Laser Raman identification of an interaction site on DNA for arginine containing histones in chromatin

Raman microspectroscopy: shining a new light on reproductive medicine

BACKGROUND The last 20 years have seen an enormous upsurge in the number of publications reporting findings obtained by Raman spectroscopy, a non-invasive, non-destructive method which uses the inelastic scattering of light to provide a 'fingerprint' of the sample's chemical composition and constituents. Long neglected because of practical difficulties, the technique has been transformed by recent technological advances into a powerful analytical tool capable of opening avenues of investigation that were previously out of the reach of biomedical scientists. Beyond introducing the approach and describing its relative merits and weaknesses, the aim of this review is to provide a spur for discussion of what may become an invaluable tool for biomedical investigations. METHODS A comprehensive review of the literature was conducted searching PubMed and Ovid databases using numerous MeSH terms associated with reproductive medicine. Furthermore, the reference lists of all reported literature were explored. The searches were restricted to English language articles published in the last 50 years. RESULTS Beginning with simple characterizations of biologically and medically important substances, aided by increasing technological sophistication, the use of Raman spectroscopy in biomedicine has quickly expanded to the investigation of complex biochemical interactions, the assessment of organelles and now the evaluation of living cells and tissue. The first Raman investigations of reproductive organs were primarily oncological in nature; however, the past few years have seen an increase in the application of the technique for the assessment and evaluation of both male and female gametes. In particular, progress has been made in the characterization, identification and localization of sperm nuclear DNA damage. CONCLUSIONS The use of Raman spectroscopy has already provided many tantalizing glimpses into the potential that the technique has to answer many of the unresolved issues in investigative and therapeutic reproductive medicine. However, without stringent assessment and the clear representation of the methods' findings, their true meaning cannot be revealed nor should any conclusions be hastily derived. For the potential of Raman microspectroscopy to be truly realized, the dependability and reliability of the technique and its results can only be ascertained by multidisciplinary collaborations that undertake carefully conducted, controlled and analysed studies.

Are there molecules of nucleoprotamine?

A short critical review of the data related to protamine and nucleoprotamine (DNP) structure is given. A new model is proposed for DNP structure in which protamine molecules are located in channels between the DNA molecules. DNA molecules are arranged hexagonally in the x-y plane, whereas their relative positions with respect to the z-axis are shifted by 0, 1/3, and 2/3 of the pitch of the double helix. As a result, large cavities are formed in three out of six channels surrounding each DNA molecule where the large grooves are juxtaposed. Protamine molecules are also proposed to have some secondary/tertiary structure prior to complex formation. Inside the channels, a protamine molecule modifies its shape to fill the large grooves of all of the three surrounding DNA molecules simultaneously, and might possibly be in touch with other protamine molecules in neighbouring positions as well. This disposition allows the protamine molecules to be located between DNA molecules without a significant increase in the lattice parameters.

Evidence of novel secondary structure in DNA-bound protamine is revealed by Raman spectroscopy

Raman spectroscopy studies of protamine-DNA complexes are reported for samples in the solid state at 98% relative humidity. Previous reports utilizing other physical techniques have indicated the presence of B-form DNA in protamine-DNA complexes. The present Raman data support the assignment of a modified B-form which is characterized by appreciable unstacking of the bases. The quality of the present spectra has made it possible, for the first time, to obtain the Raman spectrum of DNA-bound protamine by digital spectral subtraction. The difference spectrum indicates that protamine adopts an unusual secondary structure upon binding to DNA. A dominant amide I band is observed at 1683 cm-1 which is indicative of neither an alpha-helix or beta-sheet conformation. An amide I band at this position has been associated with the 1-->3 hydrogen bond that occurs within a gamma-turn [Bandekar, J., & Krimm, S. (1985) Int. J. Pept. Protein Res. 26, 158-165]. On the basis of this assignment, as well as preliminary results obtained by computer modeling, we propose a new model for the secondary structure of DNA-bound protamine that is rich in 1-->3 hydrogen bonding. Spectral data demonstrate that this structure is absent in protamine molecules in solution. Analyses of spectra of polyarginine-DNA complexes suggest that polyarginine, although similar to protamine in primary structure, assumes a conformation when bound to DNA that is distinct from that adopted by protamine.

