Nucleotides, base-pairing

Because of the double helical nature of DNA molecules, their size can be represented in terms of the numbers of nucleotide base pairs they contain. For example, the E. coli chromosome consists of 4.64 X 10 base pairs (abbreviated bp) or 4.64 X 10 kilobase pairs (kbp). DNA is a threadlike molecule. The diameter of the DNA double helix is only 2 nm, but the length of the DNA molecule forming the E. coli chromosome is over 1.6 X 10 nm (1.6 mm). Because the long dimension of an E. coli cell is only 2000 nm (0.002 mm), its chromosome must be highly folded. Because of their long, threadlike nature, DNA molecules are easily sheared into shorter fragments during isolation procedures, and it is difficult to obtain intact chromosomes even from the simple cells of prokaryotes. 

The 2.9 billion letter nucleotide base pair sequence of the human genome is now available as a fundamental resource for scientific and medical discovery on many fronts [1, 2]. Pharmacogenomics (the science of individualized prevention and therapy) is no exception. 

Abbreviation Bp, nucleotide base pairs cDNA, complementary DNA ChIP, chromatin Immunoprecipi-tation Cy5, cyanine 5-dCTP Cy3, cyanine 3-dCTP ESTs, expressed sequence tags FDR, false discovery rate MIAME, minimum information about a microarray experiment mRNA, RNA, messenger NIA, National Institutes of Aging RFUs, relative fluorescence units RT-PCR, reverse transcriptase polymerase chain reaction SAGE, serial analysis of gene expression SAM, significance analysis of microarrays... 

To facilitate high-quality hybridization that demonstrates both specificity of nucleotide base pairing... 

The first thing that we note is that there is a lot of variation in genome content within individual phyla. Consider the birds for example. At one extreme, there are birds that have genomes containing 700 million (7x10 ) nucleotide base pairs and at the other extreme there are some that contain 2 billion (2 x 10 ) base pairs, a variation of about a factor of three. The variation is considerably greater for the amphibians 600 million base pairs at one end of the spectrum to 80 billion (8 x 10 ) at the other end. 

Table 2.1. Genome size (expressed as the number of nucleotide base pairs present in the entire genome of various microorganisms whose genome sequencing is complete/near complete). MB (megabase) = million bases...

Figure 19-17 also indicates that flat, aromatic molecules can be inserted between the flat, hydrogen-bonded nucleotide base pairs of DNA. We say that the flat molecule is intercalated between the base pairs. One of many analytical applications of aptamers utilizes a molecular light switch intercalated in the aptamer. 

Organism see footnotes for sequence information Millions of nucleotide base pairs (Mb) Number of chromosomes (haploid) Estimated number of genes... 

The nucleotide base pairs of DNA specifically direct the two DNA helices in a predictable orientation. The predictability arises because the base pairs are complementary in only those arrangements that pair donors with acceptors. Unlike carboxylic acids which are free to rotate after dimer formation, the base pairs are constrained by their heterocyclic backbones to retain their mutual orientations, with both X-substituents pointing in the same direction, as shown. 

DNA (deoxyribonucleic acid) The basic genetic material found in all living cells (and some viruses), providing the blueprint (i.e. genes) for construction of proteins. DNA is composed of sugars, phosphates, and bases arranged in a double helix, a double stranded, chain-like molecules composed of nucleotide base pairs. 

Biezo, G, J. Ladik, and J. Gergely Approximate calculation of the tunnelling frequencies of the proton in the N-H---0 hydrogen bond of the nucleotide base pairs. Physics Letters 13, 317 (1964). 

In order to understand the effects of radiation damage to DNA it is necessary to consider larger model systems such as nucleotides, base pairs, and stacked bases. The question then becomes whether or not it is possible to do reliable calculations on such large systems. The literature is full of various attempts to study these complex systems. Some attempts have been more successful than others. 

DNA synthesis is catalysed by DNA polymerases and requires the precursor dNTPs (dATP, dGTP, dCTP and dTTP, each of these existing as Mg2+ complexes), a template (i.e. the dsDNA being copied) and a primer (an initial deoxyribose 3 -OH to enable the reaction to insert the first new nucleotide). The reaction proceeds in a 5 to 3 direction, that is, at the end of the synthesis there is a vacant deoxyribose 3 -OH. The fidelity of the replication process is based on the incoming nucleotides base pairing with the correct base on the antiparallel template. DNA synthesis is semi-conservative (i.e. the newly synthesized strand partners its antiparallel complementary strand) and is bidirectional (because both original strands are replicated). 

Such as is seen in so-called triplet repeat disorders (TRDs) where for unknown specific reasons, a triplet of nucleotide base pairs—such as CGG in Fragile-X syndrome—expands between generations. There might be 5 to 50 repeats in the general population, but when this expands to 45 to 200 repeats this can become a genetic catalyst—a premutation —and if over 230, and up to several thousand repeats are in the male offspring, the boy will have mental retardation that becomes apparent in late infancy. 

H] = carboxylic acid dimers, nucleotide base pairs,... 

DNA—Strands of DNA, or deoxyribonucleic acid, are like long sentences of words composed of a four letter alphabet of nucleotide base pairs A (adenine) T (thymine) C (guanine) and C (cyto-... 

Nucleic acid hybridization is based on the precise nucleotide base pairing and hydrogen bonding between one string of nucleotides and a complementary nucleotide sequence. Any diagnostic nucleic acid hybridization test has three essential elements the DNA probe, the target DNA and the signal detection system. Recent developments in detection systems and improvements in safety have enabled... 

DFT modeling has also been applied to the interaction energy calculations between nucleotide base pairs in DNA. Hesselmann et al. [32] examined the interaction energy between purines and pyrimidines using MP2, CCSD(T), and DFT in combination with symmetry-adapted perturbation theory (SAPT). This study demonstrated agreement between the results produced by the three methods, demonstrating the potential for DFT modified with SAPT. 

Figure 102. Common nucleotide base-pairing motifs and acronyms used throughout this section.

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