Temperature dependence polynucleotides

It is known that interactions between polynucleotides also depend on temperature the complex formation is favored at lower temperatures39. For the free-radical copolymerization of MAOA with MAOT, the relative rate is increased as the polymerization temperature is lowered37. In the case of template polymerization, however, a reverse temperature dependency has been observed (Fig. 12) the relative conversion tends to increase with rising temperatures. 

Polynucleotide helices are known to dissociate reversibly (Lipsett et al., 1960 Doty et al., 1959) upon heating, the melting temperature depending upon the polymers used and upon the kind and concentration of salt. By using heated solutions. Miles (1960) has followed the thermal dissociation of these three-stranded helices (Fig. 12.9 and Table 12.3) by their infrared spectra. The hot solution of tetra A -I- 2 poly U... 

The values of the internal motion correlation time are nearly the same for DNA and poly(I) poly(C), showing that this motion is not substantially coupled to the overall conformation of the polynucleotide because DNA exhibits B-form structure and poly(I) poly(C) exhibits A-form structure (Bolton and James, 1980a). In addition, the slower motion correlation time found for poly(I) poly(C) had the same value and temperature dependence of the larger DNA, providing additional support for the suggestion that t reflects a bending motion that is independent of chain length. 

P-NMR spectra of poly(I) at 36.4 and 111.6 MHz were examined by Neumann and Tran-Dinh (1981). Assuming that the relaxation could be effected by a single random isotropic motion, it was concluded from P-NMR r, and NOE measurements that the CSA contribution to relaxation amounted to 12% at 36.4 MHz and 72% at 111.6 MHz. From the P T, and NOE data, a temperature-dependent correlation time of 1 ns was calculated. 3with poly(U), poly(A), and poly(C) as a function of temperature (Akasaka et al., 1977). Again, assuming random, isotropic motion, it was estimated that the CSA mechanism may account for 20% of the P relaxation for these three polynucleotides at 40.5 MHz and 72 C. 

Akasaka et d. (1977) investigated the temperature dependence of the P NOE and T, for poly(C). In comparison with results from poly(A) and poly(U), it was suggested that the flexibility of these single-stranded polynucleotides increased in the order poly(U) < poly(C) < poly(A), which is inversely correlated with the tendency for base stacking. 

Cai et al. [7e] investigated electron and hole transfer in various polynucleotide duplexes and compared them with previous results found for salmon sperm DNA, to examine the effect of base sequence on excess electron and hole transfer along the DNA 71-way at low temperature. Electron and hole transfer in DNA was found to be clearly base sequence dependent. In glassy aqueous systems (7M LiBr glasses at 77 K), excess electron-transfer rates increase in the order polydIdC-polydIdC<salmon testes DNAexcess electron and hole transfer rates increase in the order polyC-polyG<salmon testes DNATransfer distances at 1 min and distance decay constants for electron and hole transfer from base radicals to MX in polynucleotides-MX and DNA-MX at 77 K are derived and compiled in Table 3. This table clearly shows that the electron-transfer rate from donor sites decreases in... 

Base Sequence Effects on Excess Electron Transfer. Cai et al.69 investigated low temperature electron and hole transfer to intercalator trapping sites in various polynucleotide duplexes and compared them with previous results found for salmon sperm DNA. Electron and hole transfer in DNA was found to be base sequence dependent. In glassy aqueous systems (7 M LiBr, D20 glasses at 77 K), excess electron-transfer rates increase in the order polydldC-polydldC < DNA... 

Like double-stranded DNA, synthetic polynucleotide complexes containing complementary bases show cooperative melting curves, i.e., the property studied (UV absorption, optical activity, viscosity, etc.) shows a sharp transition at a specific temperature. This Tm depends on ionic strength and, to a certain degree, on pH. If the temperature is increased above the Tm, however, a further continuous variation in the property studied will be observed. It is only in recent years that an understanding of such noncooperative phenomena is emerging. Here the studies of oligomers by CD and NMR were of critical importance. 

Most of the compounds mentioned above are electrically neutral and therefore poorly soluble in water at neutral pH. There are exceptions, such as poly (9-vinyladenine), and poly(l-vinyluracil). All compounds are stable to chemical and enzymatic hydrolysis, and they form complexes with complementary polynucleotides. However, these complexes do not have the simple stoichiometry found in natural nucleic acids. Stability and stoichiometry of complexes do depend on solvent, temperature, and pH of the system (36). Again, because of the complexity of the field, the reader is referred to the review articles mentioned above (36-38). Poly(A -vinyl) derivatives have been carefully tested for their biological and antiviral activity by Pitha (38) in enzyme assays, cell cultures, and in organisms. 

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