Raman microspectroscopic approach to the study of human granulocytes

A sensitive confocal Raman microspectrometer was employed to record spectra of nuclei and cytoplasmic regions of single living human granulocytes. Conditions were used that ensured cell viability and reproducibility of the spectra. Identical spectra were obtained from the nuclei of neutrophilic, eosinophilic, and basophilic granulocytes, which yield information about DNA and protein secondary structure and DNA-protein ratio. The cytoplasmic Raman spectra of the three cell types are very different. This was found to be mainly due to the abundant presence of peroxidases in the cytoplasmic granules of neutrophilic granulocytes (myeloperoxidase) and eosinophilic granulocytes (eosinophil peroxidase). Strong signal contributions of the active site heme group(s) of these enzymes were found. This paper illustrates the potentials and limitations for Raman spectroscopic analysis of cellular constituents and processes.

Sequence dependent conformations of oligomeric DNA's in aqueous solutions and in crystals

In order to determine the sequence dependence of the conformation of deoxynucleotides, Raman spectra have been obtained for the following oligodeoxynucleotides in aqueous salt solutions and in crystals: d(CpG)(I), d(TGCGCGCA)(II), d(CACGCGTG)(III), d(CGTGCACG)(IV), d(CGCATGCG)(V), d(ACGCGCGT)(VI), d(CGCGTACGCG)(VII), d(CGCACGTGCG)(VIII) and d(CGTGCGCACG)(IX), d(GCTATAGC) (X), d(GCATATGC) (XI), d(GGTATACC) (XII) and d(GGATATCC) (XIII). The normal B type conformation is observed for all the oligomer DNA's at low salt (0.1-1.0 M NaCl) concentration in the temperature range of 0-25 degrees C. It was considered possible that all of the first nine oligomers could go into the Z form in aqueous high salt (5.0-6.0 M NaCl) solutions, and under these conditions the last four were considered candidates to go into the A form. The B-type conformation was found to exist in high salt solutions for (I), (IV), (V), (VI), (X), (XI) and (XIII); the Z or partial Z conformation appears in high salt solution for the oligomers, (II), (III), (VII), (VIII) and (IX); an A or partial A conformation appears in high salt solution for (XII). In the crystalline state, (IV), (VIII), (X), and (XI) stay in the B-form and all of the other oligomers adopt the complete Z-form except for (XII) which crystallizes in the A form. In both the crystal and in aqueous solutions, the identification of the conformation genus was made by means of Raman spectroscopy. In the crystal of (I), grown at pH7.0, guanosine is found to be in C3'-endo/syn conformation and cytidine in C2'-endo/anti, which may be taken as the ideal building block of the typical Z conformation. At pH4, (I) crystallizes in a conformation similar to the B genus. A study of the thermally induced B to Z transition has been carried out for (II) and (III). Based on the analysis of Raman spectra of the alternating pyrimidine-purine oligomers which might be expected to go into the Z form, the tendency for these oligonucleotides to adopt the Z form can be ranked as: d(CGCGCGCG) greater than (II) greater than (III) greater than (V) approximately (VI) greater than (IV) for octamers and (VII) greater than (VIII) greater than (IX) for the decamers. Similarly, those oligomers which might have a tendency to go into the A form could be ranked as (XII) greater than (XIII) approximately (X) greater than (XI). These data should provide help in formulating rules for predicting the sequence dependence of the B to A and B to Z transitions. Some possible rules are explored, but precautions should be taken.

Modelling and refinement of the crystal structure of nucleoprotamine from Gibbula divaricata

The molecular structure of nucleoprotamine from Gibbula divaricata and its packing in oriented fibers has been modelled both to fit the X-ray diffraction pattern and to avoid steric compression. The representative model consists of 51 poly (dinucleotide) B-DNA helices with 51 poly(hexapeptide) chains associated with the major grooves. The prevailing peptide conformation is beta. The four arginine residues present are hydrogen-bonded to DNA phosphates while neutral peptides protrude into the minor grooves of neighboring nucleoprotamine molecules which are packed 2.61 nm apart in a screw-disordered, quasi-hexagonal lattice. This model reconciles a number of earlier, apparently conflicting experimental results and explains the remarkable stability of nucleoprotamines.

