Macromolecular order in biology

1994 ◽  
Vol 348 (1686) ◽  
pp. 167-178 ◽  
Keyword(s):  
Nucleic Acids ◽  
Living Cell ◽  
Double Helix ◽  
Higher Order ◽  
Biochemical Processes ◽  
Large Molecules ◽  
Functional Efficiency ◽  
Physical Necessity ◽  
Dna Double Helix ◽  
Almost All

Within a living cell there take place a large number and variety of biochemical processes, almost all of which involve large molecules, particularly proteins and nucleic acids. These macromolecules often interact to form ordered aggregates or specific complexes. A number of examples are discussed which show how different kinds of order develop on grounds of geometrical or physical necessity or for reasons of functional efficiency. Examples are taken from the structure and assembly of simple viruses and the higher-order organization of the DNA double helix in chromosomes.

Mercury Electrodes in Nucleic Acid Electrochemistry: Sensitive Analytical Tools and Probes of DNA Structure. A Review

2004 ◽  
Vol 69 (4) ◽  
pp. 715-747 ◽  
Author(s):  
Miroslav Fojta
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Double Helix ◽  
Dna Structure ◽  
Electrochemical Analysis ◽  
Label Free ◽  
Helix Formation ◽  
Mercury Electrodes ◽  
Dna Strand ◽  
Dna Double Helix

This review is devoted to applications of mercury electrodes in the electrochemical analysis of nucleic acids and in studies of DNA structure and interactions. At the mercury electrodes, nucleic acids yield faradaic signals due to redox processes involving adenine, cytosine and guanine residues, and tensammetric signals due to adsorption/desorption of polynucleotide chains at the electrode surface. Some of these signals are highly sensitive to DNA structure, providing information about conformation changes of the DNA double helix, formation of DNA strand breaks as well as covalent or non-covalent DNA interactions with small molecules (including genotoxic agents, drugs, etc.). Measurements at mercury electrodes allow for determination of small quantities of unmodified or electrochemically labeled nucleic acids. DNA-modified mercury electrodes have been used as biodetectors for DNA damaging agents or as detection electrodes in DNA hybridization assays. Mercury film and solid amalgam electrodes possess similar features in the nucleic acid analysis to mercury drop electrodes. On the contrary, intrinsic (label-free) DNA electrochemical responses at other (non-mercury) solid electrodes cannot provide information about small changes of the DNA structure. A review with 188 references.

scholarly journals Water–DNA interactions as studied by X–ray and neutron fibre diffraction

2004 ◽  
Vol 359 (1448) ◽  
pp. 1237-1248 ◽  
Author(s):  
Watson Fuller ◽  
Trevor Forsyth ◽  
Arumugam Mahendrasingam
Keyword(s):  
Structural Information ◽  
Double Helix ◽  
Water Environment ◽  
Structural Features ◽  
Molecular Conformations ◽  
X Ray ◽  
Biochemical Processes ◽  
Fibre Diffraction ◽  
Dna Double Helix ◽  
High Degree

X–ray fibre–diffraction studies indicate a high degree of stereochemical specificity in interactions between water and the DNA double helix. Evidence for this comes from data that show that the molecular conformations assumed by DNA in fibres are highly reproducible and that the hydration–driven transitions between these conformations are fully reversible. These conformational transitions are induced by varying the relative humidity of the fibre environment and hence its water content. Further evidence for stereochemical specificity comes from the observed dependence of the conformation assumed on the ionic content of the fibre and the nucleotide sequence of the DNA. For some transitions, information on stereochemical pathways has come from real–time X–ray fibre diffraction using synchrotron radiation; information on the location of water with respect to the double helix for a number of DNA conformations has come from neutron fibre diffraction. This structural information from fibre–diffraction studies of DNA is complemented by information from X–ray single–crystal studies of oligonucleotides. If the biochemical processes involving DNA have evolved to exploit the structural features observed in DNA fibres and oligonucleotide single crystals, the challenges in developing alternatives to a water environment can be expected to be very severe.

scholarly journals Heterogeneity in Nucleosome Spacing Governs Chromatin Elasticity

2019 ◽  
Author(s):  
Bruno Beltran ◽  
Deepti Kannan ◽  
Quinn MacPherson ◽  
Andrew J. Spakowitz
Keyword(s):  
Time Scales ◽  
Living Cell ◽  
Double Helix ◽  
Chromatin Organization ◽  
Chromatin Loop ◽  
Loop Formation ◽  
Dominant Source ◽  
Wormlike Chain ◽  
Dna Double Helix ◽  
Nucleosome Binding

Within a living cell, the myriad of proteins that bind DNA introduce heterogeneously spaced kinks into an otherwise semiflexible DNA double helix. To investigate the effects of heterogeneous nucleosome binding on chromatin organization, we extend the wormlike chain (WLC) model to include statistically spaced, rigid kinks. On time scales where nucleosome positions are fixed, we find that the probability of chromatin loop formation can differ by up to six orders of magnitude between two sets of nucleosome positions drawn from the same distribution. On longer time scales, we show that continuous re-randomization due to nucleosome turnover results in chromatin tracing out an effective WLC with a dramatically smaller Kuhn length than bare DNA. Together, these observations demonstrate that heterogeneity in nucleosome spacing acts as the dominant source of chromatin elasticity and governs both local and global chromatin organization.

