• Volume 8, Issue 3-4

      August 1985,   pages  507-835

    • Polymorphism in B-DNA: X-ray diffraction studies on Li-DNA fibres

      P Parrack M Sundaramoorthy V Sasisekharan

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      From X-ray diffraction studies it is generally believed that B-DNA has the structural parameters n = 10 and h = 3.4 Å. However, for the first time we report that polymorphism in the B-form can be observed in DNA fibres. This was achieved by the precise control of salt and humidity in fibres and by the application of the precession method of X-ray diffraction to DNA fibres. The significant result obtained is that n = 10 is not observed for crystalline fibre patterns. In fact, n = 10 and h = 3.4 Å are not found to occur simultaneously. Instead, a range of values, n = 9.6–10.0 and h = 3.35 Å–3.41 Å is observed.

    • Structural implications of electric-field induced dichroism of nucleic acids: Studies of alternating purine-pyrimidines

      Elliot Charney

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      Transient and steady-state electric dichroism measurements of double helical poly(dG-dC) and its 5-methyl guanosine analogue and transient electric dichroism measurements of double helical poly(dA-dT) are shown to give the following information on the structural and dynamical properties of these molecular systems: (i) the Z form structure of the alternating guanosine-cytidine moieties has the same inter base-pair separation in solution as it does in the fibre and crystalline forms; (ii) the mean normal to the base pairs (and thus their average tilt and twist) of the B and Z forms of the guanosine-cytidine moieties is very nearly the same despite the large difference in their secondary structure; (iii) the alternating adenosinethymidine nucleic acid is at least twice as flexible as random-sequence DNA.

    • Some effects of metal ions on DNA structure and genetic information transfer

      G L Eichhorn J J Butzow Y A Shin

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      The reaction of metal ions with nucleic acids can lead to a variety of dramatic effects on nucleic acid structure, e.g., crosslinking of the polymer strands, degradation to oligomers and monomers, stabilization or destabilization, and the mispairing of bases. These effects have important implications for genetic information transfer. Metal ions are involved in many aspects of this transfer; we are presently concerned with the effect of metal ions on the orientation of the active site of RNA polymerase.

      Many of the effects of metal ions on nucleic acid structure involve changes in the conformation of the macromolecules. We have found that conditions that have been used to convert B DNA to Z DNA lead to at least two other conformational changes, and phase diagrams delineate the realms of stability of each of the forms. We have carried out a number of studies that demonstrate that the conversion of B to Z DNA is very closely correlated with a substantial decrease in the ability of the DNA to act as a template for RNA synthesis.

    • Nuclear magnetic resonance studies on oligo-deoxyribonucleotides containing thedam methylation site GATC. Adenine methylation of d(GGATCC) does not change the helix geometry

      G Victor Fazakerley Andre Guy Robert Teoule Wilhelm Guschlbauer

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      We have studied the conformation of two hexanucleotides d(GGATCC) and d(GGm6ATCC) using proton nuclear magnetic resonance. Nuclear Overhauser effect measurements show that d(GGATCC) assumes a normal right handed B helix. The single and double strand resonances are in fast exchange on a proton nuclear magnetic resonance time scale. For d(GGm6ATCC), up to the Tm separate resonances are observed for each state, indicating slow exchange, though above the Tm it becomes more rapid. The orientation of the adenosine methyl-amino group, preferentiallycis to N1, hinders base pair formation.The connectivities of the resonances of the two states were established by saturation transfer experiments. At 0°C irradiation of the m6 A-T imino proton gives an nuclear Overhauser effect to AH2 showing that base pairing is Watson-Crick. Intra and interresidue nuclear Overhauser effects starting from the 3′ terminus show that the helix is right handed and in the B-form.The results on the two oligomers demonstrate that adenosine methylation induces little or no change in the conformation of the helix, but reduces the Tm from 45° to 32°C and slows the opening and closing of the m6A.T base pair by a factor of about 100.

