembly of nucleic acid structures DNA of arbitrary sequences are available by convenient solid support synthesis . Established chemistries to produce modifications , such as biotin groups, fluorescent labels, and linking functions are available. DNA can be manipulated and modified by a large battery of enzymes that include DNA ligases, restriction endonucleases, kinases, and exonucleases.

17. DNA Nanotechnology DNA origami - nanoscale folding of DNA to create arbitrary 2D & 3D shapes at nanoscale S pecificity of interactions between complementary base pairs make DNA a useful construction material , through design of its base sequences. DNA is a well- understood material that is suitable for creating scaffolds that hold other molecules in place or to create structures all on its own. I dea of using DNA as a construction material was first introduced in the early 1980s by Nadrian Seeman In 2006, Rothemund developed a new strategy to form self- assembled DNA nanostructures, which was termed DNA origami P rocess involves folding of long single strand of viral DNA aided by multiple smaller "staple" strands.

18. DNA Nanotechnology Structural DNA nanotechnology (SDN) Focuses on synthesizing and characterizing nucleic acid complexes and materials that assemble into a static, equilibrium end state . C omplexes constructed in SDN use topologically branched nucleic acid structures containing junctions. One of the simplest branched structures is a junction that consists of three/four individual DNA strands, portions of which are complementary in a specific pattern.

19. DNA Nanotechnology Dynamic DNA Nanotechnology (DDN) Focuses on complexes with useful non-equilibrium behavior such as the ability to reconfigure based on a chemical or physical stimulus. Others Some complexes, such as nucleic acid nanomechanical devices, combine features of both the structural and dynamic subfields.

20. DNA Nanotechnology Structural DNA Nanotechnology A correct form of DNA nanostructure can be achieved through three main ideas: Hybridization (by use of double and triple crossover motifs or sticky-ended cohesion) Stably branched DNA Synthesis of designed sequences

21. DNA Nanotechnology DNA origami method. (a) The single- stranded DNA ‘scaffold’ strand (purple) is folded and held in place by specifically hybridizing ‘staple’ strands (red and green). (b) Resultant rectangular origami tile once all the staples have bound to the scaffold. (c) Triple crossover motifs demonstrated by the staples interacting with the scaffold. (d) 5’ ends of the staples are extended to create overhangs, which then can be decorated with partially complementary oligonucleotides (purple).

22. Preparation of DNA based Nanostructure Nucleic-acid- based nanostructures for cancer therapy.

23. DNA Nanotechnology U se of DNA for fabrication of nanostructures is rapidly expanding in three main different directions: F abrication of artificial networks consisting of native DNA. A ttachmen t or integration of DNA onto solid state surfaces. 3. F ormation of metal or semiconductor nanoparticle assemblies along DNA.

24. Application: DNA Nanotechnology