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Huang R, Feng Y, Gao Z, Ahmed A, Zhang W. The Epigenomic Features and Potential Functions of PEG- and PDS-Favorable DNA G-Quadruplexes in Rice. Int J Mol Sci 2024; 25:634. [PMID: 38203805 PMCID: PMC10779103 DOI: 10.3390/ijms25010634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/26/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
A G-quadruplex (G4) is a typical non-B DNA structure and involved in various DNA-templated events in eukaryotic genomes. PEG and PDS chemicals have been widely applied for promoting the folding of in vivo or in vitro G4s. However, how PEG and PDS preferentially affect a subset of G4 formation genome-wide is still largely unknown. We here conducted a BG4-based IP-seq in vitro under K++PEG or K++PDS conditions in the rice genome. We found that PEG-favored IP-G4s+ have distinct sequence features, distinct genomic distributions and distinct associations with TEGs, non-TEGs and subtypes of TEs compared to PDS-favored ones. Strikingly, PEG-specific IP-G4s+ are associated with euchromatin with less enrichment levels of DNA methylation but with more enriched active histone marks, while PDS-specific IP-G4s+ are associated with heterochromatin with higher enrichment levels of DNA methylation and repressive marks. Moreover, we found that genes with PEG-specific IP-G4s+ are more expressed than those with PDS-specific IP-G4s+, suggesting that PEG/PDS-specific IP-G4s+ alone or coordinating with epigenetic marks are involved in the regulation of the differential expression of related genes, therefore functioning in distinct biological processes. Thus, our study provides new insights into differential impacts of PEG and PDS on G4 formation, thereby advancing our understanding of G4 biology.
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Affiliation(s)
| | | | | | | | - Wenli Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (R.H.); (Y.F.); (Z.G.); (A.A.)
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2
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Dutta N, Deb I, Sarzynska J, Lahiri A. Inosine and its methyl derivatives: Occurrence, biogenesis, and function in RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 169-170:21-52. [PMID: 35065168 DOI: 10.1016/j.pbiomolbio.2022.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/11/2021] [Accepted: 01/11/2022] [Indexed: 05/21/2023]
Abstract
Inosine is one of the most common post-transcriptional modifications. Since its discovery, it has been noted for its ability to contribute to non-Watson-Crick interactions within RNA. Rapidly accumulating evidence points to the widespread generation of inosine through hydrolytic deamination of adenosine to inosine by different classes of adenosine deaminases. Three naturally occurring methyl derivatives of inosine, i.e., 1-methylinosine, 2'-O-methylinosine and 1,2'-O-dimethylinosine are currently reported in RNA modification databases. These modifications are expected to lead to changes in the structure, folding, dynamics, stability and functions of RNA. The importance of the modifications is indicated by the strong conservation of the modifying enzymes across organisms. The structure, binding and catalytic mechanism of the adenosine deaminases have been well-studied, but the underlying mechanism of the catalytic reaction is not very clear yet. Here we extensively review the existing data on the occurrence, biogenesis and functions of inosine and its methyl derivatives in RNA. We also included the structural and thermodynamic aspects of these modifications in our review to provide a detailed and integrated discussion on the consequences of A-to-I editing in RNA and the contribution of different structural and thermodynamic studies in understanding its role in RNA. We also highlight the importance of further studies for a better understanding of the mechanisms of the different classes of deamination reactions. Further investigation of the structural and thermodynamic consequences and functions of these modifications in RNA should provide more useful information about their role in different diseases.
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Affiliation(s)
- Nivedita Dutta
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Indrajit Deb
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India.
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3
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Lomidze L, Yang M, Khutsishvili D, Metreveli N, Musier-Forsyth K, Kankia B. Structure of Tetrahelical DNA Homopolymers Supports Quadruplex World Hypothesis. ACS OMEGA 2022; 7:4311-4316. [PMID: 35155924 PMCID: PMC8829921 DOI: 10.1021/acsomega.1c06026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
We previously reported a tetrahelical monomolecular architecture of DNA, tmDNA, which employs G-quartets and an all-parallel GGGTGGGTGGGTGGG (G3T) quadruplex as the repeating unit. Based on thermodynamic and kinetic studies, we proposed that covalently joined (G3T) n units formed an uninterrupted programmable homopolymer; however, structural evidence for the tmDNA architecture was lacking. Here, we used NMR spectroscopy of wild-type and single-inosine-substituted constructs to characterize both monomolecular (G3T)2 and bimolecular quadruplex-Mg-coupled versions of tmDNA. The NMR results support an architecture consisting of uninterrupted stacked G-tetrads in both the monomolecular constructs and bimolecular assemblies. Taken together, these data support the formation of a stable programmable homopolymeric tmDNA architecture, which may have been a precursor to the modern-day Watson-Crick DNA duplex.