    • Quantitative internuclear distancesvia two-dimensional nuclear magnetic resonance spectra: A test case and a DNA octamer duplex

      Thomas L James Gregory B Young Michelle S Broido Joe W Keepers Nadege Jamin Gerald Zon

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      Two-dimensional proton nuclear magnetic resonance nuclear Overhauser effect experiments have been performed at a series of mixing times on proflavine and on a DNA octamer duplex [d-(GGAATTCC)]2 in solution. Using the complete matrix approach recently explored theoretically (Keepers and James, 1984), proton-proton internuclear distances were determined quantitatively for proflavine from the two-dimensional nuclear Overhauser effect results. Since proflavine is a rigid molecule with X-ray crystal structure determined, interproton distances obtained from the two-dimensional nuclear Overhauser effect experiments in solution can be compared with those for the crystalline compound agreement is better than 10 %. Experimental two-dimensional nuclear Overhauser effect spectral data for [d-(GGAATTCC)]2 were analyzed by comparison with theoretical two-dimensional nuclear Overhauser effect spectra at each mixing time calculated using the complete 70 × 70 relaxation matrix. The theoretical spectra were calculated using two structures: a standard B-form DNA structure and an energy-minimized structure based on similarity of the octamer's six internal residues with those of [d-(CGCGAATTCGCG)]2, for which the crystal structure has been determined. Neither the standard B-DNA nor the energy-minimized structure yield theoretical two-dimensional nuclear Overhauser effect spectra which accurately reproduce all experimental peak intensities. But many aspects of the experimental spectra can be represented by both the B-DNA and the energy-minimized structure. In general, the energy-minimized structure yields theoretical two-dimensional nuclear Overhauser effect spectra which mimic many, if not all, features of the experimental, spectra including structural characteristics at the purine-pyrimidine junction.

    • Left handed DNA in synthetic and topologically constrained form V DNA and its implications in protein recognition

      Y S Shouche P K Latha N Ramesh K Majumder V Mandyan Samir K Brahmachari

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      We have investigated structural transitions in Poly(dG-dC) and Poly(dG-Me5dC) in order to understand the exact role of cations in stabilizing left-handed helical structures in specific sequences andthe biological role, if any, of these structures. From a novel temperature dependent Z ⇌ B transition it has been shown that a minor fluctuation in Na+ concentration at ambient temperature can bring about B to Z transition. Forthe first time, wehave observed a novel Z⇌B⇌Zuble transition in poly(dG-Me5dC) as the Na+ concentration is gradually increased. This suggests that a minor fluctuation in Na+ concentration in conjunction with methylation may transform small stretches of CG sequences from one conformational state to another. These stretches could probably serve as sites for regulation. Supercoiled formV DNA reconstituted from pBR322 and pβG plasmids have been studied as model systems, in order to understand the nature and role of left-handed helical conformation in natural sequences. A large portion of DNA in form V, obtained by reannealing the two complementary singlestranded circles is forced to adopt left-handed double helical structure due to topological constraints (Lk = 0). Binding studies with Z-DNA specific antibody and spectroscopic studies confirm the presence of left-handed Z-structure in the pβG and pβR322 form V DNA. Cobalt hexamine chloride, which induces Z-form in Poly(dG-dC) stabilizes the Z-conformation in form V DNA even in the non-alternating purine-pyrimidine sequences. A reverse effect is observed with ethidium bromide. Interestingly, both topoisomerase I and II (from wheat germ) act effectively on form V DNA to give rise to a species having an electrophoretic mobility on agarose gel similar to that of open circular (form II) DNA. Whether this molecule is formed as a result of the left-handed helical segments of form V DNA undergoing a transition to the right-handed B-form during the topoisomerase action remains to be solved.

    • The conformations and energetics of photodamaged DNA

      David A Pearlman Sung-Hou Kim

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      Energy minimization techniques are used in conjunction with the results of small molecule crystallographic studies on relevant compounds to propose structural models for photodamaged DNAs. Specifically, we present models both for a DNA molecule containing a psoralen photo-crosslink and for a DNA molecule containing a thymine photodimer. In both models, significant distortions of the nucleic acid helix are observed, including kinking and unwinding at the damage site and numerous changes in the backbone torsion angles relative to their standard conformations. Both the torsion angle geometries and the energetics of the models are presented in detail.

