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Krall JB, Nichols PJ, Henen MA, Vicens Q, Vögeli B. Structure and Formation of Z-DNA and Z-RNA. Molecules 2023; 28:843. [PMID: 36677900 PMCID: PMC9867160 DOI: 10.3390/molecules28020843] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/08/2023] [Accepted: 01/12/2023] [Indexed: 01/17/2023] Open
Abstract
Despite structural differences between the right-handed conformations of A-RNA and B-DNA, both nucleic acids adopt very similar, left-handed Z-conformations. In contrast to their structural similarities and sequence preferences, RNA and DNA exhibit differences in their ability to adopt the Z-conformation regarding their hydration shells, the chemical modifications that promote the Z-conformation, and the structure of junctions connecting them to right-handed segments. In this review, we highlight the structural and chemical properties of both Z-DNA and Z-RNA and delve into the potential factors that contribute to both their similarities and differences. While Z-DNA has been extensively studied, there is a gap of knowledge when it comes to Z-RNA. Where such information is lacking, we try and extend the principles of Z-DNA stability and formation to Z-RNA, considering the inherent differences of the nucleic acids.
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Affiliation(s)
- Jeffrey B. Krall
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Parker J. Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Morkos A. Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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2
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Jaffrey SR, Haile DJ, Klausner RD, Harford JB. The interaction between the iron-responsive element binding protein and its cognate RNA is highly dependent upon both RNA sequence and structure. Nucleic Acids Res 1993; 21:4627-31. [PMID: 8233801 PMCID: PMC311201 DOI: 10.1093/nar/21.19.4627] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
To assess the influence of RNA sequence/structure on the interaction RNAs with the iron-responsive element binding protein (IRE-BP), twenty eight altered RNAs were tested as competitors for an RNA corresponding to the ferritin H chain IRE. All changes in the loop of the predicted IRE hairpin and in the unpaired cytosine residue characteristically found in IRE stems significantly decreased the apparent affinity of the RNA for the IRE-BP. Similarly, alteration in the spacing and/or orientation of the loop and the unpaired cytosine of the stem by either increasing or decreasing the number of base pairs separating them significantly reduced efficacy as a competitor. It is inferred that the IRE-BP forms multiple contacts with its cognate RNA, and that these contacts, acting in concert, provide the basis for the high affinity of this interaction.
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Affiliation(s)
- S R Jaffrey
- Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
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3
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Le SY, Chen JH, Maizel JV. Prediction of alternative RNA secondary structures based on fluctuating thermodynamic parameters. Nucleic Acids Res 1993; 21:2173-8. [PMID: 7684834 PMCID: PMC309481 DOI: 10.1093/nar/21.9.2173] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In this paper we present a new method for predicting a set of RNA secondary structures that are thermodynamically favored in RNA folding simulations. This method uses a large number of 'simulated energy rules' (SER) generated by perturbing the free energy parameters derived experimentally within the range of the experimental errors. The structure with the lowest free energy is computed for each SER. Structural comparisons are used to avoid multiple generation of similar structures. Computed structures are evaluated using the energy distribution of the lowest free energy structures derived in the simulation. Predicted be graphically displayed with their occurring frequencies in the simulation by dot-plot representations. On average, about 90% of phylogenetic helixes in the known models of tRNA, Group I self-splicing intron, and Escherichia coli 16 S rRNA, were predicted using the method.
