1
|
Ora M, Martikainen K, Lautkoski K. Hydrolytic reactions of cyclic bis(3′-5′)diadenylic acid (c-di-AMP). J PHYS ORG CHEM 2012. [DOI: 10.1002/poc.3070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mikko Ora
- University of Turku; Department of Chemistry; Turku Finland
| | | | | |
Collapse
|
2
|
Laing C, Wen D, Wang JTL, Schlick T. Predicting coaxial helical stacking in RNA junctions. Nucleic Acids Res 2011; 40:487-98. [PMID: 21917853 PMCID: PMC3258123 DOI: 10.1093/nar/gkr629] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
RNA junctions are important structural elements that form when three or more helices come together in space in the tertiary structures of RNA molecules. Determining their structural configuration is important for predicting RNA 3D structure. We introduce a computational method to predict, at the secondary structure level, the coaxial helical stacking arrangement in junctions, as well as classify the junction topology. Our approach uses a data mining approach known as random forests, which relies on a set of decision trees trained using length, sequence and other variables specified for any given junction. The resulting protocol predicts coaxial stacking within three- and four-way junctions with an accuracy of 81% and 77%, respectively; the accuracy increases to 83% and 87%, respectively, when knowledge from the junction family type is included. Coaxial stacking predictions for the five to ten-way junctions are less accurate (60%) due to sparse data available for training. Additionally, our application predicts the junction family with an accuracy of 85% for three-way junctions and 74% for four-way junctions. Comparisons with other methods, as well applications to unsolved RNAs, are also presented. The web server Junction-Explorer to predict junction topologies is freely available at: http://bioinformatics.njit.edu/junction.
Collapse
Affiliation(s)
- Christian Laing
- Department of Chemistry, Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
| | | | | | | |
Collapse
|
3
|
Abstract
Since the year 2000 a number of large RNA three-dimensional structures have been determined by X-ray crystallography. Structures composed of more than 100 nucleotide residues include the signal recognition particle RNA, group I intron, the GlmS ribozyme, RNAseP RNA, and ribosomal RNAs from Haloarcula morismortui, Escherichia coli, Thermus thermophilus, and Deinococcus radiodurans. These large RNAs are constructed from the same secondary and tertiary structural motifs identified in smaller RNAs but appear to have a larger organizational architecture. They are dominated by long continuous interhelical base stacking, tend to segregate into domains, and are planar in overall shape as opposed to their globular protein counterparts. These findings have consequences in RNA folding, intermolecular interaction, and packing, in addition to studies of design and engineering and structure prediction.
Collapse
Affiliation(s)
- Stephen R Holbrook
- Structural Biology Department, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
| |
Collapse
|
4
|
Pretti M. RNA-like polymer model: exact calculation on the Bethe lattice. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 74:051803. [PMID: 17279932 DOI: 10.1103/physreve.74.051803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Indexed: 05/13/2023]
Abstract
We consider a lattice polymer model (random walk), in which the walk is allowed to visit lattice bonds at most twice. Such a model might have some relevance to describe statistical properties of RNA molecules. In order to mimic base pairing, we assign an attractive energy term to each doubly visited bond, and a further contribution to each pair of consecutive doubly visited bonds. The latter term is expected to mimic the stacking effect, whereas no effect of sequence, that is, of chemical specificity, is taken into account. The phase diagram is worked out exactly on a Bethe lattice, in a grand-canonical formulation. In the single molecule limit, the system undergoes two different phase transitions upon decreasing temperature: a Theta-like collapse from a swollen "coil" state to a "molten" state, with a low fraction of doubly visited bonds, and subsequently to a "paired" state, with empty or doubly visited bonds only. The stacking effect drives the latter transition from second to first order.