    • Rigorous conformational analysis of right and left DNA helices and junction between them

      V G Tumanyan Yu A Neyfack M K Pirtskhalava J H Männik

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      On the basis of complete scanning through conformational space of dihedral angles, twelve structural genera were obtained. Subsequent energy minimization within these genera yielded a limited set of duplexes with stacking: right-handed B-form (Wilkins type), B2-form (Watson and Crick type) and left-handed Ll-form (Sasisekharan type) and the new L2-form. In the polymeric DNA only right-handed double-helices are possible, the left-handed helices are forbidden due to poor 1–5 interchain contacts. In contrast, for short fragments the left- and right-handed helicek have practically the same energies providing some physical ground for side-by-side form, which biologically is possible as recombination form and may be as replication form.

    • Comparison of interproton distances in DNA models with nuclear Overhauser enhancement data

      B Gopalakrishnan Manju Bansals

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      The conformational flexibility inherent in the polynucleotide chain plays an important role in deciding its three-dimensonal structure and enables it to undergo structural transitions in order to fulfil all its functions. Following certain stereochemical guidelines, both right and left handed double-helical models have been built in our laboratory and they are in reasonably good agreement with the fibre patterns for various polymorphous forms of DNA. Recently, nuclear magnetic resonance spectroscopy has become an important technique for studying the solution conformation and polymorphism of nucleic acids. Several workers have used 1H nuclear magnetic resonance nuclear Overhauser enhancement measurements to estimate the interproton distances for the various DNA oligomers and compared them with the-interproton distances for particular models of A and B form DNA. In some cases the solution conformation does not seem to fit either of these models. We have been studying various models for DNA with a view to exploring the full conformational space allowed for nucleic acid polymers. In this paper, the interproton distances calculated for the different stereochemically feasible models of DNA are presented and they are compared and correlated against those obtained from1H nuclear magnetic resonance nuclear Overhauser enhancement measurements of various nucleic acid oligomers.

    • Chain flexibility and configurational dimensions of left handed Z- DNA and right handed B-DNA helices

      R Malathi N Yathindra

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      The configurational behaviour of flexible helices of right handed B- and left handed Z-types have been analysed using statistical mechanical procedures. The configuration-dependent parameter, most importantly, the persistence length has been computed, using the heminucleotide scheme of treating polynucleotide chains under the approximation that perturbations in the backbone torsions produce sufficient flexibility in these helices. The values of persistence lengths obtained for Z-helices are very much higher than that of B-helices indicating that former is less flexible compared to the latter. These are in accordance with the results obtained recently on B- and Z-forms of poly(dG-dC). (dG-dC) using light scattering studies. Also the persistence lengths of BII-DNA helices characterised by a skew 3'-hemiucleotide (ε-270°), and also when they coexist with B-DNA have been computed and the values lie within the range of experimentally reported values on B-helices. It is argued that the decrease in the persistence length values of B-DNA at higher salt concentration is due to additional small fluctuations in sugar residue torsions induced due to neutralisation of electrostatic repulsions between adjacent phosphates of the nucleotide. Noteworthy is that these are correlated to winding angle variations and the consequent bending of the helix.

    • Simple theoretical models for biochemical systems, with applications to DNA

      R Bonaccorsi E Scrocco J Tomasi

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      A set oflogically connected models, to study chemical systems ofbiological interest, is presented. The sequence in the set is dictated by a progressive reduction of details with a corresponding enlargement of the field of application. The exposition starts with models suitable for interactions among a finite number of molecules, passes then to models considering also solvent effects and ends with models specialized for DNA containing systems.

