Polynucleotide duplexes

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... 

The successful application of high resolution nuclear magnetic resonance (NMR) spectroscopy to monitor the structure and dynamics of the helix-coil transition of oligonucleotide duplexes (1.-4) and transfer RNA (5—9) in solution have prompted efforts in our laboratory to extend these investigations to the polynucleotide duplex level in solution (10,11.). 

The NMR resonances of the polynucleotide duplexes at the Watson-Crick protons, the base and sugar protons and the backbone phosphates would provide sufficient markers to monitor ligand-nucleic acid interactions in solution. Such an approach has great potential in adding to our current knowledge of the interactions... 

The experimental pyrimidine H-3 upfield shift represents the difference between the observed resonance chemical shift in the polynucleotide duplex extrapolated to the transition midpoint and the 14.7 ppm intrinsic position for an isolated base pair. 

If cytosine is hemiprotonated, it can form a centrosymmetrical base pair with three hydrogen bonds (Fig. 16.3), as observed in the crystal structures of cytosine-5-acetic acid [CYACET1, of bis 1-methylcytosine hydroiodide ([MCYTIM101 and [530]), and in the polynucleotide duplex poly(C) poly(CH+) [531]. 

This tabulation is probably not exhaustive. Numerous studies have been published on 7 values of polynucleotide duplexes. They are frequently duplications and often only the most reliable values (in this author s opinion) have been included. In some of the most usual cases several sets of data - generally the most complete and most recent ones - have been included to show the scatter one can expect in these data. Therefore many of the classics from the 50 s and early 60 s do not show up, since preparations have improved and recent data are more reliable. 

DNA ligase (NAD+) [EC 6.5.1.2] (also referred to as polydeoxyribonucleotide synthase (NAD+), polynucleotide ligase (NAD+), DNA repair enzyme, and DNA join-ase) catalyzes the reaction of NAD+ with (deoxyribo-nucleotide) and (deoxyribonucleotide) to produce AMP, nicotinamide nucleotide, and (deoxyribonucleo-tide)( +m). This forms a phosphodiester at the site of a single-strand break in duplex DNA. RNA can also act as substrate to some extent. 

Adds a phosphate to the 5 -0H end of a polynucleotide to label it or permit ligation Adds homopolymer tails to the 3 -0H ends of a linear duplex Removes nucleotide residues from the 3 ends of a DNA strand Removes nucleotides from the 5 ends of a duplex to expose single-stranded 3 ends Removes terminal phosphates from either the 5 or 3 end (or both)... 

The cross-stranded structure shown in Fig. 27-22 can be formed with all base pairs in both duplexes intact.526 527 All that is required is formation of a nick in each of the two polynucleotide chains and a rejoining of the backbones across the close gap between the duplexes. This model also accounts for the cutting of the two crossed strands at exactly equivalent points to terminate the process. Various mechanisms of recombination exist, and most make use of the key... 

Fig. 4. Scheme of the preparation containing P-labeled phosphomonoesters at single-strand breaks. The two strands of Ti DNA duplex are schematically represented by two parallel lines and only the 5 termini are designated. After the introduction of single-strand breaks into DNA by incubation with pancreatic DNase, the phosphomonoesters formed are removed by phosphatase at 65°. The 5 termini are then labeled by incubation with polynucleotide kinase. From Weiss el al. (56). 

In the laboratory, double-stranded DNA can be separated into single strands. The process of separating the polynucleotide strands of duplex nucleic acid structures is called de-naturation. Denaturation disrupts the secondary binding forces that hold the strands together. Recall that the second-... 

Watson-Crick model for DNA replication. The double helix unwinds at one end. New strand synthesis begins by absorption of mononucleotides to complementary bases on the old strands. These ordered nucleotides are then covalently linked into a polynucleotide chain, a process resulting ultimately in two daughter DNA duplexes. 

Crick when they proposed the duplex structure for DNA (fig. 26.1). First, the double helix unwinds next, mononucleotides are absorbed into complementary sites on each polynucleotide strand and finally these mononucleotides become linked to yield two identical daughter DNA duplexes. What could be simpler Subsequent biochemical investigations showed that in many respects this model for DNA replication was correct, but they also indicated a much greater complexity than was initially suspected. Part of the reason for the complications is that replication must be very fast to keep up with the cell division rate, and it must be very accurate to ensure faithful transfer of information from one cell generation to the next. 

Z form. A duplex DNA structure in which the usual type of hydrogen bonding occurs between the base pairs but in which the helix formed by the two polynucleotide chains is left-handed rather than right-handed. 

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