Collapse
Affiliation(s)
- M Pretti
- Consiglio Nazionale delle Ricerche-Istituto Nazionale per la Fisica della Materia (CNR-INFM), Dipartimento di Fisica, Politecnico di Torino, Corso Duca degli Abruzzi 24, I-10129 Torino, Italy
| |
Collapse
|
5
|
Gendron P, Lemieux S, Major F. Quantitative analysis of nucleic acid three-dimensional structures. J Mol Biol 2001; 308:919-36. [PMID: 11352582 DOI: 10.1006/jmbi.2001.4626] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A new computer program to annotate DNA and RNA three-dimensional structures, MC-Annotate, is introduced. The goals of annotation are to efficiently extract and manipulate structural information, to simplify further structural analyses and searches, and to objectively represent structural knowledge. The input of MC-Annotate is a PDB formatted DNA or RNA three-dimensional structure. The output of MC-Annotate is composed of a structural graph that contains the annotations, and a series of HTML documents, one for each nucleotide conformation and base-base interaction present in the input structure. The atomic coordinates of all nucleotides and the homogeneous transformation matrices of all base-base interactions are stored in the structural graph. Symbolic classifications of nucleotide conformations, using sugar puckering modes and nitrogen base orientations around the glycosyl bond, and base-base interactions, using stacking and hydrogen bonding information, are introduced. Peculiarity factors of nucleotide conformations and base-base interactions are defined to indicate their marginalities with all other examples. The peculiarity factors allow us to identify irregular regions and possible stereochemical errors in 3-D structures without interactive visualization. The annotations attached to each nucleotide conformation include its class, its torsion angles, a distribution of the root-mean-square deviations with examples of the same class, the list of examples of the same class, and its peculiarity value. The annotations attached to each base-base interaction include its class, a distribution of distances with examples of the same class, the list of examples of the same class, and its peculiarity value. The distance between two homogeneous transformation matrices is evaluated using a new metric that distinguishes between the rotation and the translation of a transformation matrix in the context of nitrogen bases. MC-Annotate was used to build databases of nucleotide conformations and base-base interactions. It was applied to the ribosomal RNA fragment that binds to protein L11, which annotations revealed peculiar nucleotide conformations and base-base interactions in the regions where the RNA contacts the protein. The question of whether the current database of RNA three-dimensional structures is complete is addressed.
Collapse
Affiliation(s)
- P Gendron
- Département d'Informatique et de Recherche Opérationnelle, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada
| | | | | |
Collapse
|
6
|
McKay SL, Haptonstall B, Gellman SH. Beyond the hydrophobic effect: attractions involving heteroaromatic rings in aqueous solution. J Am Chem Soc 2001; 123:1244-5. [PMID: 11456685 DOI: 10.1021/ja003256d] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- S L McKay
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | | | | |
Collapse
|
7
|
Itahara T. Effect of the N6-Methyl Group of the Adenine Ring on the Stacking Interaction. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2000. [DOI: 10.1246/bcsj.73.1621] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
8
|
Pang YP, Miller JL, Kollman PA. Computational and Experimental Studies of (2,2)-Bis(indol-1-yl-methyl)acetate Suggest the Importance of the Hydrophobic Effect in Aromatic Stacking Interactions. J Am Chem Soc 1999. [DOI: 10.1021/ja9828410] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuan-Ping Pang
- Contribution from the Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143
| | - Jennifer L. Miller
- Contribution from the Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143
| | - Peter A. Kollman
- Contribution from the Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143
| |
Collapse
|
9
|
Rife JP, Cheng CS, Moore PB, Strobel SA. N 2-methylguanosine is iso-energetic with guanosine in RNA duplexes and GNRA tetraloops. Nucleic Acids Res 1998; 26:3640-4. [PMID: 9685477 PMCID: PMC147776 DOI: 10.1093/nar/26.16.3640] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Modified nucleotides are resource-intensive alternatives to the four nucleotides that constitute the bulk of natural RNAs. Yet, even in cases where modifications are highly conserved, their functions are difficult to identify. One possible function might be to modulate the stability of RNA structures. To investigate this possibility for N 2-methylguanosine (m2G), which is present in a wide variety of RNAs, we have determined the thermodynamic consequences of substituting m2G for G in G-C Watson-Crick pairs and G@U wobble pairs within RNA duplexes. The m2G substitution is iso-energetic with G in all cases, except for aninternal m2G@U pair, where it has a modest (0.3 kcal/mol) stabilizing effect. We have also examined theconsequences of replacing G by m2G, and A by N 6, N 6-dimethyladenosine (m26A) in the helix 45 tetraloop of 16S rRNA, which would otherwise be a standard GNRA tetraloop. This loop is a conserved, hypermethylated region of the ribosome where methylation appears to modulate activity. m26A substitution destabilizes the tetraloop, presumably because it prevents the formation of the G@A sheared pair it would otherwise contain. m2G substitution has no effect on tetraloop stability. Together, these results suggest that m2G is equally stable as either the s-cis or s-trans rotamer. The lack of a significant effect on secondary structural stability in these systems suggests that m2G is introduced into naturally occurring RNAs for reasons other than modulation of duplex stability.