    • Interaction of twoLAC repressor protein segments with polynucleotides

      M V R Rao M Atreyi G Suresh Kumar Satish Kumar V S Chauhan

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      The interaction of the oligopeptides Ala-Gln-GIn-Leu-Ala-Gly-OH and Gln-Leu-Ala-Gly-OMe corresponding, respectively, to the sequence 53–58 and 55–58 oflac repressor protein with four polynucleotides was studied. The two peptides did not interact with poly dA. poly dT, poly d(A-T)·poly d(A-T) or poly d(A-G)·poly d(C-T). But they interacted in a characteristic way with poly d(A-C). poly d (G-T), the sequences of which are in abundance in thelac operator region. Both the peptides stabilised the melting of poly d (A-C). poly d (G-T) at a peptide to nucleotide ratio (P/N) of 4; at lower ratios, they destabilised the DNA slightly. The circular dichroism of the alternating polynucleotide with CAC/GTG sequences was perturbed by both the oligopeptides. The hexapeptide at a P/N of 4 caused the transformation of the B-form circular dichroism spectrum to a new state, characterised by strong 220 and 240 nm bands, and a rather weak long wavelength spectrum.

    • Recognition schemes for protein-nucleic acid interactions

      Girjesh Govil N Y Kumar M Ravi Kumar R V Hosur Kunal B Roy H Todd Miles

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      The molecular forces involved in protein-nucleic acid interaction are electrostatic, stacking and hydrogen-bonding. These interactions have a certain amount of specificity due to the directional nature of such interactions and the spatial contributions of the steric effects of different substituent groups. Quantum chemical calculations on these interactions have been reported which clearly bring out such features.

      While the binding energies for electrostatic interactions are an order of magnitude higher, the differences in interaction energies for structures stabilised by hydrogen-bonding and stacking are relatively small. Thus, the molecular interactions alone cannot explain the highly specific nature of binding observed in certain segments of proteins and nucleic acids. It is therefore logical to assume that the sequence dependent three dimensional structures of these molecules help to place the functional groups in the correct geometry for a favourable interaction between the two molecules.

      We have carried out 2D-FT nuclear magnetic resonance studies on the oligonucleotide d-GGATCCGGATCC. This oligonucleotide sequence has two binding sites for the restriction enzyme Bam H1. Our studies indicate that the conformation of this DNA fragment is predominantly B-type except near the binding sites where the ribose ring prefers a3E conformation. This interesting finding raises the general question about the presence of specificity in the inherent backbone structures of proteins and nucleic acids as opposed to specific intermolecular interactions which may induce conformational changes to facilitate such binding.

    • New light on tautomerism of purines and pyrimidines and its biological and genetic implications

      David Shugar Borys Kierdaszuk

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      The tautomerism of the natural 1-substituted pyrimidines and 9-substituted purines found in nucleic acids has been re-examined in the light of new experimental data on various nitrogen heterocycles in solution, in the gas phase and, in part, in low-temperature inert matrices. The results are compared with those obtained by quantum chemical calculations, including improved versions of the latter. Examples are presented of natural nucleosides which exhibit appreciable tautomerism in solution,e.g. formycins A and B, isoguanosine, but are not found in DNA. Illustrations are given of synthetic promutagenic nucleosides with pronounced tautomerism in solution relevant to their role in mutagenesis, such as the N4-hydroxy-and N4-methoxy cytidines. The amino-imino tautomeric equilibria of the promutagenic N6-hydroxy-and N6 -methoxy-adenosines are highly dependent on the solvent medium, the proportion of the imino species varying from 10% in CCl4 to 90% in aqueous medium. The type of base pairing of these is dependent on the conformation of the exocyclic hydroxy or methoxy groups. At the monomer level, addition of a potentially complementary base leads to a shift in the tautomeric equilibrium in favour of the species which pairs with this base. Biological and genetical implications of the foregoing are described.

