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Herbert A. Simple Repeats as Building Blocks for Genetic Computers. Trends Genet 2020; 36:739-750. [PMID: 32690316 DOI: 10.1016/j.tig.2020.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/17/2020] [Accepted: 06/22/2020] [Indexed: 11/15/2022]
Abstract
Processing of RNA involves heterogeneous nuclear ribonucleoproteins. The simple sequence repeats (SSRs) they bind can also adopt alternative DNA structures, like Z DNA, triplexes, G quadruplexes, and I motifs. Those SSRs capable of switching conformation under physiological conditions (called flipons) are genetic elements that can encode alternative RNA processing by their effects on RNA processivity, most likely as DNA:RNA hybrids. Flipons are elements of a binary, instructive genetic code directing how genomic sequences are compiled into transcripts. The combinatorial nature of this code provides a rich set of options for creating genetic computers able to reproduce themselves and use a heritable and evolvable code to optimize survival. The underlying computational logic potentiates a diverse set of genetic programs that modify cis-mediated heritability and disease risk.
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Affiliation(s)
- Alan Herbert
- Discovery, InsideOutBio, 42 8th Street, Charlestown, MA 02129, USA.
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2
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Shchyolkina AK, Kaluzhny DN, Borisova OF, Arndt-Jovin DJ, Jovin TM, Zhurkin VB. Conformational variability of recombination R-triplex formed by the mammalian telomeric sequence. J Biomol Struct Dyn 2015; 34:1298-306. [PMID: 26308235 PMCID: PMC4867858 DOI: 10.1080/07391102.2015.1077344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Alignment of three nucleic acids strands, in which the third strand is identical to one of the DNA duplex strands, occurs in various cellular systems. In the case of telomeric t-loops, recognition between the DNA duplex and the homologous single strand is likely to be mediated by proteins through formation of the transient recombination-type R-triplex. Earlier, using 2-aminopurine as a fluorescent reporting base, we evaluated the thermodynamic characteristics of intramolecular R-triplex formed by a mixed nucleotide sequence. Here, we used this approach to explore a propensity of the telomeric TTAGGG repeat to form the R-triplex. The circular dichroism spectral changes detected upon formation of the R-triplex suggest that this process is accompanied by specific conformational changes in DNA, including a local destabilization of the target duplex next to a GGG run revealed by the fluorescence of the reporting 2-aminopurine base. Surprisingly, stability of the R-triplex formed by telomeric sequence depends strikingly on the counter ion, being higher for Na+ than for Li+. Taken together these findings indicate a significant conformational variability of telomeric DNA in the context of recombination-type R-triplex, a phenomenon of possible biological relevance.
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Affiliation(s)
- Anna K Shchyolkina
- a Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , 119991 Moscow , Russia
| | - Dmitry N Kaluzhny
- a Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , 119991 Moscow , Russia
| | - Olga F Borisova
- a Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , 119991 Moscow , Russia
| | - Donna J Arndt-Jovin
- b Department of Molecular Biology , Max Planck Institute for Biophysical Chemistry , D-37070 Goettingen , Germany
| | - Thomas M Jovin
- b Department of Molecular Biology , Max Planck Institute for Biophysical Chemistry , D-37070 Goettingen , Germany
| | - Victor B Zhurkin
- c Laboratory of Cell Biology , National Cancer Institute, NIH , 20892 Bethesda , MD , USA
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3
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Belotserkovskii BP, Mirkin SM, Hanawalt PC. DNA sequences that interfere with transcription: implications for genome function and stability. Chem Rev 2013; 113:8620-37. [PMID: 23972098 DOI: 10.1021/cr400078y] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Beck A, Vijayanathan V, Thomas T, Thomas TJ. Ionic microenvironmental effects on triplex DNA stabilization: cationic counterion effects on poly(dT)·poly(dA)·poly(dT). Biochimie 2013; 95:1310-8. [PMID: 23454377 DOI: 10.1016/j.biochi.2013.02.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/18/2013] [Indexed: 12/18/2022]
Abstract
