Double-stranded DNA molecules

A relaxed, circular, double-stranded DNA molecule (1600 bp) is in a solution where conditions favor 10 bp per turn. What is the value of Lq for this DNA molecule Suppose DNA gyrase introduces 12 negative snpercoils into this molecule. What are the values of L, W, and T now What is the snperhelical density, cr ... 

The chromosomes of Escherichia coli and other bacteria are single, double-stranded DNA molecules with a total length of more than 1,000 pm. Relaxed DNA exists as a helical molecule, with one full turn of the helix occurring approximately every 10.4 base pairs. This molecule must undergo several folding and compaction steps to fit into an E. coli cell which is only 1-3 pm long. Despite this enormous compaction, bacterial DNA must be accessible for the bacterial enzymes that catalize DNA replication and transcription... 

Chromatin consists of very long double-stranded DNA molecules and a nearly equal mass of rather small basic proteins termed histones as well as a smaller amount of nonhistone proteins (most of which are acidic and... 

The majority of the peptides in mitochondria (about 54 out of 67) are coded by nuclear genes. The rest are coded by genes found in mitochondrial (mt) DNA. Human mitochondria contain two to ten copies of a smaU circular double-stranded DNA molecule that makes up approximately 1% of total ceUular DNA. This mtDNA codes for mt ribosomal and transfer RNAs and for 13 proteins that play key roles in the respiratory chain. The linearized strucmral map of the human mitochondrial genes is shown in Figure 36-8. Some of the feamres of mtDNA are shown in Table... 

Although the initial change may not occur in the template strand of the double-stranded DNA molecule for that gene, after repfication, daughter DNA molecules with mutations in the template strand will segregate and appear in the population of organisms. 

This enzyme is associated with the virions of RNA tumor viruses such as the Rous sarcoma virus (RSV). The enzyme has remarkable enzymatic activity in that it can catalyze several seemingly diverse steps in the synthesis of double-stranded DNA from the single-stranded RNA viral genome. The enzyme uses a tRNA for tryp-tophan as a primer to make a copy of DNA that is complementary to the viral RNA. The resulting RNA-DNA hybrid is converted to a double-stranded DNA molecule by ribon-uclease (RNase)H and DNA-dependent DNA polymerase activities that are intrinsic to reverse transcriptase. 

Plasmids are the circular double-stranded DNA molecules found in the cytoplasm of bacterial cells. To be a useful vector the plasmid must be small. The smaller the plasmid, the easier it is taken up into the bacteria. Most vectorplas-mids are about 3-4 kilobases (kb) in length. This allows incorporation of sequences of DNA up to 10-12 kb without impairing plasmid uptake. It is also helpful if the vector has a high copy number. The larger the copy number, the more molecules of DNA will be produced. 

Plasmid A relatively (cf. the chromosome) small (>20 Kb), usually circular, double-stranded DNA molecule found in prokaryotes capable of replicating independently of the chromosome. Plasmids carry genes which are usually not essential for the growth of the organism except under special conditions. Some plasmids carry genes for antibiotic resistance. See also Ti-plasmid. Some plasmids however can be very large, e.g. the plasmids in Rhizobium species. 

Gene expression and DNA replication are compared in Table I-l-l. Transcription, the first stage in gene expression, involves transfer of information found in a double-stranded DNA molecule to the base sequence of a single-stranded RNA molecule. If the RNA molecule is a messenger RNA, then the process known as translation converts the information in the RNA base sequence to the amino add sequence of a protein. 

Figure I-1-8- shows m example of a double-stranded DNA molecule. Some of the features of double-stranded DNA include ...

Thirdly, experiments concerned with the whole process of conformational change and the unzipping process (e.g., [49]) studied the mechanical stability of individual double-stranded DNA molecules. It was foimd that the B-S transition of A-DNA occurred at 65 pN, followed by a second conformational transition during which the DNA double helix melted into two... 

The process is repeated. Heating causes separation of strands, and cooling allows primer to attach to the appropriate nucleotide sequence. Enzymic chain extension then produces four double-stranded DNA molecules. 

Too many PCR cycles will result in the occurrence of multim-ers of denatured DNA molecules that will migrate in the high molecular weight range in an analyzing PAGE. These sequences cannot be renatured to double-stranded DNA molecules and are lost, as they cannot be in vitro transcribed. 

Leger JE, Robert J, Bourdieu L et al (1998) RecA binding to a single double-stranded DNA molecule a possible role of DNA conformational fluctuations. Proc Natl Acad Sci USA 95 12295-12299... 

DNA, adenine (A) pairs with thymine (T) and cytosine (C) pairs with guanine (G). Therefore, when there is an A in one strand of the double-stranded DNA molecule, there is a T in the other strand. When the genetic code is copied from DNA to RNA, the two strands of DNA molecule separate, and the RNA nucleotides pair with nucleotides on each strand of DNA. In this case, the nucleotide that pairs with adenine (A) on the DNA is uracil (U) because RNA does not contain thymine (T). Because of the exact nature of base pairing, the genetic code can be transmitted accurately at each stage of the process. 

Double-stranded DNA molecules with one or more mispairs are more easily disrupted or denatured than are properly and fully paired double helices the more mispairing, the less the stability of the molecule. If a DNA molecule, with or without mispairs, is too unstable, then the two strands will dissociate from one another to... 

DNA is a linear polymer of covalently joined deoxyribonucleotides, of four types deoxyadenylate (A), deoxyguanylate (G), deoxycytidy-late (C), and deoxythymidylate (T). Each nucleotide, with its unique three-dimensional structure, can associate very specifically but non-covalently with one other nucleotide in the complementary chain A always associates with T, and G with C. Thus, in the double-stranded DNA molecule, the entire sequence of nucleotides in one strand is complementary to the sequence in the other. The two strands, held together by hydrogen bonds (represented here by vertical blue lines) between each pair of complementary nucleotides, twist about each other to form the DNA double helix. In DNA replication, the two strands separate and two new strands are synthesized, each with a sequence complementary to one of the original strands. The result is two double-helical molecules, each identical to the original DNA. 

FIGURE 24-15 Linking number, Lk. Here, as usual, each blue ribbon represents one strand of a double-stranded DNA molecule. For the molecule in (a), Lk = 1. For the molecule in (b), Lk = 6. One of the strands in (b) is kept untwisted for illustrative purposes, to define the border of an imaginary surface (shaded blue). The number of times the twisting strand penetrates this surface provides a rigorous definition of linking number. 

FIGURE 25-39 Effects of site-specific recombination. The outcome of site-specific recombination depends on the location and orientation of the recombination sites (red and green) in a double-stranded DNA molecule. Orientation here (shown by arrowheads) refers to the order of nucleotides in the recombination site, not the 5 —>3 direction. 

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