    • The mutation buffering concept of biomolecular structure

      Michael Conrad

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      Redundant elements in proteins and nucleic acids serve to buffer the effect of point mutations on features of conformation critical for function. Mutation buffering associated with mechanistically redundant amino acids facilitates the evolution of proteins. Such redundant amino acids accumulate by hitch-hiking along with the evolutionary advances which they facilitate. Redundancies in DNA (such as introns and repetitive DNA) prevent extraneous sequence dependent conformational effects from interfering with readout. They also facilitate regulatory evolution. According to the mutation buffering concept biological organizations are selected to facilitate evolution. As a consequence biological information processing is very different from information processing in man-made computers. The link between molecular conformation, evolutionary processes, and information processing is formulated in terms of a tradeoff principle. By utilizing mutation buffering biological systems sacrifice programmability; by achieving programmability digital computers make mutation buffering computationally expensive and hence sacrifice evolutionary adaptability.

    • Specificity in the interaction of non intercalative groove binding ligands with nucleic acids

      B Pullman

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      This paper presents results of theoretical computations on the interaction energies and geometries for the binding to nucleic acids of a number of representative groove binding non intercalating drugs: netropsin, distamycin A, SN 18071, etc. The computations account for the specificity of binding in all cases and demonstrate that the formation of hydrogen bonds is not necessary neither for binding nor for the preference for the minor groove of AT sequences of B-DNA. It appears that if a relatively good steric fit can be obtained in the minor groove, the interaction will be preferentially stabilized there by the favorable electrostatic potential generated in this groove by the AT sequences. The computation of the interaction energies in free space does not reproduce, however, the order of affinities of the ligands studied and yields too great values of the binding energies. The introduction of the solvent effect, through the computation of the hydration and cavitation effects, confirms the specificity, improves the ordering and brings the values of the energies close to the experimental ones. The theoretical account of the “surprising” effect of netrospin binding to the major groove of theTψC stem of tRNAPhe confirms the decisive significance of the distribution of the molecular electrostatic potential for the selection of the binding site. The inclusion in the computations of the flexibility of DNA enables to predict correctly the main features of the macromolecular deformation upon the binding of the ligand.

    • Conformational aspects of drug-DNA interactions: Studies on anthracycline antibiotics and psoralen derivatives

      M Palumbo L Capasso G Palù S Marcianimagno

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      The interaction of anticancer agents, analogues of adriamycin and of photo-chemotherapeutic compounds of the psoralen structural type with DNA was investigated using spectroscopic, hydrodynamic and chiroptical techniques. The nucleic acid may undergo conformational changes from the B form to more compact structures as a result of the binding process to charged compounds. Different complex geometries adopted byvarious drugs were observed and discussed in terms of intercalation into the polynucleotide double helix and orientation of the ligand in the base-pair pocket. The binding of chemotherapeutic agents to functionally organized DNA was also studied. Lower binding affinities and modified spectral responsesareindicativeofdifferent drug-DNA complexation patternsinthiscase. The results of these studies allow a better understanding of drug-nucleic acid interactions at a molecular level.

    • Interaction of 4′-6-diamidino-2-phenylindole 2HCl with synthetic and natural deoxy- and ribonucleic acids

      G Manzini L Xodo M L Barcellona F Quadrifoglio

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      The interaction of 4′-6-diamidino-2-phenylindole · 2 HCl with natural and synthetic polydeoxy- and polyribonucleotides of different base content and sequences was studied with circular dichroism, ultracentrifugation, viscosity and calorimetry. All the polymers show two types of binding. The strength of interaction and its resistence to ionic strength are related to the content of AT clusters in the chain. On the other hand, sedimentation measurements rule out an intercalation mechanism. A model of 4'-6-diamidino-2-phenylindole · 2 HCl interaction with DNA and double stranded RNA, similar to that displayed by distamycin and netropsin, is proposed.