Collapse
Affiliation(s)
- J P Rife
- Department of Chemistry and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | | | | |
Collapse
|
10
|
Abstract
BACKGROUND Ribosomal RNAs contain many modified nucleotides. The functions of these nucleotides are poorly understood and few of them are strongly conserved. The final stem loop in 16S-like rRNAs is an exception in both regards. In both prokaryotes and eukaryotes, the tetranucleotide loop that caps the 3'-terminal stem contains two N6, N6-dimethyladenosine residues. The sequence and pattern of methylation are conserved within the loop, and there is evidence that these methylated nucleotides play an important role in subunit association and the initiation of protein synthesis. Because of the integral role that helix 45 plays in ribosome function, it is important to know what consequences these methylated nucleotides have on its structure. RESULTS We have solved the solution structure of a 14-nucleotide analog of the terminal stem loop of bacterial 16S rRNA, which contains N2-methylguanosine as well as two N6,N6-dimethyladenosines. CONCLUSIONS The methylation of the 16S rRNA stem loop completely alters its conformation, which would otherwise be a GNRA tetraloop. It is likely that the conformation of this loop is crucial for its function, having implications for its interaction with ribosomal subunits and its role in the initiation of protein synthesis.
Collapse
Affiliation(s)
- J P Rife
- Department of Chemistry, Yale University New Haven, CT 06520, USA
| | | |
Collapse
|
11
|
Itahara T. NMR and UV Study of 1,1′-(α,ω-Alkanediyl)bis[thymine] and 1,1′-(α,ω-Alkanediyl)bis[uracil]. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1997. [DOI: 10.1246/bcsj.70.2239] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
12
|
Gellman SH, Haque TS, Newcomb LF. New evidence that the hydrophobic effect and dispersion are not major driving forces for nucleotide base stacking. Biophys J 1996; 71:3523-6. [PMID: 8968621 PMCID: PMC1233839 DOI: 10.1016/s0006-3495(96)79547-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
|
13
|
Zimmerman SC. Molecular Tweezers: Synthetic Receptors for π-Sandwich Complexation of Aromatic Substrates. BIOORGANIC CHEMISTRY FRONTIERS 1991. [DOI: 10.1007/978-3-642-76241-3_2] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
14
|
Structural and Functional Aspects of the N 6,N 6 Dimethyladenosines in 16S Ribosomal RNA. ACTA ACUST UNITED AC 1986. [DOI: 10.1007/978-1-4612-4884-2_23] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
|
15
|
van Knippenberg PH, Heus HA. The conformation of a conserved stem-loop structure in ribosomal RNA. J Biomol Struct Dyn 1983; 1:371-81. [PMID: 6400879 DOI: 10.1080/07391102.1983.10507448] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The RNA of small ribosomal subunits contains a conserved stem-loop structure near the 3' end. Characteristics for the hairpins are: (a) a nine-basepairs stem: (b) a conserved A-UU-G junction in the stem: (c) a conserved sequence Gm6(2)AM6(2)A sequence in the loop (except yeast mitochondria and mutants from bacteria). We are using UV-optics, micro-calorimetry and 500 MHz-NMR to investigate fragments of about 50 nucleotides cleaved from the 3' ends of small ribosomal subunit RNA's by bacteriocins. Our preliminary conclusions are: (1) Dimethylation of the adenines in the loop destabilizes the hairpin because of an increased stacking; (2) melting of the hairpin starts at the ends as well as in the middle at the A-UU-G junction; (3) basepair substitutions have an unexpectedly large effect on thermal stability.