The structure and conformation of nucleic acids are influenced by metal ions, polyamines, and the microenvironment. In poly(purine) · poly(pyrimidine) sequences, triplex DNA formation is facilitated by metal ions, polyamines and other ligands. We studied the effects of mono- and di-valent metal ions, and ammonium salts on the stability of triple- and double-stranded structures formed from poly(dA) and poly(dT) by measuring their respective melting temperatures. In the presence of metal ions, the absorbance versus temperature profile showed two transitions: Tm1 for triplex to duplex and single stranded DNA, and Tm2 for duplex DNA melting to single stranded DNA. Monovalent cations (Li(+), Na(+), K(+), Rb(+), Cs(+) and [Formula: see text] ) promoted triplex DNA at concentrations ≥150 mM. Tm1 varied from 49.8 °C in the presence of 150 mM Li(+) to 30.6 °C in the presence of 150 mM K(+). [Formula: see text] was very effective in stabilizing triplex DNA and its efficacy decreased with increasing substitution of the hydrogen atoms with methyl, ethyl, propyl and butyl groups. As in the case of monovalent cations, a concentration-dependent increase in Tm1 was observed with divalent ions and triplex DNA stabilization decreased in the order: Mg(2+) > Ca(2+) > Sr(2+) > Ba(2+). All positively charged cations increased the melting temperature of duplex DNA. Values of Δn (number of ions released) on triplex DNA melting were 0.46 ± 0.06 and 0.18 ± 0.02, respectively, for mono- and di-valent cations, as calculated from 1/Tm1 versus ln[M(+,2+)] plots. The corresponding values for duplex DNA were 0.25 ± 0.02 and 0.12 ± 0.02, respectively, for mono- and di-valent cations. Circular dichroism spectroscopic studies showed distinct conformational changes in triplex DNA stabilized by alkali metal and ammonium ions. Our results might be useful in developing triplex forming oligonucleotide based gene silencing techniques.
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Affiliation(s)
- Amanda Beck
- Department of Medicine, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, 125 Paterson St, New Brunswick, NJ 08903, USA
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Caporale LH. Overview of the creative genome: effects of genome structure and sequence on the generation of variation and evolution. Ann N Y Acad Sci 2012; 1267:1-10. [PMID: 22954209 DOI: 10.1111/j.1749-6632.2012.06749.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
This overview of a special issue of Annals of the New York Academy of Sciences discusses uneven distribution of distinct types of variation across the genome, the dependence of specific types of variation upon distinct classes of DNA sequences and/or the induction of specific proteins, the circumstances in which distinct variation-generating systems are activated, and the implications of this work for our understanding of evolution and of cancer. Also discussed is the value of non text-based computational methods for analyzing information carried by DNA, early insights into organizational frameworks that affect genome behavior, and implications of this work for comparative genomics.
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Kolganova NA, Shchyolkina AK, Chudinov AV, Zasedatelev AS, Florentiev VL, Timofeev EN. Targeting duplex DNA with chimeric α,β-triplex-forming oligonucleotides. Nucleic Acids Res 2012; 40:8175-85. [PMID: 22641847 PMCID: PMC3439883 DOI: 10.1093/nar/gks410] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 04/19/2012] [Accepted: 04/20/2012] [Indexed: 11/14/2022] Open
Abstract
Triplex-directed DNA recognition is strictly limited by polypurine sequences. In an attempt to address this problem with synthetic biology tools, we designed a panel of short chimeric α,β-triplex-forming oligonucleotides (TFOs) and studied their interaction with fluorescently labelled duplex hairpins using various techniques. The hybridization of hairpin with an array of chimeric probes suggests that recognition of double-stranded DNA follows complicated rules combining reversed Hoogsteen and non-canonical homologous hydrogen bonding. In the presence of magnesium ions, chimeric TFOs are able to form highly stable α,β-triplexes, as indicated by native gel-electrophoresis, on-array thermal denaturation and fluorescence-quenching experiments. CD spectra of chimeric triplexes exhibited features typically observed for anti-parallel purine triplexes with a GA or GT third strand. The high potential of chimeric α,β-TFOs in targeting double-stranded DNA was demonstrated in the EcoRI endonuclease protection assay. In this paper, we report, for the first time, the recognition of base pair inversions in a duplex by chimeric TFOs containing α-thymidine and α-deoxyguanosine.