The structure of nucleosome core particles as revealed by difference Raman spectroscopy

Raman spectra have been observed of nucleosome core particles (I) prepared from chicken erythrocyte chromatin, its isolated 146 bp DNA (II), and its isolated histone octamer (H2A+H2B+H3+H4)2 (III). By examining the difference Raman spectra, (I)-(II), (I)-(III), and (I)-(II)-(III), several pieces of information have been obtained on the conformation of the DNA moiety, the conformation of the histone moiety, and the DNA-histone interaction in the nucleosome core particles. In the nucleosome core particles, about 15 bp (A.T rich) portions of the whole 146 bp DNA are considered to take an A-form conformation. These are considered to correspond to its bent portions which appear at intervals of 10 bp.

Laser Raman spectra of calf thymus chromatin and its constituents

Extensive Raman measurements have been made on calf thymus chromatin, core chromatin, the (H3,H4)/DNA complex, and isolated DNA. The results indicate that the alpha-helical content of the nucleosomal histones gradually increases as they form the heterocomplexes that lead to the formation of the octameric nucleosome core. The secondary structure of the latter is not modified as it binds to DNA. The spectra indicate that the DNA essentially retains its B conformation in nucleosomes, although slight changes probably occur in the ribose-phosphate backbone. No specific interactions between the nucleosomal histones and DNA can be established from the spectra, but histone H1 possibly interacts selectively with the thymine bases.

X-ray diffraction study of DNA complexes with arginine peptides and their relation to nucleoprotamine structure

It is shown that the formation of complexes with several arginine peptides stabilizes the B-form of DNA with 10 (+/- 0.15) base-pairs per turn at all relative humidities, even upon complete dehydration. From an analysis of the packing arrangement and from the calculated diffraction patterns, it is concluded that arginine is associated with DNA in its major groove. It is also shown that the diffraction pattern of nucleoprotamine can be interpreted by placing the protamine on the major groove of DNA. The strong intensity on the first layer-line is due to the influence of neutral residues on the diffraction pattern. Thus, we conclude that protamine is bound to the major groove of DNA.

Laser Raman studies of the 5 S rRNA-protein L5 complex of rat liver ribosomes

The effects of ribosomal protein L5 on the conformation of 5 S rRNA in the 5 S rRNA-protein L5 complex extracted from rat liver ribosomes have been studied by laser Raman spectroscopy. A comparison of the spectra shows small protein-induced conformational changes in the 5 S rRNA, but most of the base-paired regions appear to be present in the complex with protein L5 as well as in the free 5 S rRNA. Furthermore specific interactions between 5 S rRNA and protein L5 are indicated. Cytosine (and/or uracil) residues in single-stranded regions and the N(7) of guanine are engaged in interactions with the protein as suggested by the Raman data.

In vitro recognition of DNA base pairs by histones in histone-DNA complexes and reconstituted core particles: an ultraviolet resonance Raman study

Resonance Raman spectra of complexes between DNA and the four core histones, alone or associated, have been investigated in vitro using excitations at 300 and 257 nm, which give complementary informations about the DNA bases. H2A and H2B fractions recognize the G-C base pairs, while H3 and H4 (arginine rich fractions) recognize the A-T base pairs. The associated fractions form complexes with DNA which yield about the same DNA spectral modifications as the DNA-H4 complexes. This reveals the important role of the arginine rich fractions in the core particle formation and confirms the preferential in vitro assembly of nucleosome cores on A-T rich regions of DNA (25).

Stabilization of Z-DNA by polyarginine near physiological ionic strength

The identification of left handed or Z-DNA in solutions of poly d(GC) in high salt suggests that left handed DNA may exist in biological systems if stabilized at lower ionic strength. In the present study we show that binding of polyarginine to the Z form of poly d(GC) results in a protein-Z-DNA complex stable near physiological ionic strength. The percentage of Z-DNA in the low salt polyarginine-poly d(GC) complex was measured from the DNA circular dichroism spectrum. The ratio of Z to B-DNA is a linear function of polyarginine concentration and is sensitive to proteolytic digestion by trypsin. These results suggest that arginine-rich proteins may stabilize Z-DNA in vivo.