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Affiliation(s)
- Levan Lomidze
- Institute of Biophysics, Ilia State University, Tbilisi 0162, Republic of Georgia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mengkun Yang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - David Khutsishvili
- Institute of Biophysics, Ilia State University, Tbilisi 0162, Republic of Georgia
| | - Nunu Metreveli
- Institute of Biophysics, Ilia State University, Tbilisi 0162, Republic of Georgia
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Besik Kankia
- Institute of Biophysics, Ilia State University, Tbilisi 0162, Republic of Georgia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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4
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Gajsiewicz JM, Smith SA, Morrissey JH. Polyphosphate and RNA Differentially Modulate the Contact Pathway of Blood Clotting. J Biol Chem 2016; 292:1808-1814. [PMID: 28007958 DOI: 10.1074/jbc.m116.754325] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 12/21/2016] [Indexed: 11/06/2022] Open
Abstract
The contact pathway of the plasma clotting cascade is dispensable for normal hemostasis, but contributes to thrombosis and serves as a bridge between inflammation and coagulation. This pathway is triggered upon exposure of plasma to certain anionic polymers and artificial surfaces. Recently, extracellular nucleic acids and inorganic polyphosphate (polyP) have been implicated as being important (patho)physiologically relevant activators of this pathway. However, mechanistic details regarding how nucleic acids or polyP modulate the individual reactions of the contact pathway have been lacking. In this study, we investigate the ability of RNA homopolymers and polyP to bind the primary constituents of the contact pathway: factor XIa, factor XIIa, and plasma kallikrein, in the presence and absence of high molecular weight kininogen (HK), an important cofactor in this pathway. We examine seven proteolytic activation reactions within the contact pathway and report that polyP greatly enhances the rate of all seven, while RNA is effective in supporting only a subset of these reactions. HK both enhances and suppresses these proteolytic activation reactions, depending on the specific reaction evaluated. Overall, we find that polyP is a potent mediator of contact pathway activation reactions in general, that RNA secondary structure may be important to its procoagulant activity, and that nucleic acids versus polyP may differentially modulate specific enzyme activation events within the contact pathway.
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Affiliation(s)
- Joshua M Gajsiewicz
- From the Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Stephanie A Smith
- From the Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - James H Morrissey
- From the Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.
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5
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Miller MC, Ohrenberg CJ, Kuttan A, Trent JO. Separation of Quadruplex Polymorphism in DNA Sequences by Reversed-Phase Chromatography. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2015; 61:17.7.1-17.7.18. [PMID: 26344226 PMCID: PMC4561857 DOI: 10.1002/0471142700.nc1707s61] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This unit describes a method for the separation of a mixture of quadruplex conformations formed from the same parent sequence via reversed-phase chromatography (RPC). Polymorphism is inherent to quadruplex formation and even relatively simple quadruplex-forming sequences can fold into a cornucopia of possible conformations and topologies. Isolation of a specific conformation for study can be problematic. This is especially true for conformations of the human telomere sequence d(GGG(TTAGGG)3). High performance liquid chromatography (HPLC), especially reversed-phase chromatography, has been a mainstay of nucleic acid research and purification for many decades. We have successfully applied this method to the problem of separating individual quadruplex species in the ensemble from the same parent sequence.
