1
|
Subbaiah S P V, Uttamrao PP, Das U, Sundaresan S, Rathinavelan T. Concentration and time-dependent amyloidogenic characteristics of intrinsically disordered N-terminal region of Saccharomyces cerevisiae Stm1. Front Microbiol 2023; 14:1206945. [PMID: 37928673 PMCID: PMC10620681 DOI: 10.3389/fmicb.2023.1206945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023] Open
Abstract
Saccharomyces cerevisiae Stm1 protein is a ribosomal association factor, which plays an important role in preserving ribosomes in a nutrition-deprived environment. It is also shown to take part in apoptosis-like cell death. Stm1 N-terminal region (Stm1_N1-113) is shown to recognize purine motif DNA triplex and G-quadruplex. Circular dichroism (CD) spectra of Stm1_N1-113 (enriched in positively-charged Lysine and Arginine; negatively-charged Aspartate; polar-uncharged Threonine, Asparagine, Proline and Serine; hydrophobic Alanine, Valine, and Glycine) collected after 0 and 24 h indicate that the protein assumes beta-sheet conformation at the higher concentrations in contrast to intrinsically disordered conformation seen for its monomeric form found in the crystal structure. Thioflavin-T kinetics experiments indicate that the lag phase is influenced by the salt concentration. Atomic force microscopy (AFM) images collected for a variety of Stm1_N1-113 concentrations (in the range of 1-400 μM) in the presence of 150 mM NaCl at 0, 24, and 48 h indicate a threshold concentration requirement to observe the time-dependent amyloid formation. This is prominent seen at the physiological salt concentration of 150 mM NaCl with the fibrillation observed for 400 μM concentration at 48 h, whereas oligomerization or proto-fibrillation is seen for the other concentrations. Such concentration-dependent fibrillation of Stm1_N1-113 explains that amyloid fibrils formed during the overexpression of Stm1_N1-113 may act as a molecular device to trigger apoptosis-like cell death.
Collapse
Affiliation(s)
- Venkata Subbaiah S P
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Patil Pranita Uttamrao
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Uttam Das
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Sruthi Sundaresan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | | |
Collapse
|
2
|
Lu B, Woloszyn K, Ohayon YP, Yang B, Zhang C, Mao C, Seeman NC, Vecchioni S, Sha R. Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles. Angew Chem Int Ed Engl 2023; 62:e202213451. [PMID: 36520622 DOI: 10.1002/anie.202213451] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Non-canonical interactions in DNA remain under-explored in DNA nanotechnology. Recently, many structures with non-canonical motifs have been discovered, notably a hexagonal arrangement of typically rhombohedral DNA tensegrity triangles that forms through non-canonical sticky end interactions. Here, we find a series of mechanisms to program a hexagonal arrangement using: the sticky end sequence; triangle edge torsional stress; and crystallization condition. We showcase cross-talking between Watson-Crick and non-canonical sticky ends in which the ratio between the two dictates segregation by crystal forms or combination into composite crystals. Finally, we develop a method for reconfiguring the long-range geometry of formed crystals from rhombohedral to hexagonal and vice versa. These data demonstrate fine control over non-canonical motifs and their topological self-assembly. This will vastly increase the programmability, functionality, and versatility of rationally designed DNA constructs.
Collapse
Affiliation(s)
- Brandon Lu
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Bena Yang
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Cuizheng Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA
| |
Collapse
|
3
|
El Deeb S, Al-Harrasi A, Khan A, Al-Broumi M, Al-Thani G, Alomairi M, Elumalai P, Sayed RA, Ibrahim AE. Microscale thermophoresis as a powerful growing analytical technique for the investigation of biomolecular interaction and the determination of binding parameters. Methods Appl Fluoresc 2022; 10. [PMID: 35856854 DOI: 10.1088/2050-6120/ac82a6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/20/2022] [Indexed: 11/12/2022]
Abstract
The in vitro panel of technologies to address biomolecular interactions are in play, however microscale thermophoresis is continuously increasing in use to represent a key player in this arena. This review highlights the usefulness of microscale thermophoresis in the determination of molecular and biomolecular affinity interactions. This work reviews the literature from January 2016 to January 2022 about microscale thermophoresis. It gives a summarized overview about both the state-of the art and the development in the field of microscale thermophoresis. The principle of microscale thermophoresis is also described supported with self-created illustrations. Moreover, some recent advances are mentioned that showing application of the technique in investigating biomolecular interactions in different fields. Finally, advantages as well as drawbacks of the technique in comparison with other competing techniques are summarized.