Recognition of base pairs by polar peptides in double stranded DNA

The resonance Raman spectrum of native DNA has been obtained using excitation at 257 nm. In a first part, the spectral lines are assigned to the different nucleotide bases which provide the resonance effect. In a second part, the interactions of DNA with basic peptides (Arginine Methylester, Lysine Methylester, Arginyl-Arginine) are investigated using excitation at 300 nm and 257 nm, which give complementary information about the DNA. Both Arginine Methylester and Arginyl-arginine recognize the A-T base pairs, the first one in the large groove, the second one in the narrow groove of DNA. The DNA-Lysine Methylester interaction is very likely not specific but can take place in the large groove of DNA.

On mechanisms determining the interrelationships between DNA and histone components of chromatin

The relative affinity of histones for DNA was studied by the analysis of competitive histone binding to DNA in whole histone/DNA mixtures at physiological and low ionic strengths as well as in water. Use of polyphosphate in similar experiments, as a model of DNA deprived of hydrophobic functional groups allowed us to reject the hypothesis that hydrophobic DNA-histone interaction plays a decisive role in the determination of the relative affinity of histones for DNA, because the orders of histone preference for DNA and for polyphosphate were the same. The relative histone affinity for DNA does not depend on the secondary structure of DNA or on the ionic strength of salt solutions, though the differences in the histone affinities for DNA decrease on lowering the salt concentration. The binding orders of the first and the last molecules of histone type to DNA, studied at various DNA/histone ratios in the medium of physiological ionic strength, are the following: H3+H4, H2A+H2B, H1 and H3+H4, H2A, H2B, H1. In water the binding orders of the first and the last histone molecules to DNA are identical: H3+H4, H2A, H2B+H1. It is concluded that the relative histone affinity for DNA in water/salt solutions is determined by non-ionic interactions between histones bound to DNA. The folding of DNA induced by histone-histone interaction seems to lead to the increase in the correlation between amino acid residues in the histone regions bound to DNA and the ionic DNA-histone interaction becoming stronger.

Nucleosomes structure and its dynamic transitions

The discovery of nucleosomes as a basic repeating unit of the chromatin structure organizing the major part of eukaryotic DNA greatly catalyzes the expansion of our knowledge on chromatin. Several lines of experimental evidence have led to the formulation of the nucleosome conception: the observation of chains of globular particles in electron micrographs of chromatin (Olins & Olins, 1974); the demonstration that DNA is released as a set of discrete sizes upon digestion of chromatin with endogenous nucleases (Hewish & Burgoyne, 1973); the isolation of discrete nucleoprotein particles upon digestion of chromatin with micrococcal nuclease (Rill & Van Holde, 1973).

Form of DNA and the nature of interactions with proteins in chromatin

Studies of native chromatins and of isolated nucleosomes (from calf thymus) show that the DNA is in the B form or modified B form. This was determined by Raman spectroscopy of chromatins, of nucleosomes (from calf thymus) and of DNA fibres and directly correlated with X-ray diffraction studies. The Raman spectra of three forms of DNA (A, B and C) have been characterized in fibres both by X-ray diffraction and Raman spectroscopy on the same sample. In particular, the Raman spectrum of the C form of DNA is characterized by a band of about 870 cm(-1). For the first time, chromatins of different origins with increasing content of non-histone proteins have been investigated by Raman spectroscopy. The site of interaction of the non-histone proteins appears to involve the N7 position of guanine while the histone core does not interact at this site. It is proposed that the mechanism of specific recognition in chromatin involves the large groove.

Secondary structure of histones and DNA in chromatin

Laser Raman spectroscopy indicates that the inner histones which are bound to DNA in chromatin or in isolated nu bodies are similar in conformation to the inner histones which are dissociated from DNA in high-salt solutions. This structure contains, on the average, 51+/-5% alpha-helix and no substantial beta-sheet conformation. It is proposed that the protein core of the nu body has a high alpha-helix content.