Publisher Summary This chapter discusses the structure and function of DNA. DNA occupies a critical role in cells, because it is the source of all intrinsic genetic information. Chemically, DNA is a very stable molecule, a characteristic important for a macromolecule that may have to persist in an intact form for a long period of time before its information is accessed by the cell. Although DNA plays a critical role as an informational storage molecule, it is by no means as unexciting as a computer tape or disk drive. The structure of the DNA described by Watson and Crick in 1953 is a right handed helix of two individual antiparallel DNA strands. Hydrogen bonds provide specificity that allows pairing between the complementary bases (A.T and G.C) in opposite strands. Base stacking occurs near the center of the DNA helix and provides a great deal of stability to the helix (in addition to hydrogen bonding). The sugar and phosphate groups form a “backbone” on the outside of the helix. There are about 10 base pairs (bp) per turn of the double helix.

DNA Structure and Function

The carcinoembryonic antigen (CEA) gene family belongs to the immunoglobulin supergene family and can be divided into two main subgroups based on sequence comparisons In humans it is clustered on the long arm of chromosome 19 and consists of approximately 20 genes The CEA subgroup genes code for CEA and its classical crossreacting antigens, which are mainly membrane-bound, whereas the other subgroup genes encode the pregnancy-specific glycoproteins (PSG), which are secreted Splice variants of individual genes and differential post-translational modifications of the resulting proteins, eg, by glycosylation, indicate a high complexity in the number of putative CEA-related molecules So far, only a limited number of CEA-related antigens in humans have been unequivocally assigned to a specific gene Rodent CEA-related genes reveal a high sequence divergence and, in part, a completely different domain organization than the human CEA gene family, making it difficult to determine individual gene counterparts However, rodent CEA-related genes can be assigned to human subgroups based on similarity of expression patterns, which is characteristic for the subgroups Various functions have been determined for members of the CEA subgroup in vitro, including cell adhesion, bacterial binding, an accessory role for collagen binding or ecto-ATPases activity Based on all that is known so far on its biology, the clinical outlook for the CEA family has been reassessed

/pdf/carcinoembryonic-antigen-gene-family-molecular-biology-and-2n71cbhbw6.pdf

Carcinoembryonic antigen gene family: molecular biology and clinical perspectives.

Biologists were puzzled by the discovery of left-handed Z-DNA because it seemed unnecessary. Z-DNA was stabilized by the negative supercoiling generated by transcription, which indicated a transient localized conformational change. Few laboratories worked on the biology of Z-DNA. However, the discovery that certain classes of proteins bound to Z-DNA with high affinity and great specificity indicated a biological role. The most recent data show that some of these proteins participate in the pathology of poxviruses.

Z-DNA: the long road to biological function

Publisher Summary This chapter summarizes the current knowledge about the structure–function relationships of the globin gene system as derived from studies at the level of DNA and RNA. It discusses some of the sequence comparisons that relate to the evolution of this gene system and reviews the status of the applications of this molecular genetic knowledge to the understanding of the human hemoglobinopathies. The bulk of literatureon globin precludes anything approaching exhaustive coverage. Hemoglobin is a metalloprotein tetramer consisting of two α-like globin polypeptides and two β-like globin chains. The striking achievements of the past five years has been the rapid definition at the DNA level of the heterogeneous collection of mutations that lead to α- and β-thalassemia, which have themselves provided crucial information about the control of gene expression in vivo. The recognition of linked polymorphisms, the development of mutation-specific oligonucleotide probes, and the possibility of first-trimester chrionic villus biopsy have made the prenatal diagnosis of sickle-cell anemia and β-thalassemias of immediate applicability, and appropriate resources must be marshaled to offer this technology to the areas of the world where it is most needed.

The molecular genetics of human hemoglobin.

A fundamental principle of exponential bacterial growth is that no more ribosomes are produced than are necessary to support the balance between nutrient availability and protein synthesis. Although this conclusion was first expressed more than 40 years ago, a full understanding of the molecular mechanisms involved remains elusive and the issue is still controversial. There is currently agreement that, although many different systems are undoubtedly involved in fine-tuning this balance, an important control, and in our opinion perhaps the main control, is regulation of the rate of transcription initiation of the stable (ribosomal and transfer) RNA transcriptons. In this review, we argue that regulation of DNA supercoiling provides a coherent explanation for the main modes of transcriptional control - stringent control, growth-rate control and growth-phase control - during the normal growth of Escherichia coli.

DNA supercoiling - a global transcriptional regulator for enterobacterial growth?