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Affiliation(s)
- M. Clarke Miller
- Department of Chemistry and Biochemistry, University of North Georgia, 3820 Mundy Mill Road, Oakwood, Georgia 30566
- James Graham Brown Cancer Center, Clinical Translational Research Building, University of Louisville, 505 South Hancock Street, Louisville, KY 40202
| | - Carl J. Ohrenberg
- Department of Chemistry and Biochemistry, University of North Georgia, 3820 Mundy Mill Road, Oakwood, Georgia 30566
| | - Ashani Kuttan
- James Graham Brown Cancer Center, Clinical Translational Research Building, University of Louisville, 505 South Hancock Street, Louisville, KY 40202
| | - John O. Trent
- James Graham Brown Cancer Center, Clinical Translational Research Building, University of Louisville, 505 South Hancock Street, Louisville, KY 40202
- Department of Medicine, University of Louisville, Clinical Translational Research Building, University of Louisville, 505 South Hancock Street, Louisville, KY 40202
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Le HT, Buscaglia R, Dean WL, Chaires JB, Trent JO. Calculation of hydrodynamic properties for G-quadruplex nucleic acid structures from in silico bead models. Top Curr Chem (Cham) 2013; 330:179-210. [PMID: 22886555 PMCID: PMC3580009 DOI: 10.1007/128_2012_351] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Nucleic acids enriched in guanine bases can adopt unique quadruple helical tertiary structures known as G-quadruplexes. G-quadruplexes have emerged as attractive drug targets as many G-quadruplex-forming sequences have been discovered in functionally critical sites within the human genome, including the telomere, oncogene promoters, and mRNA processing sites. A single G-quadruplex-forming sequence can adopt one of many folding topologies, often resulting in a lack of a single definitive atomic-level resolution structure for many of these sequences and a major challenge to the discovery of G-quadruplex-selective small molecule drugs. Low-resolution techniques employed to study G-quadruplex structures (e.g., CD spectroscopy) are often unable to discern between G-quadruplex structural ensembles, while high-resolution techniques (e.g., NMR spectroscopy) can be overwhelmed by a highly polymorphic system. Hydrodynamic bead modeling is an approach to studying G-quadruplex structures that could bridge the gap between low-resolution techniques and high-resolution molecular models. Here, we present a discussion of hydrodynamic bead modeling in the context of studying G-quadruplex structures, highlighting recent successes and limitations to this approach, as well as an example featuring a G-quadruplex structure formed from the human telomere. This example can easily be adapted to the investigation of any other G-quadruplex-forming sequences.
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Affiliation(s)
- Huy T Le
- Clinical and Translation Research Building, University of Louisville, 505 S. Hancock St, Louisville, KY, 40202, USA
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7
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Le HT, Miller MC, Buscaglia R, Dean WL, Holt PA, Chaires JB, Trent JO. Not all G-quadruplexes are created equally: an investigation of the structural polymorphism of the c-Myc G-quadruplex-forming sequence and its interaction with the porphyrin TMPyP4. Org Biomol Chem 2012; 10:9393-404. [PMID: 23108607 PMCID: PMC3501587 DOI: 10.1039/c2ob26504d] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
G-quadruplexes, DNA tertiary structures highly localized to functionally important sites within the human genome, have emerged as important new drug targets. The putative G-quadruplex-forming sequence (Pu27) in the NHE-III(1) promoter region of the c-Myc gene is of particular interest as stabilization of this G-quadruplex with TMPyP4 has been shown to repress c-Myc transcription. In this study, we examine the Pu27 G-quadruplex-forming sequence and its interaction with TMPyP4. We report that the Pu27 sequence exists as a heterogeneous mixture of monomeric and higher-order G-quadruplex species in vitro and that this mixture can be partially resolved by size exclusion chromatography (SEC) separation. Within this ensemble of configurations, the equilibrium can be altered by modifying the buffer composition, annealing procedure, and dialysis protocol thereby affecting the distribution of G-quadruplex species formed. TMPyP4 was found to bind preferentially to higher-order G-quadruplex species suggesting the possibility of stabilization of the junctions of the c-Myc G-quadruplex multimers by porphyrin end-stacking. We also examined four modified c-Myc sequences that have been previously reported and found a narrower distribution of G-quadruplex configurations compared to the parent Pu27 sequence. We could not definitively conclude whether these G-quadruplex structures were selected from the original ensemble or if they are new G-quadruplex structures. Since these sequences differ considerably from the wild-type promoter sequence, it is unclear whether their structures have any actual biological relevance. Additional studies are needed to examine how the polymorphic nature of G-quadruplexes affects the interpretation of in vitro data for c-Myc and other G-quadruplexes. The findings reported here demonstrate that experimental conditions contribute significantly to G-quadruplex formation and should be carefully considered, controlled, and reported in detail.
