Nucleic acids circular structures

Not all the cellular DNA is in the nucleus some is found in the mitochondria. In addition, mitochondria contain RNA as well as several enzymes used for protein synthesis. Interestingly, mitochond-rial RNA and DNA bear a closer resemblance to the nucleic acid of bacterial cells than they do to animal cells. For example, the rather small DNA molecule of the mitochondrion is circular and does not form nucleosomes. Its information is contained in approximately 16,500 nucleotides that func-tion in the synthesis of two ribosomal and 22 transfer RNAs (tRNAs). In addition, mitochondrial DNA codes for the synthesis of 13 proteins, all components of the respiratory chain and the oxidative phosphorylation system. Still, mitochondrial DNA does not contain sufficient information for the synthesis of all mitochondrial proteins most are coded by nuclear genes. Most mitochondrial proteins are synthesized in the cytosol from nuclear-derived messenger RNAs (mRNAs) and then transported into the mito-chondria, where they contribute to both the structural and the functional elements of this organelle. Because mitochondria are inherited cytoplasmically, an individual does not necessarily receive mitochondrial nucleic acid equally from each parent. In fact, mito-chondria are inherited maternally. 

Several direct methods are available to analyze the tertiary structure of ODNs like nuclear magnetic resonance (NMR) and X-ray crystallographic (XRC) techniques, which needs a sophisticated setup and infrastructure. An alternative but indirect method to study the structure and conformations of nucleic acids is circular dichroism spectroscopy (CD spectroscopy) (25, 26), where circular dichroism refers to the differential absorption of left and right circularly polarized light (27). 

Baase WA, Johnson WC Jr (1979) Circular dichroism and DNA secondary structure. Nucleic Acids Res 2 797-814... 

Abstract Now an incisive probe of biomolecular structure, Raman optical activity (ROA) measures a small difference in Raman scattering from chiral molecules in right- and left-circularly polarized light. As ROA spectra measure vibrational optical activity, they contain highly informative band structures sensitive to the secondary and tertiary structures of proteins, nucleic acids, viruses and carbohydrates as well as the absolute configurations of small molecules. In this review we present a survey of recent studies on biomolecular structure and dynamics using ROA and also a discussion of future applications of this powerful new technique in biomedical research. 

Bioactive macromolecules like peptides, proteins, and nucleic acids have been successfully embedded in planar LbL films. An important question is the retention of the bioactivity of the film-embedded biomolecules. The structural properties and stability of the LbL films formed from synthesized polypeptides of various amino acid sequences were recently reported [50]. The authors showed that control over the amino acid sequence enables control over non-covalent interpolypeptide interaction in the film, which determines the film properties. Haynie and coworkers showed by circular dichroism spectroscopy that the extent of adsorption of poly(L-glutamic acid) (PGA) and poly(L-lysine) (PLL) in the LbL films scales with the extent of secondary structure of the polypeptides in solution [51]. Boulmedais demonstrated that the secondary structure of the film composed of these polypeptides is the same as the peptide structure in the complex formed in solution [52], as found by Fourier transform IR spectroscopy (FUR). 

Protein-DNA Complexes. Circular dichroism has been used to characterize protein secondary structure in many kinds of nucleic acid-binding proteins, their mutants, and derivatives. Similarly, CD has been employed to characterize the structural changes which occur in the nucleic acids as well, but these are beyond the scope of the present work. Our discussion here will center on a few examples of the use of CD for characterizing structural changes which occur in DNA-binding proteins. 

Raman optical activity (RO A) Due to molecular chirality there is a difference in the intensity of Raman scattered right and left circularly polarized light. Raman optical activity (ROA) is a vibrational spectroscopic technique that is reliant on this difference and the spectrum of intensity differences recorded over a range of wavenumbers reveals information about chiral centers within a sample molecule. It is a useful probe to study biomolecular structures and their behavior in aqueous solution especially those of proteins, nucleic acids, carbohydrates, and viruses. The information obtained is in realistic conditions... 

Figure 27.19. Linking Number. The relations between the linking number (Lk), twisting number (Tw), and writhing number (Wr) of a circular DNA molecule revealed schematically. [After W. Saenger, Principles of Nucleic Acid Structure (Springer-Verlag, 1984), p. 452.]...

Combined SAXS/Circular dichroism beamline. Biological macromolecules, such as proteins, carbohydrates and nucleic acids, are composed of many optically active or chiral units that exhibit large Circular Dichroism (CD) signals. CD spectroscopy has therefore been used extensively in the study of proteins, where asymmetric carbon atoms in their amino acid backbone give rise to a CD spectrum. The shape of the spectrum depends on the protein s secondary structure content and allows the proportions of helix, beta structure, turns and random to be determined. 

Aside from the intrinsic circular dichroism originating from the molecular structure, a so-called induced optical activity may result when a molecule is situated in an asymmetric environment. Magnetic circular dichroism, for instance, maybe produced by applying an external magnetic field to an absorbing sample. Adsorption of pigment molecules on nucleic acids or protein molecules may also induce circular dichroism. 

The loop sequence of the tpy-modified DNA strand was designed such that the strand could hybridize to a molecular beacon [Fig. 16(a)] only when in its extended, linear form [Fig. 16(h)]. Upon hybridization to the tpy-modified DNA, the molecular beacon switches from its closed, nonfluorescent form to its open, fluorescent form [Fig. 16(h)]. Both Fe and Zn form very stable [M(qjy)2] complexes and consequently, the circular structure adopted by the tpy-modified DNA strands in the presence of 1 equiv of these metal ions represented a steric barrier for its hybridization to the molecular beacon. The metal ion acted as an allosteric off switch for DNA hybridization (148). This study demonstrated that the incorporation of metal-binding ligands in nucleic acid strands can be used to create metal-dependent allosteric switches for the Watson-Crick interactions between the nucleic acid strands, a mechanism that may find applications in creating artificial systems with regulatory function. In contrast, in the presence of Cu + the DNA hybridization to the molecular beacon was energetically more favorable than the formation of circular stmctures from the tpy-containing DNA strands. Therefore, hybridization of a complementary ssDNA to the... 

Circular dichroism measurements can give information about secondary structure in proteins and nucleic acids. 

The application of absorption and circular dichroism spectra to the study of nucleic acids is discussed by Gray et al. [3]. Examples of the advantages of circular dichroism spectra over absorption spectra in analysis of the stoichiometry and structure of DNA, RNA, and hybrid duplexes and triplexes are given. 

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