Structure Of Ribonucleic Acid Research Articles

Amino acid-directed nucleic acid synthesis. A possible mechanism in the origin of life.

The fact that proteins contain only alpha-amino acids and that protein structure is determined by 3' leads to 5' linked ribonucleotides is postulated to be the result of the copolymerization of these molecules in the prebiotic environment. Ribonucleotides therefore represent partial degradation products and proteins represent a side reaction developing from copolymerization. The basic structural unit of copolymerization is a nucleotide substituted with an amino acid at the 2' postion. Characteristics of modern amino and ribonucleic acid structure are all consistent with and necessary for this hypothesis. The characteristics and individual base assignemnts of the code also provide strong support for origin from the postulated copolymers. All characteristics of the code can be accounted for by this single hypothesis.

The Structure of Tobacco Rattle Virus Ribonucleic Acids: Comparison of Large Oligonucleotides Derived from the 3' Ends

SUMMARY The RNA species of the CAM isolate of tobacco rattle virus have been labelled at their 3′ termini and partially digested with T1 ribonuclease. The two RNAs give an identical pattern of labelled fragments following acrylamide gel electrophoresis, showing considerable structural similarity between the 3′ ends of these molecules. RNA fragments derived from the 3′ ends of short particle RNA and long particle RNA labelled in vitro with 125I were tested for their ability to anneal to complementary long particle RNA. Fragments derived from short particle RNA failed to hybridize, showing that despite their structural similarity, the 3′ sequences of these RNAs are not homologous and that the homologous sequence known to be shared by TRV RNAs are not at the 3′ ends of the molecules.

Effect of aminoacylation on the conformation of yeast phenylalanine tRNA

MUCH effort has been devoted to analysing the effect of aminoacylation on the structure of transfer ribonucleic acid (tRNA). While it is generally held that changes in conformation provide the basis for the discrimination between acylated and non-acylated tRNA in tRNA: aminoacyl tRNA synthetase, tRNA: ribosome and tRNA: co-repressor interactions, the evidence to support this view to date is in serious conflict. We have been using the technique of laser light scattering to investigate the tertiary structure of tRNA (ref. 1). This technique is particularly well suited for analysing structural changes in macromolecules such as tRNA as it can detect changes of as little as 1 % in the translational diffusion constant. The method has the advantage of allowing rapid, continual data monitoring making it possible to study dynamic changes in conformation. We describe here the use of this technique to monitor the diffusion coefficient of aminoacylated tRNA in conditions where deacylation occurs spontaneously. The results clearly demonstrate that: (1) large changes in the conformation of yeast phenylalanine tRNA do occur on aminoacylation, (2) the change can be reduced to an undetectable value by small changes in the solution parameters, and (3), the results apparently provide an explanation for many of the discrepancies observed by others.

The primary structure of non-initiator methionine transfer ribonucleic acid from Bakers' yeast. I. Purification and complete digestion with ribonuclease T1 and pancreatic ribonuclease A.

The methionine acceptor activity of a crude tRNA from bakers' yeast was resolved into two peaks (I and II) by column chromatography on DEAE-Sephadex A-25 with a 1 M phosphate system. Methionine tRNA from peak II was not formylated by E. coli methionyl-tRNA transformylase [EC 2.1.2.9.] after being charged with methionine, whereas that from peak I was formylatable under the same conditions. A substantial amount of unlabelled methionine tRNA, tRNAMetm, was highly purified from the peak II fraction by successive chromatographic procedures. The purified tRNAMetm was digested with pancreatic ribonuclease A [EC 3.1.4.22] and ribonuclease T1 [EC 3.1.4.8]. The digestion products were isolated into individual components and completely sequenced. The results of sequence analysis of the two RNase digests were in good agreement and indicated that the chain length of this tRNA is 76, including 13 modified nucleotides. These oligonucleotide fragments can be constructed into a unique total sequence, assuming a few conventional features of clover leaf structure for the tRNA was established by analyses of partial digestion products with RNase T1, as reported in the accompanying paper.

The primary structure of non-initiator methionine transfer ribonucleic acid from Bakers' yeast. II. Partial digestion with ribonuclease T1 and derivation of the complete sequence.

Large oligonucleotides obtained from partial RNase T1 digestion of tRNAMetm from bakers' yeast (S. cerevisiae, strain Y 185) were isolated by chromatographic procedures and sequenced. The complete sequence of the tRNAMetm was established from the results of this partial digestion, together with those of the complete RNase T1 and A [EC 3.1.4.8 and 22] digestions of tRNAMetm reported in the preceding paper. The structure of this tRNAMetm was arranged into a clover leaf comparable with those of other tRNAMet species including bakers' yeast initiator tRNA.

The relation of structure and function of transfer ribonucleic acid, with special reference to phenylalanine and methionine transfer ribonucleic acids.

