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Khan S, Singh A, Nain N, Gulati S, Kukreti S. Sequence-specific recognition of a coding segment of human DACH1 gene via short pyrimidine/purine oligonucleotides. RSC Adv 2021; 11:40011-40021. [PMID: 35494143 PMCID: PMC9044637 DOI: 10.1039/d1ra06604h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/03/2021] [Indexed: 12/18/2022] Open
Abstract
With growing in vivo evidence of the roles of triplexes in biological processes, oligonucleotide-directed targeting of double-helical DNA for selective modulation of gene functions has become imperative in their therapeutic aspects. This study comprises a comparative investigation of 17-mer Py- and Pu-TFO for the formation of an intermolecular triplex with a 27-bp genomic homopurine-homopyrimidine track present in the transcriptional element of the human DACH1 gene. The biochemical and biophysical studies have revealed that triplex formation takes place only with Py-TFO and not with its Pu-counterpart. Non-denaturating gel electrophoresis indicated the formation of an intermolecular triplex in Py-motif with an increasing amount of Py-TFO, whereas no such interaction was observed for the Pu-counterpart. UV-thermal melting (T m), circular dichroism (CD) and thermal difference spectra (TDS) studies confirmed the pyrimidine motif triplex formation, which was observed to be significantly pH-dependent and stable at acidic pH (5.2) in the presence of 100 mM Na+ ions. Contrarily, Pu-TFO was not found to bind to the target predominantly, owing to its self-association properties. Further studies have revealed that the GA-rich Pu-TFO adopts a homoduplex structure leading to a limit in its availability for triplex formation. These results may add to our understanding of sequence-specific gene targeting and give insight into designing more specific TFOs depending on genomic targets.
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Affiliation(s)
- Shoaib Khan
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
| | - Anju Singh
- Department of Chemistry, Ramjas College, University of Delhi Delhi-110007 India
| | - Nishu Nain
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
| | - Srishty Gulati
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
| | - Shrikant Kukreti
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
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Ajjugal Y, Rathinavelan T. Conformational distortions induced by periodically recurring A…A in d(CAG).d(CAG) provide stereochemical rationale for the trapping of MSH2.MSH3 in polyQ disorders. Comput Struct Biotechnol J 2021; 19:4447-4455. [PMID: 34471491 PMCID: PMC8379282 DOI: 10.1016/j.csbj.2021.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 11/25/2022] Open
Abstract
CAG repeat instability causes a number of neurodegenerative disorders. The unusual hairpin stem structure formed by the CAG repeats in DNA traps the human mismatch repair MSH2.MSH3 (Mutsβ) complex. To understand the mechanism behind the abnormal binding of Mutsβ with the imperfect hairpin stem structure formed by CAG repeats, molecular dynamics simulations have been carried out for Mutsβ-d(CAG)2(CAG)(CAG)2.d(CTG)2(CAG)(CTG)2 (1 A…A mismatch) and Mutsβ-d(CAG)5.d(CAG)5 (5 mismatches, wherein, A…A occurs periodically) complexes. The interaction of MSH3 residue Tyr245 at the minor groove side of A…A, an essential interaction responsible for the recognition by Mutsβ, are retained in both the cases. Nevertheless, the periodic unwinding caused by the nonisostericity of A…A with the flanking canonical base pairs in d(CAG)5.d(CAG)5 distorts the regular B-form geometry. Such an unwinding exposes one of the A…A mismatches (that interacts with Tyr245) at the major groove side and also facilitates the on and off hydrogen bonding interaction with Lys546 sidechain (MSH2-domain-IV). In contrast, kinking of the DNA towards the major groove in Mutsβ-d(CAG)2(CAG)(CAG)2.d(CTG)2(CAG)(CTG)2 doesn’t facilitate such an exposure of the bases at the major groove. Further, the unwinding of the helix in d(CAG)5.d(CAG)5 enhances the tighter binding between MSH2-domain-I and d(CAG)5.d(CAG)5 at the major groove side as well as between MSH3-domain-I and MSH3-domain-IV. Markedly, such enhanced interactions are absent in Mutsβ-d(CAG)2(CAG)(CAG)2.d(CTG)2(CAG)(CTG)2 that has a single A…A mismatch. Thus, the above-mentioned enhancement in intra- and inter- molecular interactions in Mutsβ-d(CAG)5.d(CAG)5 provide the stereochemical rationale for the trapping of Mutsβ in CAG repeat expansion disorders.