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Affiliation(s)
| | | | | | | | | | - E. N. Timofeev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow, 119991, Russia
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Kowal EA, Ganguly M, Pallan PS, Marky LA, Gold B, Egli M, Stone MP. Altering the electrostatic potential in the major groove: thermodynamic and structural characterization of 7-deaza-2'-deoxyadenosine:dT base pairing in DNA. J Phys Chem B 2011; 115:13925-34. [PMID: 22059929 PMCID: PMC3225014 DOI: 10.1021/jp207104w] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
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As part of an ongoing effort to explore the effect of major groove electrostatics on the thermodynamic stability and structure of DNA, a 7-deaza-2′-deoxyadenosine:dT (7-deaza-dA:dT) base pair in the Dickerson–Drew dodecamer (DDD) was studied. The removal of the electronegative N7 atom on dA and the replacement with an electropositive C–H in the major groove was expected to have a significant effect on major groove electrostatics. The structure of the 7-deaza-dA:dT base pair was determined at 1.1 Å resolution in the presence of Mg2+. The 7-deaza-dA, which is isosteric for dA, had minimal effect on the base pairing geometry and the conformation of the DDD in the crystalline state. There was no major groove cation association with the 7-deaza-dA heterocycle. In solution, circular dichroism showed a positive Cotton effect centered at 280 nm and a negative Cotton effect centered at 250 nm that were characteristic of a right-handed helix in the B-conformation. However, temperature-dependent NMR studies showed increased exchange between the thymine N3 imino proton of the 7-deaza-dA:dT base pair and water, suggesting reduced stacking interactions and an increased rate of base pair opening. This correlated with the observed thermodynamic destabilization of the 7-deaza-dA modified duplex relative to the DDD. A combination of UV melting and differential scanning calorimetry experiments were conducted to evaluate the relative contributions of enthalpy and entropy in the thermodynamic destabilization of the DDD. The most significant contribution arose from an unfavorable enthalpy term, which probably results from less favorable stacking interactions in the modified duplex, which was accompanied by a significant reduction in the release of water and cations from the 7-deaza-dA modified DNA.
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Affiliation(s)
- Ewa A Kowal
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
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8
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Site-specific fluorescent probing of RNA molecules by unnatural base-pair transcription for local structural conformation analysis. Nat Protoc 2010; 5:1312-23. [DOI: 10.1038/nprot.2010.77] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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9
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Shukshina IZ, Minyat EE. Effect of aminoglycoside antibiotics on the conformation of the unpaired loop adenine of avian leucosis virus RNA as revealed using 2-aminopurine fluorescence. Mol Biol 2009. [DOI: 10.1134/s0026893309060132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Kaluzhny DN, Minyat EE. Interaction of the dimeric form of retroviral RNA with paromonycin and magnesium as revealed using 2-aminopurine fluorescence. Mol Biol 2009. [DOI: 10.1134/s0026893309040141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Kaluzhny DN, Borisova OF, Shchyolkina AK. Diverse modes of 5'-[4-(aminoiminomethyl)phenyl]-[2,2'-bifuran]-5-carboximidamide (DB832) interaction with multi-stranded DNA structures. Biopolymers 2009; 93:8-20. [PMID: 19642208 DOI: 10.1002/bip.21287] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The modes of binding of 5'-[4-(aminoiminomethyl)phenyl]-[2,2'-Bifuran]-5-carboximidamide (DB832) to multi-stranded DNAs: human telomere quadruplex, monomolecular R-triplex, pyr/pur/pyr triplex consisting of 12 T*(T x A) triplets, and DNA double helical hairpin were studied. The optical adsorption of the ligand was used for monitoring the binding and for determination of the association constants and the numbers of binding sites. CD spectra of DB832 complexes with the oligonucleotides and the data on the energy transfer from DNA bases to the bound DB832 assisted in elucidating the binding modes. The affinity of DB832 to the studied multi-stranded DNAs was found to be greater (K(ass) approximately 10(7)M(-1)) than to the duplex DNA (K(ass) approximately 2 x 10(5)M(-1)). A considerable stabilizing effect of DB832 binding on R-triplex conformation was detected. The nature of the ligand tight binding differed for the studied multi-stranded DNA depending on their specific conformational features: recombination-type R-triplex demonstrated the highest affinity for DB832 groove binding, while pyr/pur/pyr TTA triplex favored DB832 intercalation at the end stacking contacts and the human telomere quadruplex d[AG(3)(T(2)AG(3))(3)] accommodated the ligand in a capping mode. Additionally, the pyr/pur/pyr TTA triplex and d[AG(3)(T(2)AG(3))(3)] quadruplex bound DB832 into their grooves, though with a markedly lesser affinity. DB832 may be useful for discrimination of the multi-sranded DNA conformations and for R-triplex stabilization.
