Lecture 7 Biomotors Linear motors on tracks

Examples of Biomolecular Motors Karplus and Gao, Curr Opin. Struct. Biol (2004)

Actin and Myosin - Muscle power Myosin motor pulls on actin filaments

Myosin power strokke driven by ATP hydrolysis

Watching individual actin filaments driven by myosin Actin filaments - 8nm in diameter

Kinesin

The motor protein kinesin walks along microtubules, one tubulin subunit at a time using an optical trap, one can follow its steps 1 monomer Watching kinesin walk.

Tubulin - a self-assembling, re-modellable track

Lecture 8 Designed self-assembly with Biomolecules Polypeptide vs DNA

Rajagopal and Schneider Curr Opin. Struct. Biol (2004) 14 p480-6 Self-assembly of polypeptides - fibres and tubes

MacPhee and Woolfson Curr Opin. Solid-state and Materials Science (2004) 8 p  -sheet ‘amyloid’-type Protein fibrils  -helix coiled-coil-type protein fibrils Self-assembly of polypeptide secondary structures

Peptide Aggregation NucleusProtofilamentPeptide fibril Fibre ‘Amyloid’ fibres - a generic protein/peptide aggregate

Peptide nanotubes - a silver cloud with a peptide lining Reches and Gazit Science (2003) 300, p625

Lecture 8 Designed self-assembly with Biomolecules Polypeptide vs DNA

Nucleic acid bases Adenine (A)Guanine (G) Purines Cytosine (C)Thymine (T; R = CH 3 ) Pyrimidines NB – structural similarity Nucleic Acid - the Basics

Nomenclature base + sugar = nucleoside deoxyribose cytosine 2´-deoxyribonucleoside deoxycytidine deoxyadenosine deoxyguanosine thymidine (or deoxythymidine) (deoxyuridine) Nucleic Acid - the Basics

Nomenclature deoxyribose cytosine 2´-deoxyribonucleotide deoxycytidine-5´-monophosphate 5´-dCMP (or just dCMP) base + sugar + phosphate = nucleotide Nucleic Acid - the Basics

DNA strands Long polymer Base Sugar Phosphate Phosphodiester bond Sugar-phosphate backbone Nucleotide Nucleic Acid - the Basics

Base pairing Nucleic Acid - the Basics

Canonical W-C structure B-DNA Physiologically significant conformation Right handed helix Diameter is ~20 Å Base tilt to helix axis ~6° Helical twist per base pair ~34° 3.4 Å /bp 10.5 bp /turn Nucleic Acid - the Basics

DNA structure - variations Bases are not flat, but are twisted with respect to each other The rotation from one bp to the next is also variable (27-40°) Structure of DNA is therefore sequence dependent – identifiable binding sites for regulatory proteins? Nucleic Acid - the Basics

DNA energetics DNA can be reversibly denatured ("melting") –Cooperative transition from helix  random coil; the change in absorbance at =260 nm can be used to monitor this transition. The absorbance (A260) increases when the DNA melts –Tm (the midpoint) increases with G + C content –Tm increases with increased salt concentration Base pairing –Watson-Crick H-bonding is only a minor contribution to stability but is essential for specificity Repulsion between phosphates is minimized by maximizing P - P distance and by interactions with cations Nucleic Acid - the Basics

DNA energetics Base stacking is the major contribution to helix stability. Planar aromatic bases overlap geometrically and electronically. Energy gain by base stacking is due to: –Hydrophobic effect, water is excluded from the central part of the helix, but still fills the grooves. This is a minor contribution to the energy. –Direct interaction between the nucleotide bases. This is the major favourable contribution to the energetics of DNA folding. Nucleic Acid - the Basics

Supercoiling Supercoil Coil Nucleic Acid - the Basics

Replication

Translation

Nucleic Acid - the Basics Sticky ended ligation Annealing Ligation

Nucleic Acid - the Basics Strand exchange - junctions and branches Holliday Junctions Double Crossover Molecules

Nanostructured Nucleic Acid Materials - Ned Seeman Nature 421 (2003) p427

Tiling with DNA

DNA ‘motors’ - DNA as fuel Seeman

DNA ‘motors’ - DNA as fuel Seeman ‘Biped’ Nanoletters 4 (2004) p Proof?? Tuberfield Nature 406 (2000) P605-8 Video Liao and Seeman Science 306 (2004) Links to DNA synthesis

Assembly of a nanoscale quadruple helix Balasubramanian and co-workers J. Am. Chem. Soc. 126, (2004) J. Am. Chem. Soc. 125, (2004) Alternative DNA structures - G-quadruplexes

OH - H+H+ H2OH2O H2OH2O i-motif Proton driven single molecule DNA motor Balasubramanian and co-workers Angew. Chem. Intl. Ed., 42, (2003) DNA ‘motors’ - Protons as fuel

Copying DNA - the polymerase chain reaction

Attaching things to DNA 1.Biotin Streptavidin interaction - generic molecular adapters 2.Thiols - Nanoparticles 3.Fluorohores - for sensitive detection 4.Proteins - protein/DNA recognition 5.Proteins - semi-synthetic conjugation 6.Metal - metallisation for conductors

DNA detection using nanoparticle assembly Chad MirkinThiol terminated ssDNA Sensitivity - femtomol(ar) Selectivity - 100,000 : 1 for point mutations (singlr base pair changes)

Chad Mirkin DNA detection using nanoparticle assembly

Chad Mirkin Using DNA bar codes to detect proteins Science 2003, 301,

Chad Mirkin Using DNA bar codes to detect proteins Science 2003, 301, aM 30 aM Sensitivity aM = attomolar = M

NiemeyerDNA protein conjugates - ImmunoPCR Protein diagnostics using DNA

DNA as a scaffold for something else Biotin Streptavidin interaction - generic molecular adapters

NiemeyerDNA directed immobilisation (DDI) DNA as a scaffold for something else NiemeyerEnzyme locaisation

Niemeyer Protein directed DNA organisation ChainsRingsNetworks Ionic strength dependent supercoliing

DNA directed Protein organisation NiemeyerEnzyme localisation ChemBioChem (2003) 2, p

DNA (and protein) metallisation Braun, Finkelstein and others Yan et al Science (2003) 301 p1882

DNA (and protein) metallisation Braun, Finkelstein and others Yan et al Science (2003) 301 p1882