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Affiliation(s)
- Yogeeshwar Ajjugal
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State 502285, India
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Ajjugal Y, Kolimi N, Rathinavelan T. Secondary structural choice of DNA and RNA associated with CGG/CCG trinucleotide repeat expansion rationalizes the RNA misprocessing in FXTAS. Sci Rep 2021; 11:8163. [PMID: 33854084 PMCID: PMC8046799 DOI: 10.1038/s41598-021-87097-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 03/22/2021] [Indexed: 11/09/2022] Open
Abstract
CGG tandem repeat expansion in the 5'-untranslated region of the fragile X mental retardation-1 (FMR1) gene leads to unusual nucleic acid conformations, hence causing genetic instabilities. We show that the number of G…G (in CGG repeat) or C…C (in CCG repeat) mismatches (other than A…T, T…A, C…G and G…C canonical base pairs) dictates the secondary structural choice of the sense and antisense strands of the FMR1 gene and their corresponding transcripts in fragile X-associated tremor/ataxia syndrome (FXTAS). The circular dichroism (CD) spectra and electrophoretic mobility shift assay (EMSA) reveal that CGG DNA (sense strand of the FMR1 gene) and its transcript favor a quadruplex structure. CD, EMSA and molecular dynamics (MD) simulations also show that more than four C…C mismatches cannot be accommodated in the RNA duplex consisting of the CCG repeat (antisense transcript); instead, it favors an i-motif conformational intermediate. Such a preference for unusual secondary structures provides a convincing justification for the RNA foci formation due to the sequestration of RNA-binding proteins to the bidirectional transcripts and the repeat-associated non-AUG translation that are observed in FXTAS. The results presented here also suggest that small molecule modulators that can destabilize FMR1 CGG DNA and RNA quadruplex structures could be promising candidates for treating FXTAS.
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Affiliation(s)
- Yogeeshwar Ajjugal
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State, 502285, India
| | - Narendar Kolimi
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State, 502285, India
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Ajjugal Y, Tomar K, Rao DK, Rathinavelan T. Spontaneous and frequent conformational dynamics induced by A…A mismatch in d(CAA)·d(TAG) duplex. Sci Rep 2021; 11:3689. [PMID: 33574412 PMCID: PMC7878774 DOI: 10.1038/s41598-021-82669-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 01/20/2021] [Indexed: 01/20/2023] Open
Abstract
Base pair mismatches in DNA can erroneously be incorporated during replication, recombination, etc. Here, the influence of A…A mismatch in the context of 5′CAA·5′TAG sequence is explored using molecular dynamics (MD) simulation, umbrella sampling MD, circular dichroism (CD), microscale thermophoresis (MST) and NMR techniques. MD simulations reveal that the A…A mismatch experiences several transient events such as base flipping, base extrusion, etc. facilitating B–Z junction formation. A…A mismatch may assume such conformational transitions to circumvent the effect of nonisostericity with the flanking canonical base pairs so as to get accommodated in the DNA. CD and 1D proton NMR experiments further reveal that the extent of B–Z junction increases when the number of A…A mismatch in d(CAA)·d(T(A/T)G) increases (1–5). CD titration studies of d(CAA)·d(TAG)n=5 with the hZαADAR1 show the passive binding between the two, wherein, the binding of protein commences with B–Z junction recognition. Umbrella sampling simulation indicates that the mismatch samples anti…+ syn/+ syn…anti, anti…anti & + syn…+ syn glycosyl conformations. The concomitant spontaneous transitions are: a variety of hydrogen bonding patterns, stacking and minor or major groove extrahelical movements (with and without the engagement of hydrogen bonds) involving the mismatch adenines. These transitions frequently happen in anti…anti conformational region compared with the other three regions as revealed from the lifetime of these states. Further, 2D-NOESY experiments indicate that the number of cross-peaks diminishes with the increasing number of A…A mismatches implicating its dynamic nature. The spontaneous extrahelical movement seen in A…A mismatch may be a key pre-trapping event in the mismatch repair due to the accessibility of the base(s) to the sophisticated mismatch repair machinery.
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Affiliation(s)
- Yogeeshwar Ajjugal
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy District, Telangana State, 502285, India
| | - Kripi Tomar
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy District, Telangana State, 502285, India
| | - D Krishna Rao
- Tata Institute of Fundamental Research, 36/P, Gopanpally Mandal, Ranga Reddy District, Hyderabad, Telangana State, 500107, India
| | - Thenmalarchelvi Rathinavelan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy District, Telangana State, 502285, India.