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Affiliation(s)
- Huy T. Le
- Department of Biochemistry & Molecular Biology, School of Medicine, University of Louisville, HSC-A Building, Room 616 Louisville, Kentucky 40292; Phone: (502) 852-6221; Fax: (502) 852-6222
| | - M. Clarke Miller
- James G. Brown Cancer Center, University of Louisville, 529 South Jackson Street Louisville, KY 40202; Phone:(502) 562-4375
| | - Robert Buscaglia
- Department of Biochemistry & Molecular Biology, School of Medicine, University of Louisville, HSC-A Building, Room 616 Louisville, Kentucky 40292; Phone: (502) 852-6221; Fax: (502) 852-6222
| | - William L. Dean
- James G. Brown Cancer Center, University of Louisville, 529 South Jackson Street Louisville, KY 40202; Phone:(502) 562-4375
- Department of Medicine, School of Medicine, University of Louisville, 550 South Jackson Street, Louisville, KY 40202; Phone: (502) 852-5241; Fax: (502) 852-6233
| | - Patrick A. Holt
- Department of Biochemistry & Molecular Biology, School of Medicine, University of Louisville, HSC-A Building, Room 616 Louisville, Kentucky 40292; Phone: (502) 852-6221; Fax: (502) 852-6222
| | - Jonathan B. Chaires
- Department of Biochemistry & Molecular Biology, School of Medicine, University of Louisville, HSC-A Building, Room 616 Louisville, Kentucky 40292; Phone: (502) 852-6221; Fax: (502) 852-6222
- James G. Brown Cancer Center, University of Louisville, 529 South Jackson Street Louisville, KY 40202; Phone:(502) 562-4375
- Department of Medicine, School of Medicine, University of Louisville, 550 South Jackson Street, Louisville, KY 40202; Phone: (502) 852-5241; Fax: (502) 852-6233
| | - John O. Trent
- Department of Biochemistry & Molecular Biology, School of Medicine, University of Louisville, HSC-A Building, Room 616 Louisville, Kentucky 40292; Phone: (502) 852-6221; Fax: (502) 852-6222
- James G. Brown Cancer Center, University of Louisville, 529 South Jackson Street Louisville, KY 40202; Phone:(502) 562-4375
- Department of Medicine, School of Medicine, University of Louisville, 550 South Jackson Street, Louisville, KY 40202; Phone: (502) 852-5241; Fax: (502) 852-6233
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8
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Miller MC, Trent JO. Resolution of quadruplex polymorphism by size-exclusion chromatography. ACTA ACUST UNITED AC 2011; Chapter 17:Unit17.3. [PMID: 21638270 DOI: 10.1002/0471142700.nc1703s45] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This unit describes a method for separation of quadruplex species formed from the same sequence via size-exclusion chromatography (SEC). Polymorphism is inherent to quadruplex formation, and even relatively simple quadruplex-forming sequences, such as the human telomere sequence d(GGG(TTAGGG)(3)), can form a myriad of possible configurations. HPLC, especially using reversed-phase and anion-exchange methods, has been a mainstay of nucleic acids research and purification for many decades. These methods have been applied for separation of individual quadruplex species formed in a mixture from the same parent sequence.
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Affiliation(s)
- M Clarke Miller
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, USA
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9
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Miller MC, Le HT, Dean WL, Holt PA, Chaires JB, Trent JO. Polymorphism and resolution of oncogene promoter quadruplex-forming sequences. Org Biomol Chem 2011; 9:7633-7. [PMID: 21938285 DOI: 10.1039/c1ob05891f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We report the separation of several quadruplex species formed by ten promoter sequences by Size Exclusion Chromatography (SEC). Modification at the 5' or 3' ends or in loop regions of quadruplex forming sequences has become the standard technique for dealing with quadruplex polymorphism. However, conformations produced employing this method or by other means of artificially shifting the equilibrium may not represent the species that are present in vivo. This method enables an unperturbed view of the structural polymorphism inherent to quadruplex formation. Separation via SEC facilitates studies on quadruplex structure and biophysical properties without the need for sequence modification.