scholarly journals Mapping life's reactions: A brief history of metabolic pathways and their regulation

2009 ◽  
Vol 31 (3) ◽  
pp. 4-7
Author(s):  
Philip Newsholme
Keyword(s):  
Nucleic Acids ◽  
Chemical Reactions ◽  
Chemical Reaction ◽  
Metabolic Pathway ◽  
Metabolic Pathways ◽  
Living Cell ◽  
Complete Synthesis ◽  
History Of ◽  
A Chain ◽  
Almost All

It is now recognized that almost all chemical reactions that take place in a living cell require an enzyme to catalyse the reaction. An enzyme catalyses one (or, in rare cases, more than one closely related) chemical reaction. The complete synthesis or degradation of complex biological substances such as glycogen, nucleic acids, proteins and lipids requires a series of linked sequences of reactions. A chain of such reactions is referred to as a ‘metabolic pathway’.

SOME OBSERVATIONS ON THE DISTRIBUTION AND MOLECULAR ARRANGEMENT OF NUCLEIC ACIDS IN SALIVARY GLAND NUCLEI OF DROSOPHILA MELANOGASTER

1973 ◽  
Vol 15 (3) ◽  
pp. 509-522 ◽  
Author(s):  
Eileen Sutton Gersh ◽  
Isidore Gersh
Keyword(s):  
Drosophila Melanogaster ◽  
Salivary Gland ◽  
Electron Microscope ◽  
Nucleic Acids ◽  
Double Helix ◽  
Second Order ◽  
Selective Staining ◽  
Molecular Arrangement ◽  
A New Technique ◽  
Dna Double Helix

A new technique is described for preparation of salivary gland chromosomes for viewing with the electron microscope, with selective staining of nucleic acids. The DNA double helix is coiled in a second order helix with period and diameter of about 400A. These secondary helices are aggregated in compact masses in bands, especially in the proximal heterochromatic regions. Larger bands, however, consist of alternating DNA-rich and RNA-rich lamellae and the DNA is compacted only in the DNA-rich lamellae. In RNA-rich lamellae, as well as in interbands and puffs, the second order helices are separated from one another. In the nucleolus the DNA secondary helices form small aggregates. RNA-containing granules are found not only in the nucleolus but also in the nucleoplasm, especially around chromosomal puffs, and also in the puffs, in interbands, and in the RNA-rich lamellae of bands.

scholarly journals Kinetics and mechanism of the DNA double helix invasion by pseudocomplementary peptide nucleic acids

2002 ◽  
Vol 99 (9) ◽  
pp. 5953-5958 ◽  
Author(s):  
V. V. Demidov ◽  
E. Protozanova ◽  
K. I. Izvolsky ◽  
C. Price ◽  
P. E. Nielsen ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Peptide Nucleic Acids ◽  
Double Helix ◽  
Kinetics And Mechanism ◽  
Dna Double Helix

scholarly journals Understanding biochemistry: structure and function of nucleic acids

2019 ◽  
Vol 63 (4) ◽  
pp. 433-456 ◽  
Author(s):  
Steve Minchin ◽  
Julia Lodge
Keyword(s):  
Nucleic Acids ◽  
Genetic Information ◽  
Deoxyribonucleic Acid ◽  
Double Helix ◽  
Protein Translation ◽  
Structure And Function ◽  
Dna Molecule ◽  
Living Things ◽  
Dna Double Helix ◽  
And Function

Abstract Nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), carry genetic information which is read in cells to make the RNA and proteins by which living things function. The well-known structure of the DNA double helix allows this information to be copied and passed on to the next generation. In this article we summarise the structure and function of nucleic acids. The article includes a historical perspective and summarises some of the early work which led to our understanding of this important molecule and how it functions; many of these pioneering scientists were awarded Nobel Prizes for their work. We explain the structure of the DNA molecule, how it is packaged into chromosomes and how it is replicated prior to cell division. We look at how the concept of the gene has developed since the term was first coined and how DNA is copied into RNA (transcription) and translated into protein (translation).

Protamine-DNA interaction

1978 ◽  
Vol 36 (2) ◽  
pp. 200-201
Author(s):  
D.P. Bazett-Jones ◽  
F.P. Ottensmeyer
Keyword(s):  
Small Volume ◽  
Double Helix ◽  
Dna Interaction ◽  
Dark Field ◽  
Sperm Head ◽  
Nuclear Proteins ◽  
Field Electron Microscopy ◽  
Dark Field Electron ◽  
Dna Double Helix ◽  
Positively Charged

Dark field electron microscopy has been used for the study of the structure of individual macromolecules with a resolution to at least the 5Å level. The use of this technique has been extended to the investigation of structure of interacting molecules, particularly the interaction between DNA and fish protamine, a class of basic nuclear proteins of molecular weight 4,000 daltons.Protamine, which is synthesized during spermatogenesis, binds to chromatin, displaces the somatic histones and wraps up the DNA to fit into the small volume of the sperm head. It has been proposed that protamine, existing as an extended polypeptide, winds around the minor groove of the DNA double helix, with protamine's positively-charged arginines lining up with the negatively-charged phosphates of DNA. However, viewing protamine as an extended protein is inconsistent with the results obtained in our laboratory.

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