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Xiao S, Sharpe DJ, Chakraborty D, Wales DJ. Energy Landscapes and Hybridization Pathways for DNA Hexamer Duplexes. J Phys Chem Lett 2019; 10:6771-6779. [PMID: 31609632 DOI: 10.1021/acs.jpclett.9b02356] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Strand hybridization is not only a fundamental molecular mechanism underlying the biological functions of nucleic acids but is also a key step in the design of efficient nanodevices. Despite recent efforts, the microscopic rules governing the hybridization mechanisms remain largely unknown. In this study, we exploit the energy landscape framework to assess how sequence-specificity modulates the hybridization mechanisms in DNA. We find that GG-tracts hybridize much more rapidly compared to GC-tracts, via either zippering or slithering pathways. For the hybridization of GG-tracts, both zippering and slithering mechanisms appear to be kinetically relevant. In contrast, for the GC-tracts, the zippering mechanism is dominant. Our work reveals that even for the relatively small systems considered, the energy landscapes feature multiple metastable states and kinetic traps, which is at odds with the conventional "all-or-nothing" model of DNA hybridization formulated on the basis of thermodynamic arguments alone. Interestingly, entropic effects are found to play an important role in determining the thermal stability of competing conformational ensembles and in determining the preferred hybridization pathways.
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Affiliation(s)
- Shiyan Xiao
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , United Kingdom
| | - Daniel J Sharpe
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , United Kingdom
| | - Debayan Chakraborty
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - David J Wales
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , United Kingdom
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Leung E, Pilkington LI, Naiya MM, Barker D, Zafar A, Eurtivong C, Reynisson J. The cytotoxic potential of cationic triangulenes against tumour cells. MEDCHEMCOMM 2019; 10:1881-1891. [PMID: 32952994 PMCID: PMC7478161 DOI: 10.1039/c9md00305c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/19/2019] [Indexed: 12/20/2022]
Abstract
TOTA (trioxatriangulenium ion) is a close-shelled carbocation known to intercalate strongly with the DNA double helix (J. Reynisson, G. B. Schuster, S. B. Howerton, L. D. Williams, R. N. Barnett, C. L. Cleveland, U. Landman, N. Harrit, J. B. Chaires, J. Am. Chem. Soc. 2003, 125, 2072). The cytotoxicity of TOTA and its four close structural analogues, ADOTA, Pr-ADOTA, Pr-DAOTA and n-Butyl-TATA were tested against the breast cancer cell line MDA-MB-231 and colon cancer cell line HCT116. The most potent derivatives Pr-ADOTA and Pr-DAOTA had IC50 values of ∼80 nM for MDA-MB-231 but slightly higher for HCT116 in the low hundreds nM range. A 3D model assay of HCT116 spheroids was also used, mimicking a tumour environment, again both Pr-ADOTA and Pr-DAOTA were very active with IC50 values of 38 nM and 21 nM, respectively. Molecular modelling suggest that the planar derivatives intercalate between the base pairs of the DNA double helix. However, only modest DNA double stranded DNA cleavage was observed using the γH2AX assay as compared to camptothecin, a topoisomerase I poison suggesting a different mechanism. Finally, a robust density functional theory (DFT) model was built to predict the pK R+ stability values, i.e., to design derivatives, which predominantly have a non-intercalating buckled form in healthy tissues followed by a nucleophilic attach of water on the central carbon, but a planar form at relatively low pH values rendering them only cytotoxic in the interior of tumours.
