Helix, length types

Intercalators with asymmetric substituents, such as the phenyl and ethyl groups of ethidium bromide (21), frequently cause a smaller increase in DNA length than expected from the simple model described above. In such cases these groups are inserted into the minor groove of the DNA helix with concomitant bending of the double helix towards the major groove. This alternative type of complexation is supported by X-ray studies on model systems, 25). 

This expression is made up so that p tends to unity at the limit of random-coil (fN = 0) and approaches the value of length/diameter at the limit of intact a-helix (fN = 1), with the assumption of 15 A for the diameter of the helical rod (2). It roughly accounts for the effect that the distribution of dipoles in the molecule becomes more spherically symmetric in going from helix to random-coil. Since p appears only in the correction terms for /g, its exact values are not needed. It has been shown (117) that the calculated values of depend little on the type of equation employed for p except in the region close to fN = 0. 

The Ufson-Roig matrix theory of the helix-coil transition In polyglycine is extended to situations where side-chain interactions (hydrophobic bonds) are present both In the helix and in the random coil. It is shown that the conditional probabilities of the occurrence of any number and size of hydrophobic pockets In the random coil can be adequately described by a 2x2 matrix. This is combined with the Ufson-Roig 3x3 matrix to produce a 4 x 4 matrix which represents all possible combinations of any amount and size sequence of a-helix with random coil containing all possible types of hydrophobic pockets In molecules of any given chain length. The total set of rules is 11) a state h preceded and followed by states h contributes a factor wo to the partition function 12) a state h preceded and followed by states c contributes a factor v to the partition function (3) a state h preceded or followed by one state c contributes a factor v to the partition function 14) a state c contributes a factor u to the partition function IS) a state d preceded by a state other than d contributes a factor s to the partition function 16) a state d preceded by a state d contributes a factor r to the partition function. 

Short peptides three to five residues in length that contain one or two APhe residues adopt a fJ-bend 45"48 and 310-helical folding. For example, crystal structure studies of a three-residue peptide containing two APhe residues, Ac-APhe-Ala-APhe-NHMe, 49 and a five-residue peptide with one APhe residue, Boc-Leu-Phe-Ala-APhe-Leu-OMe, 50 show the presence of two consecutive (3-bends, corresponding to an incipient 310-helix in both peptides. Such didehydropeptides exist in both screw senses and the spacing between APhe residues does not seem to affect the type of helix formed. 51,52 ... 

With one end of a straight strip fixed, the other end deflects in direct proportion to the temperature change and the square of the length, and inversely as Lhe thickness, throughout the linear portion of Lhe deflection characteristic curve. Tf a strip of bimetal is wound into a helix or spiral and one end is fixed, the other end will rotate when heat is applied. The angular deflection varies directly with the temperature change and the length of the strip, and inversely with the thickness of the material, over the linear parts of the deflection characteristic curve. Bimetals show uniform deflection only over part of the deflection characteristic curve, as shown in Fig. 1. The three types of elements most commonly used in thermometers are shown in Fig. 2. 

---