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Ruszkowska A, Zheng YY, Mao S, Ruszkowski M, Sheng J. Structural Insights Into the 5′UG/3′GU Wobble Tandem in Complex With Ba2+ Cation. Front Mol Biosci 2022; 8:762786. [PMID: 35096964 PMCID: PMC8793689 DOI: 10.3389/fmolb.2021.762786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 11/24/2021] [Indexed: 11/25/2022] Open
Abstract
G•U wobble base pair frequently occurs in RNA structures. The unique chemical, thermodynamic, and structural properties of the G•U pair are widely exploited in RNA biology. In several RNA molecules, the G•U pair plays key roles in folding, ribozyme catalysis, and interactions with proteins. G•U may occur as a single pair or in tandem motifs with different geometries, electrostatics, and thermodynamics, further extending its biological functions. The metal binding affinity, which is essential for RNA folding, catalysis, and other interactions, differs with respect to the tandem motif type due to the different electrostatic potentials of the major grooves. In this work, we present the crystal structure of an RNA 8-mer duplex r[UCGUGCGA]2, providing detailed structural insights into the tandem motif I (5′UG/3′GU) complexed with Ba2+ cation. We compare the electrostatic potential of the presented motif I major groove with previously published structures of tandem motifs I, II (5′GU/3′UG), and III (5′GG/3′UU). A local patch of a strongly negative electrostatic potential in the major groove of the presented structure forms the metal binding site with the contributions of three oxygen atoms from the tandem. These results give us a better understanding of the G•U tandem motif I as a divalent metal binder, a feature essential for RNA functions.
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Affiliation(s)
| | - Ya Ying Zheng
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Song Mao
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Milosz Ruszkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Jia Sheng
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
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Making Molecules with Clay: Layered Double Hydroxides, Pentopyranose Nucleic Acids and the Origin of Life. Life (Basel) 2019; 9:life9010019. [PMID: 30781413 PMCID: PMC6463092 DOI: 10.3390/life9010019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 02/04/2019] [Accepted: 02/09/2019] [Indexed: 11/17/2022] Open
Abstract
A mixture of sugar diphosphates is produced in reactions between small aldehyde phosphates catalysed by layered double hydroxide (LDH) clays under plausibly prebiotic conditions. A subset of these, pentose diphosphates, constitute the backbone subunits of nucleic acids capable of base pairing, which is not the case for the other products of these LDH-catalysed reactions. Not only that, but to date no other polymer found capable of base pairing—and therefore information transfer—has a backbone for which its monomer subunits have a plausible prebiotic synthesis, including the ribose-5-phosphate backbone subunit of RNA. Pentose diphosphates comprise the backbone monomers of pentopyranose nucleic acids, some of the strongest base pairing systems so far discovered. We have previously proposed that the first base pairing interactions were between purine nucleobase precursors, and that these were weaker and less specific than standard purine-pyrimidine interactions. We now propose that the inherently stronger pairing of pentopyranose nucleic acids would have compensated for these weaker interactions, and produced an informational polymer capable of undergoing nonenzymatic replication. LDH clays might also have catalysed the synthesis of the purine nucleobase precursors, and the polymerization of pentopyranose nucleotide monomers into oligonucleotides, as well as the formation of the first lipid bilayers.
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Abstract
HIV integrase (IN) catalyzes the insertion into the genome of the infected human cell of viral DNA produced by the retrotranscription process. The discovery of raltegravir validated the existence of the IN, which is a new target in the field of anti-HIV drug research. The mechanism of catalysis of IN is depicted, and the characteristics of the inhibitors of the catalytic site of this viral enzyme are reported. The role played by the resistance is elucidated, as well as the possibility of bypassing this problem. New approaches to block the integration process are depicted as future perspectives, such as development of allosteric IN inhibitors, dual inhibitors targeting both IN and other enzymes, inhibitors of enzymes that activate IN, activators of IN activity, as well as a gene therapy approach.