Conference Article| October 01 1975 The Relation of Structure and Function of Transfer Ribonucleic Acid, with Special Reference to Phenylalanine and Methionine Transfer Ribonucleic Acids BRIAN F. C. CLARK BRIAN F. C. CLARK 1Department of Chemistry, University of Aarhus, 8000 Aarhus C, Denmark Generalized primary structure for tRNA Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1975) 3 (5): 645–649. https://doi.org/10.1042/bst0030645 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation BRIAN F. C. CLARK; The Relation of Structure and Function of Transfer Ribonucleic Acid, with Special Reference to Phenylalanine and Methionine Transfer Ribonucleic Acids. Biochem Soc Trans 1 October 1975; 3 (5): 645–649. doi: https://doi.org/10.1042/bst0030645 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1975 Biochemical Society1975 Article PDF first page preview Close Modal You do not currently have access to this content.

The three-dimensional structure of yeast phenylalanine transfer ribonucleic acid and its interaction with aminoacyl synthetases.

The three-dimensional structure of yeast phenylalanine transfer ribonucleic acid and its interaction with aminoacyl synthetases.

Changes in secondary structure of poliovirus ribonucleic acid

Infectious single-stranded RNA isolated from mature purified poliovirus was separated into three fractions by means of chromatography on an “evaporated” calcium phosphate column. RNA molecules with a higher degree of secondary structure were detected in two of the fractions as a result of the chromatography. These RNA molecules (i) were resistant to hydrolysis by pancreatic ribonuclease A, (ii) retained unchanged the original infectivity for actinomycin D-pretreated cells, (iii) were resistant to ultraviolet-light inactivation and (iv) were partially resistant to formaldehyde inactivation.

Chemical probe of structure and function of transfer ribonucleic acids.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical probe of structure and function of transfer ribonucleic acidsRam P. SinghalCite this: Biochemistry 1974, 13, 14, 2924–2932Publication Date (Print):July 1, 1974Publication History Published online1 May 2002Published inissue 1 July 1974https://doi.org/10.1021/bi00711a023RIGHTS & PERMISSIONSArticle Views39Altmetric-Citations19LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (1 MB) Get e-Alerts Get e-Alerts

Alterations in structure and function of transfer ribonucleic acid on chemical methylation.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAlterations in structure and function of transfer ribonucleic acid on chemical methylationNatalia P. Trifunac and Alvin I. KrasnaCite this: Biochemistry 1974, 13, 11, 2403–2409Publication Date (Print):May 1, 1974Publication History Published online1 May 2002Published inissue 1 May 1974https://doi.org/10.1021/bi00708a026RIGHTS & PERMISSIONSArticle Views39Altmetric-Citations5LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (889 KB) Get e-Alerts Get e-Alerts

Letter: Paramagnetic rare earth ion probes of transfer ribonucleic acid structure.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTParamagnetic rare earth ion probes of transfer ribonucleic acid structureClaude R. Jones and David R. KearnsCite this: J. Am. Chem. Soc. 1974, 96, 11, 3651–3653Publication Date (Print):May 1, 1974Publication History Published online1 May 2002Published inissue 1 May 1974https://doi.org/10.1021/ja00818a051RIGHTS & PERMISSIONSArticle Views35Altmetric-Citations24LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (385 KB) Get e-Alerts Get e-Alerts

High-resolution nuclear magnetic resonance studies of the structure of transfer ribonucleic acid and other polynucleotides in solution

ADVERTISEMENT RETURN TO ISSUEArticleNEXTHigh-resolution nuclear magnetic resonance studies of the structure of transfer ribonucleic acid and other polynucleotides in solutionDavid R. Kearns and Robert G. ShulmanCite this: Acc. Chem. Res. 1974, 7, 2, 33–39Publication Date (Print):February 1, 1974Publication History Published online1 May 2002Published inissue 1 February 1974https://doi.org/10.1021/ar50074a001RIGHTS & PERMISSIONSArticle Views61Altmetric-Citations80LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (829 KB) Get e-Alerts Get e-Alerts

The restriction in ribonuclease T2 catalysed hydrolysis of oligoribonucleotides after kethoxalation of guanine bases.

Kethoxalation produces a restriction in splitting of phosphodiester bonds between modified Gp and 3′ neighbouring nucleotide irrespectively of the chemical nature of the latter. Possible applications of this observation for analysis of primary structure of ribonucleic acids and polynucleotides are discussed.

Improved estimation of secondary structure in ribonucleic acids.

A SIMPLE method for estimating the most stable secondary structure of an RNA molecule from its sequence was proposed earlier1. This method can be used for predicting and assessing possible secondary structures for recently determined RNA sequences2–4. New experimental5–8 and theoretical9, 10 results allow us to improve the method, without making it more complicated.

The Structure of Tobacco Rattle Virus Ribonucleic Acids: Common Nucleotide Sequences in the RNA Species

SUMMARY It has been shown by competition hybridization experiments that common sequences of about 600 nucleotides are present in TRV long and short particle RNA species. Heteroduplex molecules have been formed by the hybridization of short particle RNA strands with long complementary strands derived from tissue infected with a ‘defective isolate’ of the virus. The heteroduplex molecules were shown to have a lower melting temperature than either the long-long or short-short homoduplexes, indicating some mismatching of base pairs. The results are discussed in the light of our present knowledge about the replication of viruses. Theoretical equations have been derived to describe RNA-RNA competition hybridization and duplex formation.