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Affiliation(s)
- Euphemia Leung
- Auckland Cancer Society Research Centre , University of Auckland , Grafton , Auckland 1023 , New Zealand
| | - Lisa I Pilkington
- School of Chemical Sciences , University of Auckland , City Centre , Auckland 1010 , New Zealand
| | - Mohinder M Naiya
- School of Chemical Sciences , University of Auckland , City Centre , Auckland 1010 , New Zealand
| | - David Barker
- School of Chemical Sciences , University of Auckland , City Centre , Auckland 1010 , New Zealand
| | - Ayesha Zafar
- School of Chemical Sciences , University of Auckland , City Centre , Auckland 1010 , New Zealand
| | - Chatchakorn Eurtivong
- Program of Chemical Biology , Chulabhorn Graduate Institute , Chulabhorn Royal Academy of Science , Bangkok 10210 , Thailand
| | - Jóhannes Reynisson
- School of Chemical Sciences , University of Auckland , City Centre , Auckland 1010 , New Zealand
- School of Pharmacy , Keele University , Hornbeam building , Staffordshire ST5 5BG , UK . ; Tel: +44 (0)1782 733985
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Patro LPP, Kumar A, Kolimi N, Rathinavelan T. 3D-NuS: A Web Server for Automated Modeling and Visualization of Non-Canonical 3-Dimensional Nucleic Acid Structures. J Mol Biol 2017; 429:2438-2448. [PMID: 28652006 DOI: 10.1016/j.jmb.2017.06.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 06/15/2017] [Accepted: 06/15/2017] [Indexed: 10/19/2022]
Abstract
The inherent conformational flexibility of nucleic acids facilitates the formation of a range of conformations such as duplex, triplex, quadruplex, etc. that play crucial roles in biological processes. Elucidation of the influence of non-canonical base pair mismatches on DNA/RNA structures at different sequence contexts to understand the mismatch repair, misregulation of alternative splicing mechanisms and the sequence-dependent effect of RNA-DNA hybrid in relevance to antisense strategy demand their three-dimensional structural information. Furthermore, structural insights about nucleic acid triplexes, which are generally not tractable to structure determination by X-ray crystallography or NMR techniques, are essential to establish their biological function(s). A web server, namely 3D-NuS (http://iith.ac.in/3dnus/), has been developed to generate energy-minimized models of 80 different types of triplexes, 64 types of G-quadruplexes, left-handed Z-DNA/RNA duplexes, and RNA-DNA hybrid duplex along with inter- and intramolecular DNA or RNA duplexes comprising a variety of mismatches and their chimeric forms for any user-defined sequence and length. It also generates an ensemble of conformations corresponding to the modeled structure. These structures may serve as good starting models for docking proteins and small molecules with nucleic acids, NMR structure determination, cryo-electron microscope modeling, DNA/RNA nanotechnology applications and molecular dynamics simulation studies.
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Affiliation(s)
- L Ponoop Prasad Patro
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State 502285, India
| | - Abhishek Kumar
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State 502285, India
| | - Narendar Kolimi
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State 502285, India
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Zhou H, Kimsey IJ, Nikolova EN, Sathyamoorthy B, Grazioli G, McSally J, Bai T, Wunderlich CH, Kreutz C, Andricioaei I, Al-Hashimi HM. m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs. Nat Struct Mol Biol 2016; 23:803-10. [PMID: 27478929 PMCID: PMC5016226 DOI: 10.1038/nsmb.3270] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/05/2016] [Indexed: 12/13/2022]
Abstract
The B-DNA double helix can dynamically accommodate G-C and A-T base pairs in either Watson-Crick or Hoogsteen configurations. Here, we show that G-C(+) (in which + indicates protonation) and A-U Hoogsteen base pairs are strongly disfavored in A-RNA. As a result,N(1)-methyladenosine and N(1)-methylguanosine, which occur in DNA as a form of alkylation damage and in RNA as post-transcriptional modifications, have dramatically different consequences. Whereas they create G-C(+) and A-T Hoogsteen base pairs in duplex DNA, thereby maintaining the structural integrity of the double helix, they block base-pairing and induce local duplex melting in RNA. These observations provide a mechanism for disrupting RNA structure through post-transcriptional modifications. The different propensities to form Hoogsteen base pairs in B-DNA and A-RNA may help cells meet the opposing requirements of maintaining genome stability, on the one hand, and of dynamically modulating the structure of the epitranscriptome, on the other.
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Affiliation(s)
- Huiqing Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
| | - Isaac J. Kimsey
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
| | - Evgenia N. Nikolova
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California USA
| | | | - Gianmarc Grazioli
- Department of Chemistry, University of California Irvine, Irvine, California USA
| | - James McSally
- Department of Chemistry, University of California Irvine, Irvine, California USA
| | - Tianyu Bai
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
| | | | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck Austria
| | - Ioan Andricioaei
- Department of Chemistry, University of California Irvine, Irvine, California USA
| | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
- Department of Chemistry, Duke University, Durham, North Carolina USA
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Goldsmith G, Rathinavelan T, Yathindra N. Correction: Selective Preference of Parallel DNA Triplexes Is Due to the Disruption of Hoogsteen Hydrogen Bonds Caused by the Severe Nonisostericity between the G*GC and T*AT Triplets. PLoS One 2016; 11:e0155090. [PMID: 27152600 PMCID: PMC4859481 DOI: 10.1371/journal.pone.0155090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0152102.].
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