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Affiliation(s)
- S Y Le
- Laboratory of Mathematical Biology, National Cancer Institute, NIH, Frederick, MD 21702
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Nevinsky GA, Andreola ML, Jamkovoy VI, Levina AS, Barr PJ, Tarrago-Litvak L, Tharaud D, Litvak S. Functional analysis of primers and templates in the synthesis of DNA catalyzed by human immunodeficiency virus type 1 reverse transcriptase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 207:351-8. [PMID: 1378404 DOI: 10.1111/j.1432-1033.1992.tb17057.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The kinetics of copying of poly(A).(dT)n, poly(A).(U)n, poly(dA).(dT)n and poly(A).(dT)9-U by reverse transcriptase of human immunodeficiency virus-1 (HIV-1) has been studied and the binding affinity of the enzyme, for template or primer, determined. Short oligonucleotides and dTTP served as primers in the HIV-1 reverse-transcriptase-dependent DNA synthesis. Km and Vmax were measured as functions of the primer chain length; the logarithm of the values of both Km and Vmax increased linearly up to 10. For longer primers (n = 11 to n = 24) the increase of those values changes very little. The enhanced affinity of the primers, (dT)n or (U)n due to the formation of one complementary pair, A.dT, dA.dT, A.U was estimated as a factor of 2. A specific property of HIV-1 reverse transcriptase compared with other DNA polymerases (procaryotes, eucaryotes, other retroviruses and archaebacteria) was its higher affinity to riboprimers as compared to deoxyriboprimers. Relative initial rates when copying poly(A) or poly(dA) templates using different primers and various conditions were compared; the optimal temperature for the reaction of polymerization with poly(A) or poly(dA) templates and (U)10, (dT)10 or (dT)9-U primers was determined. The maximal activity of the enzyme in the case of poly(A) and decanucleotide primers was found at temperatures between 27-31 degrees C. An increase in the primer length results in the stabilization of the template.primer duplex complexed to the enzyme, thus increasing to more than 40 degrees C the optimal temperature of polymerization. The activation energy (Ea) values of the polymerization reaction for different template.primer complexes were evaluated.
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Affiliation(s)
- G A Nevinsky
- Institut of Bioorganic Chemistry, Siberian Division of the Academy of Sciences of the CIS, Novosibirsk
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5
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Miller WA, Silver SL. Alternative tertiary structure attenuates self-cleavage of the ribozyme in the satellite RNA of barley yellow dwarf virus. Nucleic Acids Res 1991; 19:5313-20. [PMID: 1717946 PMCID: PMC328893 DOI: 10.1093/nar/19.19.5313] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A self-cleaving satellite RNA associated with barley yellow dwarf virus (sBYDV) contains a sequence predicted to form a secondary structure similar to catalytic RNA molecules (ribozymes) of the 'hammerhead' class (Miller et al., 1991, Virology 183, 711-720). However, this RNA differs from other naturally occurring hammerheads both in its very slow cleavage rate, and in some aspects of its structure. One striking structural difference is that an additional helix is predicted that may be part of an unusual pseudoknot containing three stacked helices. Nucleotide substitutions that prevent formation of the additional helix and favor the hammerhead increased the self-cleavage rate up to 400-fold. Compensatory substitutions, predicted to restore the additional helix, reduced the self-cleavage rate by an extent proportional to the calculated stability of the helix. Partial digestion of the RNA with structure-sensitive nucleases supported the existence of the proposed alternative structure in the wildtype sequence, and formation of the hammerhead in the rapidly-cleaving mutants. This tertiary interaction may serve as a molecular switch that controls the rate of self-cleavage and possibly other functions of the satellite RNA.
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Affiliation(s)
- W A Miller
- Plant Pathology Department, Iowa State University, Ames 50011
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6
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Danenberg PV, Shea LC, Danenberg KD, Horikoshi T. Inactivation of Tetrahymena rRNA self-splicing by cis-platin proceeds through dissociable complexes. Nucleic Acids Res 1991; 19:3123-8. [PMID: 1905401 PMCID: PMC328280 DOI: 10.1093/nar/19.11.3123] [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: 12/29/2022] Open
Abstract
The anti-cancer drug cis-diamminedichloroplatinum (II) (cis-DDP) reacted with Tetrahymena self-splicing rRNA ribozyme, causing loss of self-splicing activity and formation of a number of platinated RNA species. The formation of one distinct platinated product, migrating at an apparent size of 2400 nt, was closely associated with ribozyme inactivation. This platinated RNA was resistant to T1 ribonuclease digestion, suggesting the presence of inter-strand Pt cross-links. The reaction rate of cis-DDP with the ribozyme followed first order kinetics and showed a saturation effect with increasing cis-DDP concentration, characteristic of an affinity-label type of interaction rather than bimolecular collision. The apparent KI for binding of cis-DDP to the ribozyme was 62 microM. Ribozyme treated with urea was not inactivated by cis-DDP, indicating that the native structure of the RNA is required for reaction with cis-DDP. Mg++, which binds to the ribozyme and causes conformational changes in the molecule, protected the ribozyme from inactivation by cis-DDP and also prevented the formation of platinated RNA. These results suggest that binding of cis-DDP to sites formed by certain secondary or tertiary structural elements of the RNA enhance the rate and the specificity of reaction of the reagent with the ribozyme.
