Noncovalent biomolecules

When thinking about chemical reactivity, chemists usually focus their attention on bonds, the covalent interactions between atoms within individual molecules. Also important, hotvever, particularly in large biomolecules like proteins and nucleic acids, are a variety of interactions between molecules that strongly affect molecular properties. Collectively called either intermolecular forces, van der Waals forces, or noncovalent interactions, they are of several different types dipole-dipole forces, dispersion forces, and hydrogen bonds. 

The covalent bond is the strongest force that holds molecules together (Table 2-1). Noncovalent forces, while of lesser magnitude, make significant contributions to the structure, stability, and functional competence of macromolecules in living cells. These forces, which can be either attractive or repulsive, involve interactions both within the biomolecule and between it and the water that forms the principal component of the surrounding environment. 

The DNA double heUx illustrates the contribution of multiple forces to the structure of biomolecules. While each individual DNA strand is held together by covalent bonds, the two strands of the helix are held together exclusively by noncovalent interactions. These noncovalent interactions include hydrogen bonds between nucleotide bases (Watson-Crick base pairing) and van der Waals interactions between the stacked purine and pyrimidine bases. The hehx presents the charged phosphate groups and polar ribose sugars of... 

Patonay G, Salon J, Sowell J, Strekowski L (2004) Noncovalent labeling of biomolecules with red and near-infrared dyes. Molecules 9 40-49... 

Aptamers are oligonucleic acids or peptide molecules that bind to a specific target biomolecule (Fig. 2). A dye molecule can be noncovalently or covalently bound to an aptamer. 

An alternative efficient approach to disperse CNTs relies on the use of synthetic peptides. Peptides were designed to coat and solubilise the CNTs by exploiting a noncovalent interaction between the hydrophobic face of amphiphilic helical peptides and the graphitic surface of CNTs (Dieckmann et al., 2003 Zoibas et al., 2004 Dalton et al., 2004 Arnold et al., 2005). Peptides showed also selective affinity for CNTs and therefore may provide them with specifically labelled chemical handles (Wang et al., 2003). Other biomolecules, such as Gum Arabic (GA) (Bandyopadhyaya et al., 2002), salmon sperm DNA, chondroitin sulphate sodium salt and chitosan (Zhang et al., 2004 Moulton et al., 2005), were selected as surfactants to disperse CNTs (Scheme 2.1). 

Scheme 2.1 Examples of noncovalent functionalisation of carbon nanotubes (CNTs) with different biomolecules...

The alternative noncovalent functionalization does not rely on chemical bonds but on weaker Coulomb, van der Waals or n-n interactions to connect CNTs to surface-active molecules such as surfactants, aromatics, biomolecules (e.g. DNA), polyelectrolytes and polymers. In most cases, this approach is used to improve the dispersion properties of CNTs [116], for example via charge repulsion between micelles of sodium dodecylsulfate [65] adsorbed on the CNT surface or a large solvation shell formed by neutral molecule (e.g. polyvinylpyrrolidone) [117] around the CNTs. 

One of the approaches to attach a biomolecule to CNTs is to introduce a functional group that can noncovalently bind the graphene motif via n-n stacking. As in the case of polymers discussed previously, pyrene moieties proved to be very effective and they are in most cases the anchor group of choice [72]. 

Noncovalent interactions play a key role in biodisciplines. A celebrated example is the secondary structure of proteins. The 20 natural amino acids are each characterized by different structures with more or less acidic or basic, hydrophilic or hydrophobic functionalities and thus capable of different intermolecular interactions. Due to the formation of hydrogen bonds between nearby C=0 and N-H groups, protein polypeptide backbones can be twisted into a-helixes, even in the gas phase in the absence of any solvent." A protein function is determined more directly by its three-dimensional structure and dynamics than by its sequence of amino acids. Three-dimensional structures are strongly influenced by weak non-covalent interactions between side functionalities, but the central importance of these weak interactions is by no means limited to structural effects. Life relies on biological specificity, which arises from the fact that individual biomolecules communicate through non-covalent interactions." " Molecular and chiral recognition rely on... 

Noncovalent interactions in metal complexes of biomolecules may play an important role in the creation of supramolecular structures around the metal center. For instance, extensive three-dimensional hydrogen-bonded stmcmres grow around metal complexes of barbiturates, recognized as the most widely used drugs for the treatment of epilepsy.Electrostatic interactions between a cation and the Trring of an aromatic molecule (cation-tt interactions) are common motifs in protein structures. Little is known about alkali and alkali-earth cation-tt inter-... 

The chemical modification of CNTs can be endohedral (inside the cavity of the tube) or exohedral [42]. There are some examples in the literature that have demonstrated the filling of CNTs with fullerenes, biomolecules (proteins, DNA), metals and oxides that have been driven inside by capillary pressure [39, 42, 72-78]. However, in this section we will focus on exohedral functionalization, taking place just at the external walls of the tubes. Both covalent (chemical-bond formation) and noncovalent (physiadsorption) functionlizations can be carried out. In the following... 

TABLE 2-5 Four Types of Noncovalent ( Weak ) Interactions among Biomolecules in Aqueous Solvent... 

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TABLE 1.1. Energy Contribution and Distance of Noncovalent Interactions in Biomolecules... 

IMMOBILIZATION OF BIOMOLECULES WITH COVALENT AND NONCOVALENT LINKERS... 

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