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Affiliation(s)
- M Clarke Miller
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
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10
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Andrushchenko V, Bouř P. Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides. Chirality 2011; 22 Suppl 1:E96-E114. [PMID: 21038400 DOI: 10.1002/chir.20872] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The application of the Cartesian coordinate tensor transfer (CCT) technique for simulations of the IR absorption and vibrational circular dichroism (VCD) spectra of relatively large nucleic acid fragments is demonstrated on several case studies. The approach is based on direct ab initio calculations of atomic tensors, determining molecular properties, for relatively small fragments, and subsequent transfer of these tensors to the larger systems in Cartesian coordinates. This procedure enables precise computations of vibrational spectra for large biomolecular systems, currently with up to several thousands of atoms. The versatile ability of the CCT methods is emphasized on the examples of VCD and IR absorption spectra calculations for B- and Z-forms of DNA, single-, double-, and triple-stranded RNA helices and DNA structures with different base content and sequences. The development and recent improvements of the methodology are followed, including utilization of the constrained normal mode optimization (NMO) strategy and combined quantum mechanics and molecular dynamics simulations. Advantages, drawbacks, and recommendations for future improvements of the CCT method as applied to nucleic acid spectra calculations are discussed.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague, Czech Republic.
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11
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Tintoré M, Aviñó A, Ruiz FM, Eritja R, Fàbrega C. Development of a Novel Fluorescence Assay Based on the Use of the Thrombin-Binding Aptamer for the Detection of O-Alkylguanine-DNA Alkyltransferase Activity. J Nucleic Acids 2010; 2010. [PMID: 20936180 PMCID: PMC2946612 DOI: 10.4061/2010/632041] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 07/17/2010] [Indexed: 02/05/2023] Open
Abstract
Human O6-alkylguanine-DNA alkyltransferase (hAGT) is a DNA repair protein that reverses the effects of alkylating agents by removing DNA adducts from the O6 position of guanine. Here, we developed a real-time fluorescence hAGT activity assay that is based on the detection of conformational changes of the thrombin-binding aptamer (TBA). The quadruplex structure of TBA is disrupted when a central guanine is replaced by an O6-methyl-guanine. The sequence also contains a fluorophore (fluorescein) and a quencher (dabsyl) attached to the opposite ends. In the unfolded structure, the fluorophore and the quencher are separated. When hAGT removes the methyl group from the central guanine of TBA, it folds back immediately into its quadruplex structure. Consequently, the fluorophore and the quencher come into close proximity, thereby resulting in decreased fluorescence intensity. Here, we developed a new method to quantify the hAGT without using radioactivity. This new fluorescence resonance energy transfer assay has been designed to detect the conformational change of TBA that is induced by the removal of the O6-methyl group.
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Affiliation(s)
- Maria Tintoré
- Institute for Research in Biomedicine (IRB Barcelona) IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering Biomaterials and Nanomedicine, Cluster Building, Baldiri i Reixac 10, 08028 Barcelona, Spain
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12
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Urbanová M. Bioinspired interactions studied by vibrational circular dichroism. Chirality 2010; 21 Suppl 1:E215-30. [PMID: 19937957 DOI: 10.1002/chir.20803] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Vibrational circular dichroism (VCD) spectra are reliable indicators of the spatial structure of chiral molecules. The specific and characteristic feature of vibrational spectroscopy, and therefore also of VCD, where the energy of some vibrational modes is predominantly focused to a specific part of the molecule, enables monitoring both the structure of the molecule dissolved in different solvents and under different physicochemical conditions and molecular interactions. This minireview deals with recent contributions covering structural information on the bioinspired interactions obtained by means of VCD, especially in the following areas: interaction of DNA with biomolecules and biogenic metals, guanine tetramers and quadruplexes, biointeractions of bile pigments, and polypeptide and protein interactions with other biomolecules.
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Affiliation(s)
- Marie Urbanová
- Department of Physics and Measurements, Institute of Chemical Technology, Prague, Czech Republic.
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13
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Sannohe Y, Sugiyama H. Overview of formation of G-quadruplex structures. ACTA ACUST UNITED AC 2010; Chapter 17:Unit 17.2.1-17. [PMID: 20201027 DOI: 10.1002/0471142700.nc1702s40] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There are many structures that can be adopted by nucleic acids other than the Watson-Crick duplex. In particular, a noncanonical four-stranded topology, called a G-quadruplex, is of great interest because of its roles in key biological processes such as the maintenance of telomeres and regulation of gene transcription. This review describes the condition for forming the G-quadruplex structure, G-quadruplex-forming sequences, and methods for studying the structures.
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