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Affiliation(s)
- P V Danenberg
- Department of Biochemistry, University of Southern California School of Medicine, Los Angeles 90033
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7
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Lokhova IA, Nevinsky GA, Gorn VV, Veniaminova AG, Repkova MV, Kavsan VM, Rudenko NK, Lavrik OI. A comparison of the initiating abilities of ribo- and deoxyriboprimers in DNA polymerization catalyzed by AMV reverse transcriptase. FEBS Lett 1990; 274:156-8. [PMID: 1701399 DOI: 10.1016/0014-5793(90)81352-o] [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: 12/28/2022]
Abstract
The difference in optimal conditions for DNA polymerization catalyzed by AMV reverse transcriptase on poly(A) and poly(dA) templates with d(pT)10 and (pU)10 primers has been found. A comparison of the initiating abilities of d(pT)10 and (pU)10 primers under optimal conditions for various template.primer complexes has been made. The best template.primer complex was poly(A).d(pT)10 and the worst was poly(A).(pU)10. The lengthening of d(pT)n primers by a mononucleotide unit (n = 2-10) increases their affinity by a factor of about 2 and 3 in the case of poly(dA) and poly(A) templates, respectively. The affinities of d(pT) to the enzyme does not change with the primer length.
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Affiliation(s)
- I A Lokhova
- Novosibirsk Institute of Bioorganic Chemistry, Siberan Division, Academy of Sciences, USSR
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8
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Barton HA, Eisenstein RS, Bomford A, Munro HN. Determinants of the interaction between the iron-responsive element-binding protein and its binding site in rat L-ferritin mRNA. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39250-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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9
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Hartmann B, Lavery R. The conformation and stability of ribonucleic acids: modeling base sequence effects in double stranded helices. J Biomol Struct Dyn 1989; 7:363-80. [PMID: 2604910 DOI: 10.1080/07391102.1989.10507778] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Base sequence effects within double stranded RNA oligomers of A and Z conformations have been studied by molecular modeling using a methodological approach specifically adapted to nucleic acids. Calculations on symmetric oligomers having homonucleotide or dinucleotide repeating base sequences show that sequence changes can produce modifications in overall conformation, influence the degree of internal hydrogen bonding and strongly affect stability.
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Affiliation(s)
- B Hartmann
- Institut de Biologie Physico-Chimique, Paris, France
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10
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Rao AL, Dreher TW, Marsh LE, Hall TC. Telomeric function of the tRNA-like structure of brome mosaic virus RNA. Proc Natl Acad Sci U S A 1989; 86:5335-9. [PMID: 2748589 PMCID: PMC297616 DOI: 10.1073/pnas.86.14.5335] [Citation(s) in RCA: 118] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Four mutant brome mosaic virus (BMV) RNA3 transcripts, bearing single or double base changes in the 3'-CCAOH terminus of the tRNA-like structure, previously characterized as being deficient in vitro with respect to aminoacylation and replication activities, have now been assayed in vivo for their ability to replicate (in the presence of transcripts of wild-type RNA1 and -2) in barley protoplasts and plants. In tests conducted with protoplasts, irrespective of the time post-infection, all four mutants were fully viable, and the relative levels of both plus and minus strand replication for each mutant were similar to that of the wild type. Inoculation of barley plants with these mutants resulted in phenotypic symptoms and viral yields that were similar to those from wild-type infections. Analysis of each mutant progeny RNA3 indicated that the altered sequence at the 3' terminus was restored to that of wild type. These observations indicate that there is a rapid turnover and correction of the 3' termini of BMV RNAs in vivo. Such correction is commensurate with the action of tRNA nucleotidyltransferase, but it differs from recombination processes that appear to be relatively infrequent for BMV RNA3. These results support the conclusion that the 3'-CCAOH termini of viral tRNA-like structures function analogously to telomeres of chromosomal DNA.
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Affiliation(s)
- A L Rao
- Department of Biology, Texas A&M University, College Station 77843-3258
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