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Affiliation(s)
- Dmitry N Kaluzhny
- Engelhardt Institute of Molecular Biology RASc, Moscow 119991, Russia
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12
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Kaluzhny DN, Timoshin VV, Borisova OF, Zhurkin VB, Florentiev VL, Shchyolkina AK. Intramolecular recombination R-triplex in solution: stabilization by bis-intercalator YOYO. J Biomol Struct Dyn 2008; 26:301-6. [PMID: 18808196 DOI: 10.1080/07391102.2008.10507245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Recognition of double-stranded DNA with a mixed nucleotide sequence by oligonucleotide is a long-term challenge. This aim can be achieved via formation of the recombination R-triplex, accommodating two identical DNA strands in parallel orientation, and antiparallel complementary strand. In the absence of proteins the R-triplex stability is low, however, so that intermolecular R-triplex is not formed by three DNA strands in a ligand-free system. Recently, recognition of DNA with mixed base sequence by single-stranded oligonucleotide in the presence of bis-intercalator YOYO was reported. Here, we describe thermodynamic characteristics of YOYO complexes with the model oligonucleotides 5'-GT-2AP-GACTGAG TTTT CTCAGTCTACGC GAA GCGTAGACTGAG-3' (R(2AP)CW) bearing a single reporting 2-aminopurine (2AP) in place of adenine and 5'-CTCAGTCTACGC GAA GCGTAGACTGAG-3' (CW). We found that each oligonucleotide is able to bind two YOYO molecules via intercalation mode in 0.5 M LiCl. Fluorescence intensity of YOYO intercalated in triplex R(2AP)CW and in CW hairpin increased 40-fold compared to the free YOYO. Remarkably, the melting temperature of the triplex (determined using temperature dependence of the 2AP fluorescence) increased from 19 degrees C to 33 degrees C upon binding two YOYO molecules. Further increase in the YOYO concentration resulted in binding of up to five YOYO molecules to R(2AP)CW triplex and up to six YOYO molecules to CW hairpin.
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Affiliation(s)
- Dmitry N Kaluzhny
- Engelhardt Institute of Molecular Biology RASc, Vavilova 32, 119991 Moscow, Russia
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Ulyanov NB, Shefer K, James TL, Tzfati Y. Pseudoknot structures with conserved base triples in telomerase RNAs of ciliates. Nucleic Acids Res 2007; 35:6150-60. [PMID: 17827211 PMCID: PMC2094054 DOI: 10.1093/nar/gkm660] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Telomerase maintains the integrity of telomeres, the ends of linear chromosomes, by adding G-rich repeats to their 3′-ends. Telomerase RNA is an integral component of telomerase. It contains a template for the synthesis of the telomeric repeats by the telomerase reverse transcriptase. Although telomerase RNAs of different organisms are very diverse in their sequences, a functional non-template element, a pseudoknot, was predicted in all of them. Pseudoknot elements in human and the budding yeast Kluyveromyces lactis telomerase RNAs contain unusual triple-helical segments with AUU base triples, which are critical for telomerase function. Such base triples in ciliates have not been previously reported. We analyzed the pseudoknot sequences in 28 ciliate species and classified them in six different groups based on the lengths of the stems and loops composing the pseudoknot. Using miniCarlo, a helical parameter-based modeling program, we calculated 3D models for a representative of each morphological group. In all cases, the predicted structure contains at least one AUU base triple in stem 2, except for that of Colpidium colpoda, which contains unconventional GCG and AUA triples. These results suggest that base triples in a pseudoknot element are a conserved feature of all telomerases.
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Affiliation(s)
- Nikolai B. Ulyanov
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158-2517, USA and Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, 91904 Jerusalem, Israel
- *To whom correspondence should be addressed. +1 415 476 0707+1 415 502 8298 Correspondence may also be addressed to Yehuda Tzfati. +972 2 6584902+972 2 6586975
| | - Kinneret Shefer
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158-2517, USA and Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, 91904 Jerusalem, Israel
| | - Thomas L. James
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158-2517, USA and Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, 91904 Jerusalem, Israel
| | - Yehuda Tzfati
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158-2517, USA and Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, 91904 Jerusalem, Israel
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Lanzov VA. RecA homologous DNA transferase: Functional activities and a search for homology by recombining DNA molecules. Mol Biol 2007. [DOI: 10.1134/s0026893307030077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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