The DNA polymer d(GC)n . d(GC)n can undergo a transition from the usual right-handed 10.4 base pairs (bp) per turn B form to a novel left-handed 12 bp per turn Z form in response to altered environmental conditions. Several other alternating purine-pyrimidine DNA polymers with modified bases have been shown to undergo transitions from B to Z conformations, with varying degrees of difficulty. We report here that the unmodified DNA polymer d(TG)n . d(CA)n readily undergoes a transition to a Z conformation when subjected to unwinding torsional stress in ionic conditions that are close to physiological. By using a two-dimensional gel electrophoresis system, we have determined both the critical free energy of supercoiling that is required to initiate the transition and the free energy of supercoiling that is required to maintain this polymer in the Z form.

Facile transition of poly[d(TG) x d(CA)] into a left-handed helix in physiological conditions.

A 34 base pair tract of the simple repeating dinucleotide d(AT)n-d(AT)n cloned into a 2.4 kb polylinker plasmid vector undergoes a structural transition in response to negative superhelical coiling. The transition has been characterized by 2 dimensional gel electrophoresis, mapping of S1, P1 and T7 endonuclease 1 sensitive sites, and mapping of sites that are sensitive to modification by bromoacetaldehyde. After S1 nuclease treatment it is possible to trap supercoiled species that are nicked on one or both strands near the center of the palindrome. These data show that the alternate state adopted by the d(AT)n-dAT)n insert is a cruciform rather than a Z conformation. Unlike other B-cruciform transitions the transition in d(AT)n-d(AT)n has a low activation energy and the transition is facilitated by the presence of magnesium ions. Evidence from in-vivo topoisomer distributions is presented which shows that under conditions of blocked protein synthesis the d(AT)n-d(AT)n insert will spontaneously adopt the cruciform state in-vivo in E. coli.

Transition of a cloned d(AT)n-d(AT)n tract to a cruciform in vivo

The energetics of the B-Z transition of two different types of cloned alternating purine/pyrimidine DNA sequences have been analysed by a two dimensional electrophoretic technique. Since the transition between right handed and left handed forms of these polymers is detected by alterations of electrophoretic mobilities of topoisomers of the plasmid DNA molecules, the method is not dependent on Z-DNA binding ligands. The measurements reflect intrinsic properties of the DNA unperturbed by the free energy of binding such a ligand. Direct evidence from the analysis of topoisomer distributions is presented which shows that d(GC)n.d(GC)n sequence elements within an E. coli plasmid will adopt a Z conformation in-vivo under conditions of blocked protein synthesis. Evidence for the in-vivo occurrence of Z-DNA was not detected in plasmid DNA isolated from bacterial cells growing in the absence of protein synthesis inhibitors. A model is proposed for a function for the B-Z transition in ensuring the correct pairing of homologous chromosomes during meiosis.

The in-vivo occurrence of Z DNA.

The family of zinc dependent endonucleases (EC 30.1.30.x, herein referred to as SS nucleases, reviewed in 1) exemplified by S1 and mung bean nucleases, have been widely regarded as being specific for single stranded nucleic acids. These enzymes have recently been shown to recognize a variety of non-B structures in double stranded DNA (2–14). The basis for the selectivity of these enzymes is discussed with reference to their cleavage of cruciform loops in poly d(AT)n.d(AT)n and of protonated polypurine/polypyrimidine structures. Evidence is presented for a novel left handed form of d(TC) n.d (GA)n and for unexpectedly long range interactions between regions of different structure in plasmid DNA molecules. The existence of these interactions indicate that even the “normal” B-form of double stranded DNA has properties which are not predicted by classical theories of nucleic acid structure.

The Specificity of “Single Strand Specific Endonucleases”: Probes of phosphodiester conformation in double stranded nucleic acids. Left-Handed Polypurine/polypyrimidine structures. Long range transmission of conformational information in DNA.

A family of plasmids which contain d(AT)n cruciforms are sensitive to "single strand specific" (SS) endonucleases and a variety of chemical probes in a "random sequence" region centered 10-30 residues away from the cruciform junction. The SS nuclease sensitive structures are dependent on the presence of the extruded cruciform and exhibit a degree of sequence independence. Their appearance depends upon the combined effects of slightly lower than neutral pH and superhelical coiling above the minimum required to drive the extrusion of the d(AT)n cruciform arms. The nuclease sensitive structure is therefore underwound with respect to the B conformation and contains protonated bases.

David B. Haniford

Papers

Facile transition of poly[d(TG) x d(CA)] into a left-handed helix in physiological conditions.

Transition of a cloned d(AT)n-d(AT)n tract to a cruciform in vivo

The in-vivo occurrence of Z DNA.

The Specificity of “Single Strand Specific Endonucleases”: Probes of phosphodiester conformation in double stranded nucleic acids. Left-Handed Polypurine/polypyrimidine structures. Long range transmission of conformational information in DNA.

Intermediate range effects in DNA I: low pH/stress induced conformational changes in the vicinity of an extruded d(AT)n·d(AT)n cruciform