Collapse
Affiliation(s)
- Sami El Deeb
- Technische Universitat Braunschweig, Braunschweig, Braunschweig, Niedersachsen, 38106, GERMANY
| | | | - Ajmal Khan
- University of Nizwa, Nizwa, Nizwa, 616, OMAN
| | | | | | | | | | - Rania A Sayed
- Pharmaceutical analytical chemistry department, Zagazig University, Zagazig, Zagazig, 44519, EGYPT
| | - Adel Ehab Ibrahim
- Pharmaceutical Analytical Chemistry, Port Said University, Port Said, Port Said, 42526, EGYPT
| |
Collapse
|
4
|
Bhanjadeo MM, Nial PS, Sathyaseelan C, Singh AK, Dutta J, Rathinavelan T, Subudhi U. Biophysical interaction between lanthanum chloride and (CG) n or (GC) n repeats: A reversible B-to-Z DNA transition. Int J Biol Macromol 2022; 216:698-709. [PMID: 35809677 DOI: 10.1016/j.ijbiomac.2022.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/30/2022] [Accepted: 07/03/2022] [Indexed: 11/24/2022]
Abstract
The transition from right-handed to left-handed DNA is not only acts as the controlling factor for switching gene expression but also has equal importance in designing nanomechanical devices. The (CG)n and (GC)n repeat sequences are well known model molecules to study B-Z transition in the presence of higher concentration of monovalent cations. In this communication, we report a cyclic transition in (CG)6 DNA using millimolar concentration of trivalent lanthanide salt LaCl3. The controlled and reversible transition was seen in (CG)12, and (GC)12 DNA employing CD spectroscopy. While LaCl3 failed to induce B-Z transition in shorter oligonucleotides such as (CG)3 and (GC)3, a smooth B-Z transition was recorded for (CG)6, (CG)12 and (GC)12 sequences. Interestingly, the phenomenon was reversible (Z-B transition) with addition of EDTA. Particularly, two rounds of cyclic transition (B-Z-B-Z-B) have been noticed in (CG)6 DNA in presence of LaCl3 and EDTA which strongly suggest that B-Z transition is reversible in short repeat sequences. Thermal melting and annealing behaviour of B-DNA are reversible while the thermal melting of LaCl3-induced Z-DNA is irreversible which suggest a stronger binding of LaCl3 to the phosphate backbone of Z-DNA. This was further supported by isothermal titration calorimetric study. Molecular dynamics (MD) simulation indicates that the mode of binding of La3+ (of LaCl3) with d(CG)8.d(CG)8 is through the minor groove, wherein, 3 out of 11 La3+ bridge the anionic oxygens of the complementary strands. Such a tight coordination of La3+ with the anionic oxygens at the minor groove surface may be the reason for the experimentally observed irreversibility of LaCl3-induced Z-DNA seen in longer DNA fragments. Thus, these results indicate LaCl3 can easily be adopted as an inducer of left-handed DNA in other short oligonucleotides sequences to facilitate the understanding of the molecular mechanism of B-Z transition.
Collapse
Affiliation(s)
- Madhabi M Bhanjadeo
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751 013, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Partha S Nial
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751 013, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Chakkarai Sathyaseelan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi Campus, Telangana 502285, India
| | - Ajit K Singh
- Structural Biology Laboratory, DBT-Institute of Life Sciences, Bhubaneswar 751023, India; Department of Pharmacology, University of Vermont College of Medicine, Burlington 05405, USA
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education & Research, Bhubaneswar 752050, India; Homi Bhaba National Institute, Mumbai 400094, India
| | | | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751 013, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
| |
Collapse
|
5
|
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.
Collapse
Affiliation(s)
- Yogeeshwar Ajjugal
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State 502285, India
| | | |
Collapse
|
6
|
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] [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.
Collapse
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
| | | |
Collapse
|