    • Quantum mechanical studies on the activity of anticancerous drug — Ellipticine

      Nitish K Sanyal M RoyChoudhury S N Tiwari

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      Ellipticine compounds, derivatives of pyrido-(4-3b) carbazole are used in the human cancer therapy. Most of these drugs interact directly with DNA molecule. CNDO method, alongwith second order perturbation theory and multicentered-multipole approxiation have been used to compute intermolecular interaction energies of ellipticine with DNA ase pairs (GC and AT) in both normal and inverted cases. An attempt has been made to correlate the drug-nucleic acid interactions for ellipticine to locate site of drug action and binding pattern on the basis of intermolecular forces

    • Importance of DNA conformation in the reaction with cis-dichlorodiammine platinum (II)

      M Leng J M Malinge M Ptak

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      Cis-dichlorodiammine platinum (II) has been reacted with synthetic polynucleotides either in B or in Z conformation. The binding of cis-dichlorodiammine platinum (II) stabilizes the Z conformation when reacted with poly (dG-m5dC) ·poly (dG-m5dC) in the Z conformation as shown by circular dichroism and by the antibodies to Z-DNA. On the other hand, the binding of cis-dichlorodiammine platinum (II) stabilizes a new conformation when reacted with poly(dG-dC)·poly(dG-dC) or poly (dG-m5dC)·poly(dG-m5dC) in the B conformation. The antibodies to Z-DNA bind to these platinated polynucleotides. In rabbits, the injection of platinated poly (dG-dC) poly (dG-dC) induces the synthesis of antibodies which recognize Z-DNA. In low salt conditions, the circular dichroism spectra of these platinated polynucleotides differ from those of B-DNA or Z-DNA. The characteristic31P nuclear magnetic resonance spectrum of Z-DNA is not detected. It appears only at high ionic strength, as a component of a more complex spectrum.

    • Conformational aspects and functions of tRNA

      T Miyazawa S Yokoyama

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      In the process of protein biosynthesis, an aminoacyl-tRNA synthetase strictly recognizes the cognate amino acid and tRNA species. Spectroscopic and biochemical analyses have been made of a heterologous system ofThermus thermophilus glutamyl-tRNA synthetase andEscherichia coli tRNAGlu. The conformational difference between the initial complex and active complex has been observed, which is probably related with the strict recognition of aminoacyl-tRNA synthetase.

      tRNA species are post-transcriptionally modified at specific sites. Two types of modified uridine nucleosides have been found in the first position of anticodon, namely 5-hydroxyuridine derivatives (xo5U) and 5-methyl-2-thiouridine derivatives (xm5s2U). From the analyses of nuclear magnetic resonance spectra, the conformational characteristics of the two types of modified uridine nucleotides have been found to be remarkably different from each other. The conformational flexibility of xo5U nucleotides allow the multiple recognition of codons, whereas the conformational rigidity of xm5s2U nucleotides guarantees the recognition of correct codons. The modification of uridines in the first position of anticodon contributes to the correct and efficient translations of codons in protein biosynthesis.

    • Mapping the structure of macromolecular assemblies by combining chemical modification and separation methods

      C R Cantor R Benezra C-F Hui C L Smith J Welsh

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      Several examples will be described in which powerful separation methods are combined with relatively simple chemical modification techniques to provide structural information on complex macromolecular assemblies. Ribosomal RNA structure has been examined by crosslinking, separating individual crosslinked species by gel electrophoresis, and enzymatic methods for determination of crosslink positions in the nucleotide sequence. Chromatin structure has been examined by footprinting the location of individual nucleosomes by a combination of chemical nicking and DNA separations. Virus structure can be examined by using breakable crosslinkers analyzed with diagonal gel electrophoresis. Ultimately such methods may allow structural information to be obtained on systems even as complex as whole chromosomes.

    • Studies on the structure and function of 16S ribosomal RNA using structure-specific chemical probes

      Harry F Noller Barbara J Van Stolk Danesh Moazed Stephen Douthwaite Robin R Gutell

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      Recent technological developments permit us to examine the accessibility of specific atoms on any nucleotide in any large RNA molecule to certain chemical probes. This can provide detailed information about the higher order structure of large RNA molecules, including secondary and tertiary structure, protein-RNA contacts, binding sites for functional ligands and possible biologically significant conformational changes. Here, we summarize recent studies on (i) the conformation of naked 16S rRNA under a variety of ionic conditions, and (ii) the behaviour of 16S rRNA in active and inactive 30S subunits, as defined by Zamir, Elson and their colleagues. The latter study reveals a reciprocal conformational change in the vicinity of the decoding region of 16S rRNA in 30S ribosomal subunits. This conformational change appears to be a rearrangement of tertiary and/or quaternary structure involving several universally conserved nucleotides. No reproducible effects are seen elsewhere in the molecule, suggesting that the active-inactive transition is a result of the observed conformational change.