Collapse
|
16
|
Tazawa I, Inoue Y. Intramolecular stacking association and conformation properties of a 'cap' structure, m7G5'pppUm, and the related model compounds. Nucleic Acids Res 1983; 11:2907-15. [PMID: 6856481 PMCID: PMC325932 DOI: 10.1093/nar/11.9.2907] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The stacking equilibrium quotient of the m7G5'pppUm unit, which occurs as the 5'-terminal "cap" of certain eukaryotic mRNA's, was determined by temperature-dependent difference spectrophotometry as Kstack = 1.82 at 25 degrees and pH 5. In order to evaluate the contribution of different structural modifications to the net stabilization of the cap structures of mRNA, a variety of compounds related to m7G5'pppUm were synthesized and their stacking properties were studied by the same method and compared. The results are summarized as: (1) Introduction of a methyl group into N-7 of G residue results in an increase in base stacking. (2) Methylation at 2'-OH of U residue also stabilizes the stacked structure of G-containing dimers, but it does not influence stacking interaction in m7G-containing dimers. (3) The effect of different types of internucleotide linkages on the order of stacking tendencies is: N5'ppN' greater than N5'pppN' greater than NpN'. UV hypochromicity and CD spectral measurements of the relevant dimers were also conducted, and the hypochromicity values and CD spectra of dimers in their stacked conformation were estimated by making use of the determined Kstack values. The results indicate that, while 2'-O-methylation exerts very little effect on the stacked conformation of the dimers, methylation at N-7 and the nature of the internucleotide linkage strongly influence the stacked conformation, thereby forming unusual left-handed conformations in m7G5'pppU(m), m7G5'ppU(m), and G5'ppU(m).
Collapse
|
17
|
Takeuchi Y, Tazawa I, Inoue Y. Intramolecular Stacking Association of Three Dinucleoside Monophosphates Containing Naturally-occurring 1-Methyladenosine Residue(s): m1ApA, Apm1A, and m1Apm1A. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1982. [DOI: 10.1246/bcsj.55.3598] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
18
|
Takeuchi Y, Tazawa I, Inoue Y. Determination of microscopic ionization constants and microscopic stacking equilibrium quotients of adenylyl(3' → 5')adenosine. Biophys Chem 1982; 16:27-31. [PMID: 17000428 DOI: 10.1016/0301-4622(82)85004-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/1982] [Accepted: 04/25/1982] [Indexed: 11/16/2022]
Abstract
Using the basic ionization constants for a pair of isomers, m1ApA and Apm1A, and the measured values for the overlapping pK values of ApA, the microscopic ionization constants and intramolecular stacking quotients for the monoprotonated ApA were estimated. The results indicate that, in contrast to the case of GpG, ApA did not exhibit preferential protonation on either site of 3'- and 5'-linked nucleoside bases and neither enhanced nor diminished stacking was observed for ApA and ApA as compared to ApA.
Collapse
Affiliation(s)
- Y Takeuchi
- Department of Biophysics and Biochemistry, Faculty of Science, University of Tokyo, Hongo, Tokyo 113, Japan
| | | | | |
Collapse
|
19
|
Van Charldorp R, Verhoeven JJ, Van Knippenberg PH, Haasnoot CA, Hilbers CW. A carbon-13 nuclear magnetic resonance study of the 3'-terminus of 16S ribosomal RNA of Escherichia coli specifically labeled with carbon-13 in the methylgroups of the m6(2)Am6(2)A sequence. Nucleic Acids Res 1982; 10:4237-45. [PMID: 6750555 PMCID: PMC320796 DOI: 10.1093/nar/10.14.4237] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
30S ribosomes were isolated from a kasugamycin resistant mutant of E. coli that lacks methylgroups on two adjacent adenines in 16S ribosomal RNA. These ribosomes were methylated in vitro with a purified methylating enzyme and 5-S-adenosyl-(13C-methyl)-L-methionine chloride ((13C-methyl)-SAM) as methyldonor. After in situ cleavage of the 16S ribosomal RNA by the bacteriocin cloacin DF13, the 49 nucleotide fragment from the 3'-end of the RNA was isolated. The carbon-13 nuclear magnetic resonance spectra of the fragment at various temperatures were compared with those of 6-N-dimethyladenosine (m6(2)A) and 6-N-dimethyladenylyl-(3' leads to 5')-6-N-dimethyladenosine (m6(2)Am6(2)A). The data show that the two methylated adenines, which are part of a four membered hairpin loop, show a strong tendency to be stacked in analogy to the dinucleotide m6(2)Am6(2).