Structure and Function of Nucleosides and Nucleotides

AbstractThe nucleosides participating in biological processes consist of a sugar and a heterocyclic nucleobase; the nucleotides, which occur as monomers and as building units of polymeric nucleic acids, contain an additional phosphoester group. The complexity of the molecules leads to a complex stereochemistry with which the present progress report is concerned. Particular attention will be devoted to conformational considerations at the sugar groups, the syn‐anti conformation, the position of the C(5′)O(5′) bond relative to the sugar group, and the conformation of the phosphoester bonds. The article touches upon base pairing and base stacking, as well as forces stabilizing the syn conformation, and also deals with the reaction mechanism of the enzyme pancreatic ribonuclease as established from the stereochemistry of nucleotides and the mechanisms of action of the antileukemia drug 6‐azauridine and the antibiotic actinomycin D. Views on the effects of the unusual structures of the “rare” nucleosides 4‐thiouridine, isopentenyladenosine, and dihydrouridine on the structure of transfer ribonucleic acid are also presented.

Preparation, molecular weight, base composition, and secondary structure of giant nuclear ribonucleic acid.

Preparation, molecular weight, base composition, and secondary structure of giant nuclear ribonucleic acid.

Kinetics of ethidium bromide binding as a probe of transfer ribonucleic acid structure.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetics of ethidium bromide as a probe of transfer ribonucleic acid structureThomas R. Tritton and Scott C. MohrCite this: Biochemistry 1973, 12, 5, 905–914Publication Date (Print):February 27, 1973Publication History Published online1 May 2002Published inissue 27 February 1973https://doi.org/10.1021/bi00729a018RIGHTS & PERMISSIONSArticle Views50Altmetric-Citations26LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (2 MB) Get e-Alerts Get e-Alerts

Studies on the secondary structure of nuclear ribonucleic acids.

Rat liver nuclei were separated into two fractions, the nucleolus and the nucleoplasm, by a combined salt-enzymic extraction. RNA was purified from both sources and analysed on sucrose density gradients. In both fractions a prominent heterogeneous RNA class with mean sedimentation coefficient of 18S was found. This material was analysed by measuring the rate of reaction with formaldehyde, the ultraviolet absorbance-temperature profile, the spectrophotometric observation of conformational changes as a function of pH, the spectrophotometric titration of uracil and guanine residues and the effect of both temperature and ionic strength on the spectrophotometric titration of cytosine residues. Nucleoplasmic 18S RNA fraction exhibited, on heating and also by adjustment of the pH to 2.5, a hyperchromicity of about 16%, close to that observed, in control experiments, for ribosomal RNA (22%). Titration of cytosine residues in solutions containing 1mm-NaCl and 0.1m-NaCl yielded pK values equal to 4.41 and 3.84 respectively. These results suggest that this RNA fraction is composed of structurally complex polymers. The hypochromicity of the nucleolar 18S RNA fraction determined by heating or adjusting the pH to 2.5, was not greater than 6% of the initial value. The rate of reaction with formaldehyde was 88% of that observed for the hydrolysed 18S fraction which suggested only 12% hydrogen bonding. pK values for uracil and guanine residues were 10.1 and 10.05 respectively. Titration of cytosine residues yielded a pK of 4.10, which was found to be independent of temperature and ionic strength variations.

Effect of polybasic amines on the immunogenicity of mycobacterial ribonucleic acid.

The five polybasic amines, methylated bovine serum albumin (MBSA), protamine sulfate, neomycin sulfate, streptomycin sulfate, and diethylaminoethyl-dextran (DEAE-dextran), were examined to determine their effects on the immunogenic activity of mycobacterial ribonucleic acid (RNA) preparations, and whether they could substitute for Freund incomplete adjuvant (FIA) by protecting the mycobacterial RNA in vivo. These compounds were either emulsified in FIA or not emulsified in FIA. Different results were obtained when these compounds, complexed with mycobacterial RNA, were emulsified in FIA. MBSA, in ratios of mycobacterial RNA-MBSA of 1:0.2 to 1:0.4, had no effect on immunogenic activity. However, when the ratio was increased to 1:1, 1:2, or to 1:4, marked inhibition of the immunogenic activity occurred. Protamine sulfate and neomycin sulfate also inhibited the immunogenic activity of mycobacterial RNA; however, neither streptomycin sulfate nor DEAE-dextran had any effect on immunogenic activity. Without being emulsified in FIA, these five polybasic amines, with the exception of DEAE-dextran, acted only as weak adjuvants for mycobacterial RNA and, therefore, could not be used as substitutes for FIA for the protection of mycobacterial RNA from host nucleases. DEAE-dextran, although not as effective as FIA, afforded some protection for the mycobacterial RNA. DEAE-dextran alone also produced a low degree of nonspecific immunity against tuberculosis. Since MBSA, protamine sulfate, and neomycin sulfate reduce the biological activity of mycobacterial RNA after complexing with it, it is probable that these compounds "mask" the immunogenic sites on the mycobacterial RNA structure.