Melting curves structure

Whereas proteins have their low energy absorption band at 280 nm, polynucleotides typically have maxima at 260 nm (38,500 cm ). A phenomenon of particular importance in the study of nucleic acids is the hypochromic effect. In a denatured polynucleotide the absorption is approximately the sum of that of the individual components. However, when a double helical structure is formed and the bases are stacked together, there is as much as a 34% depression in the absorbance at 260 nm. This provides the basis for optical measurement of DNA melting curves (Fig. 5-45).45,86 The physical basis for the hypochromic effect is found in dipole-dipole interactions between the closely stacked base pairs.7,86,87... 

Thermal denaturation profiles were done using one of the molecular beacon structures in solution, without the alkyl chain linker attached to the 3 -thymidine residue. The fully complementary and single base pair mismatched sequence targets were investigated. The differences of Tm from the melt profiles showed that single base pair mismatches could not be discriminated from the complementary target material. Melt curves were also... 

Figure 21.2 Monovalent salt dependences for the formation of RNA tertiary structures. For both RNAs shown, log(Kobs) was calculated at 20 °C from the melting temperature (7 ln) and enthalpy (AH ) of the tertiary folding transition observed in melting curves by the formula ln(lC0i,s) = — (H /R) (1 / 7, 1/T0), where R is the gas...

The stability of double stranded nudeic adds can be determined accurately from their melting curves. These are obtained most simply from measurement of the absorbance of the solution at 260 nm which can be monitored directly as the DNA solution is heated separation of the two strands leads to de-stacking of the nucleotide residues and a concomitant increase in the absorbance (hyperchromic effect). Analogously, formation of double stranded structures from the component single strands can be monitored by following the decrease in absorbance (hypochromic effect). 

It is believed that the CNA backbone undergoes a chair inversion to adopt axial base orientations within the duplex to promote base pairing. Homo-chiral CNA complexes (d/d or l/l) of A13 or T13 are more stable than ds-DNA but show multiple transitions in the melting curve, while heterochiral CNA duplexes (d/l) are much less stable with mixed AT sequences forming only as homochiral complexes. No self-pairing of CNA strands was observed. This study demonstrates that conformational intuition of monomer structures does not easily translate to backbone conformations that favor duplex formation. Thus, CNAs are examples of nucleotidomimetics where a unique backbone conformation is only adopted through the optimization of nonadjacent contacts. 

The melting curve of sulfur with respect to metastability and experimental procedures has been critically analyzed by Vezzoli and Walsh [194]. The authors also discussed the previously reported phase boundaries of the sohd high-pressure allotropes in the range up to 4 GPa and from room temperature up to about 670 K [132]. However, the structures of these high-pressure polymorphs are unknown and their probability to exist under equilibrium conditions is still awaiting confirmation. 

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