Collapse
|
20
|
Olsthoorn CS, Doornbos J, de Leeuw HP, Altona C. Influence of the 2'-hydroxyl group and of 6-N-methylation on the conformation of adenine dinucleoside monophosphates in solution. A nuclear magnetic resonance and circular dichroism study. EUROPEAN JOURNAL OF BIOCHEMISTRY 1982; 125:367-82. [PMID: 7117238 DOI: 10.1111/j.1432-1033.1982.tb06693.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Proton NMR studies at 360 MHz are reported on the adenine dinucleoside monophosphates N6-dimethyladenyly(3'-5')-N6-dimethyladenosine (m(6)(2)Apm(6)(2)A), ApA, rApdA, dAprA and on the methyl phosphate esters of the monomers m(6)(2)Ap, pm(6)(2)A, Ap and pA. Complete 1H-NMR spectral assignments are given. The dimers were also investigated by means of circular dichroism to obtain accurate thermodynamic parameters of the stacking equilibrium. With the aid of the thermodynamic data NMR coupling constants are extrapolated to values appropriate to the stacked conformers. A modernized version of pseudorotation analysis is used to delineate the conformational behaviour of the ribose and 2'-deoxyribose rings. It is shown that the unmethylated dimers can be arranged in two groups (dApdA/dAprA vs ApA/rApdA) according to their melting temperatures. ApA and the fully N6-methylated dimer m(6)(2)Apm(6)(2)A prefer to adopt the classical right-handed N-N stacked conformation. Both dimers with a 2'-deoxyribose ring at the 5'-OH end (dApdA and dAprA) behave similarly and occur in solution as a 75:25 mixture of S-S and S-N stacked states. The fully stacked hybrid dimer rApdA displays an unexpectedly large amount of S conformers (greater than 40%) in both sugar rings. This finding is rationalized by the postulation of a right-handed helical S-S stacked state on the basis of NMR and circular dichroic data.
Collapse
|
21
|
Trempe M, Glitz D. Chloroplast ribosome structure. Electron microscopy of ribosomal subunits and localization of N6,N6-dimethyladenosine by immunoelectronmicroscopy. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)68487-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
22
|
Van Charldorp R, Heus HA, Van Knippenberg PH, Joordens J, De Bruin SH, Hilbers CW. Destabilization of secondary structure in 16S ribosomal RNA by dimethylation of two adjacent adenosines. Nucleic Acids Res 1981; 9:4413-22. [PMID: 7029465 PMCID: PMC327444 DOI: 10.1093/nar/9.17.4413] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Fragments comprising the 49 nucleotides from the 3'-end have been purified from 16S ribosomal RNA of wild-type Escherichia coli and from a kasugamycin-resistant mutant that specifically lacks dimethylation of two adjacent adenines near the 3'-terminus. These fragments, obtained after treatment of ribosomes in vitro with the bacteriocin cloacin DF13, were used to study the effect of the methyl groups on the temperature dependent unfolding of double-stranded regions. Both fragments contain at least 3 independent melting transitions, of which the one with the highest Tm corresponds with the unfolding of a nine-basepair long central hairpin. Dimethylation of the adenines in the loop of this hairpin lowers the melting temperature (Tm) by approximately 2 degrees C at 0.2 M NaCl and by about 5 degrees C at 0.15 M NaCl. It is suggested that m6(2)Am6(2)A is more antagonistic to loop formation that ApA and that the function of the methyl groups is to help to destabilize the 3'-terminal hairpin in 16S rRNA in order to facilitate intermolecular interactions.
Collapse
|
23
|
Kennedy T, Hanley-Bowdoin L, Lane B. Structural integrity of DNA and translational integrity of ribosomes in nuclease-treated cell-free protein synthesizing systems prepared from wheat germ and rabbit reticulocytes. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69278-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
24
|
Van Charldorp R, Heus HA, Van Knippenberg PH. Adenosine dimethylation of 16S ribosomal RNA: effect of the methylgroups on local conformational stability as deduced from electrophoretic mobility of RNA fragments in denaturing polyacrylamide gels. Nucleic Acids Res 1981; 9:267-75. [PMID: 7010312 PMCID: PMC326691 DOI: 10.1093/nar/9.2.267] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The electrophoretic mobility of RNA fragments derived from the 3'-end of 16S rRNA on slabs of polyacrylamide gel in the presence of urea is strongly influenced by dimethylation of the N6-aminogroup of two adjacent adenosines. This is not due to the presence of the methylgroups per se, but must be ascribed to an effect of methylation on long range intramolecular interactions at these denaturing conditions. When it is assumed that the electrophoretic mobilities of the RNA fragments in the polyacrylamide matrix are determined by the conformational state(s) of the fragments, dimethylation of the adenosines leads in the smaller fragments to a less compact average conformation and in the larger fragments to a more compact average conformation. An effort is made to comprehend the effects of adenosine dimethylation in terms of secondary structure based on nucleotide sequence.
Collapse
|