    • Do ribosomal RNAs act merely as scaffold for ribosomal proteins?

      D P Burma A K Srivastava S Srivastava D Dash D S Tewari B Nag

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      Investigations that are being carried out in various laboratories including ours clearly provide the answer which is in the negative. Only the direct evidences obtained in this laboratory will be presented and discussed. It has been unequivocally shown that the interaction between 16S and 23S RNAs plays the primary role in the association of ribosomal subunits. Further, 23S RNA is responsible for the Binding of 5S RNA to 16S.23S RNA complex with the help of three ribosomal proteins, L5, L18, L15/L25. The 16S.23S RNA complex is also capable of carrying out the following ribosomal functions, although to small but significant extents, with the help of a very limited number of ribosomal proteins and the factors involved in protein synthesis: (a) poly U-Binding, (B) poly U-dependent Binding of phenylalanyl tRNA, (c) EF-G-dependent GTPase activity, (d) initiation complex formation, (e) peptidyl transferase activity (puromycin reaction) and (f) polyphenylalanine synthesis. These results clearly indicate the direct involvement of rRNAs in the various steps of protein synthesis. Very recently it has Been demonstrated that the conformational change of 23S RNA is responsible for the translocation of peptidyl tRNA from the aminoacyl (A) site to the peptidyl (P) site. A model has Been proposed for translocation on the Basis of direct experimental evidences. The new concept that ribosomal RNAs are the functional components in ribosomes and proteins act as control switches may eventually turn out to Be noncontroversial.

    • Loopstructures in synthetic oligonucleotides. Hairpin stability and structure studied as a function of loop elongation

      C A G Haasnoot S H de Bruin C W Hilbers G A van der Marel J H van Boom

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      The formation of hairpin structures in the homologous, (partly) self-complementary DNA fragments d(ATCCTATnTAGGAT), n = 0–7, was studied by means of nuclear magnetic resonance, T-jump and ultra-violet techniques. It is shown that all compounds in the series may adopt hairpin-like conformations, albeit for n < 3 this only occurs to a significant amount at relatively low concentrations (∼ 10μM). For the present series of oligonucleotides, hairpin formation is accompanied by an apparent loop enthalpy significantly different from zero. The stability of the DNA hairpins turns out to be at its maximum for loop lengths of four or five residues, whereas earlier experiments (Tinocoet al., 1973) indicated that loop lengths of six to seven residues are most favourable for RNA hairpins. This is explained by considering the difference in geometry of A-RNA and B-DNA helices.

    • Imperfect complementarity and RNA structure

      E N Trifonov

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      Intra- and intermolecular complementary contacts in RNA are not always perfect: a significant amount of mismatch pairs is frequently found in naturally occurring RNA helices. The state of art in studies on mismatch pairs and examples of imperfect complementarity are reviewed. Two more cases are revealed by nucleotide sequence analysis techniques: imperfect complementary contacts Between ends of intervening sequences in eukaryotic mRNA precursors, and possible “stickiness” of mRNA to the ribosomes. The “stickiness” might arise from specific 3-Base periodicity of protein coding sequences which is found to be as universal as the code itself. The imperfect complementary contacts between mRNA and rRNA which monitor the coding frame provide a structural basis for the explanation of leaky frameshift phenomena.

    • Prediction of secondary structures of 16S and 23S rRNA fromEscherichia coli

      A S Kolaskar T A Thanaraj M W Pandit

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      Small and large subunits ofEscherichia coli ribosome have three different rRNAs, the sequences of which are known. However, attempts by three groups to predict secondary structures of 16S and 23S rRNAs have certain common limitations namely, these structures are predicted assuming no interactions among various domains of the molecule and only 40% residues are involved in base pairing as against the experimental observation of 60 % residues in base paired state. Recent experimental studies have shown that there is a specific interaction between naked 16S and 23S rRNA molecules. This is significant because we have observed that the regions (oligonucleotides of length 9–10 residues), in 16S rRNA which are complementary to those in 23S rRNA do not have internal complementary sequences. Therefore, we have developed a simple graph theoretical approach to predict secondary structures of 16S and 23S rRNAs. Our method for model building not only uses complete sequence of 16S or 23S rRNA molecule along with other experimental observations but also takes into account the observation that specific recognition is possible through the complementary sequences between 16S and 23S rRNA molecules and, therefore, these parts of the molecules are not used for internal base pairing. The method used to predict secondary structures is discussed. A typical secondary structure of the complex between 16S and 23S rRNA molecules, obtained using our method, is presented and compared Briefly with earlier model Building studies.

    • Filamentous Bacterial viruses

      D A Marvin

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      The filamentous bacterial virus is a simple and well-characterized model system for studying how genetic information is transformed into molecular machines. The viral DNA is a single-stranded circle coding for about 10 proteins. The major viral coat protein is largely α-helical, with about 46 amino acid residues. Several thousand identical copies of this protein in a helical array form a hollow cylindrical tube 1–2μ long, of outer diameter 60 Å and inner diameter 20 Å, with the twisted circular DNA extending down the core of the tube. Before assembly, the viral coat protein spans the cell membrane, and assembly involves extrusion of the coat from the membrane. X-ray fibre diffraction patterns of the Pf 1 species of virus at 4°C, oriented in a strong magnetic field, give three-dimensional data to 4 Å resolution. An electron density map calculated from native virus and a single iodine derivative, using the maximum entropy technique, shows a helix pitch of 5.9 Å. This may indicate a stretched A-helix, or it may indicate a partially 310 helix conformation, resulting from the fact that the coat protein is an integral membrane protein before assembly, and is still in the hydrophobic environment of other coat proteins after assembly.

    • Similarities in the genomic sequence and coat protein structure of plant virsuses

      M R N Murthy H S Savithri

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      The genomic sequences of several RNA plant viruses including cucumber mosaic virus, brome mosaic virus, alfalfa mosaic virus and tobacco mosaic virus have become available recently. The former two viruses are icosahedral while the latter two are bullet and rod shaped, respectively in particle morphology. The non-structural 3a proteins of cucumber mosaic virus and brome mosaic virus have an amino acid sequence homology of 35% and hence are evolutionarily related. In contrast, the coat proteins exhibit little homology, although the circular dichroism spectrum of these viruses are similar. The non-coding regions of the genome also exhibit variable but extensive homology. Comparison of the brome mosaic virus and alfalfa mosaic virus sequences reveals that they are probably related although with a much larger evolutionary distance. The polypeptide folds of the coat protein of three biologically distinct isometric plant viruses, tomato Bushy stunt virus, southern bean mosaic virus and satellite tobacco necrosis virus have been shown to display a striking resemblance. All of them consist of a topologically similar 8-standard β-Barrel. The implications of these studies to the understanding of the evolution of plant viruses will be discussed.

    • Conformational studies on nucleotide-amino acid interactions leading to origin of life

      R Balasubramanian

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      Living processes may be defined as the self-sustained chemical reactions based on the special chemical machinery of nucleic acid-directed protein synthesis. Its genesis may be traced to the molecular interaction between nucleotides and amino acids leading to a primitive adaptor-mediated ordered synthesis of polypeptides. A primitive decoding system is described and its characteristics are shown to imitate, in a primitive manner, the present-day elaborate machinery of protein synthesis. This molecular interaction theory may be rightly considered as the missing link between the Protochemical and biological Evolution. The origin of chiral specificity observed in living organisms is also traced to this specific molecular interaction in the protobiological milieu.

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