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Affiliation(s)
- Roberto Di Santo
- Dipartimento
di Chimica e
Tecnologie del Farmaco, Istituto Pasteur, Fondazione Cenci Bolognetti, “Sapienza” Università di Roma, P.le Aldo Moro 5, I-00185 Rome, Italy
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Halder S, Bhattacharyya D. RNA structure and dynamics: a base pairing perspective. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 113:264-83. [PMID: 23891726 DOI: 10.1016/j.pbiomolbio.2013.07.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 06/25/2013] [Accepted: 07/16/2013] [Indexed: 12/12/2022]
Abstract
RNA is now known to possess various structural, regulatory and enzymatic functions for survival of cellular organisms. Functional RNA structures are generally created by three-dimensional organization of small structural motifs, formed by base pairing between self-complementary sequences from different parts of the RNA chain. In addition to the canonical Watson-Crick or wobble base pairs, several non-canonical base pairs are found to be crucial to the structural organization of RNA molecules. They appear within different structural motifs and are found to stabilize the molecule through long-range intra-molecular interactions between basic structural motifs like double helices and loops. These base pairs also impart functional variation to the minor groove of A-form RNA helices, thus forming anchoring site for metabolites and ligands. Non-canonical base pairs are formed by edge-to-edge hydrogen bonding interactions between the bases. A large number of theoretical studies have been done to detect and analyze these non-canonical base pairs within crystal or NMR derived structures of different functional RNA. Theoretical studies of these isolated base pairs using ab initio quantum chemical methods as well as molecular dynamics simulations of larger fragments have also established that many of these non-canonical base pairs are as stable as the canonical Watson-Crick base pairs. This review focuses on the various structural aspects of non-canonical base pairs in the organization of RNA molecules and the possible applications of these base pairs in predicting RNA structures with more accuracy.
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Affiliation(s)
- Sukanya Halder
- Biophysics division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700 064, India
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5
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Abstract
Molecular docking, molecular mechanics, molecular dynamics and relaxation matrix simulation protocols have been extensively used to generate the structural details of ligand-receptor complexes in order to understand the binding interactions between the two entities. Experimental methods like NMR spectroscopy and X-ray crystallography are known to provide structural information about ligand-receptor complexes. In addition, fluorescence spectroscopy, circular dichroism (CD) spectroscopy and molecular docking have also been utilized to decode the phenomenon of the ligand-DNA interactions, with good correlation between experimental and computational results. The DNA binding affinity was demonstrated by analysing fluorescence spectral data. Structural rigidity of DNA upon ligand binding was identified by CD spectroscopy. Docking is carried out using the DNA-Dock program which results in the binding affinity data along with structural information like interatomic distances and H-bonding, etc. The complete structural analyses of various drug-DNA complexes have afforded results that indicate a specific DNA binding pattern of these ligands. It also exhibited that certain structural features of ligands can make a ligand to be AT- or GC-specific. It was also demonstrated that changing specificity from AT base pairs to GC base pairs further improved the DNA topoisomerase inhibiting activity in certain ligands. Thus, a specific molecular recognition signature encrypted in the structure of ligand can be decoded and can be effectively employed in designing more potent antiviral and antitumour agents.
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6
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Singh N, Ranjan A, Sur S, Chandra R, Tandon V. Inhibition of HIV-1 Integrase gene expression by 10-23 DNAzyme. J Biosci 2012; 37:493-502. [PMID: 22750986 DOI: 10.1007/s12038-012-9216-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
HIV Integrase (IN) is an enzyme that is responsible for the integration of the proviral genome into the human genome, and this integration step is the first step of the virus hijacking the human cell machinery for its propagation and replication. 10-23 DNAzyme has the potential to suppress gene expressions through sequence-specific mRNA cleavage. We have designed three novel DNAzymes, DIN54, DIN116, and DIN152, against HIV-1 Integrase gene using Mfold software and evaluated them for target site cleavage activity on the in vitro transcribed mRNA. All DNAzymes were tested for its inhibition of expression of HIV Integrase protein in the transiently transfected cell lines. DIN116 and DIN152 inhibited IN-EGFP expression by 80 percent and 70 percent respectively.
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MESH Headings
- Base Pairing
- Base Sequence
- DNA, Catalytic/chemistry
- DNA, Catalytic/genetics
- DNA, Catalytic/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Gene Expression
- Green Fluorescent Proteins/biosynthesis
- Green Fluorescent Proteins/genetics
- HIV Integrase/biosynthesis
- HIV Integrase/genetics
- HeLa Cells
- Humans
- Models, Molecular
- Nucleic Acid Conformation
- RNA Cleavage
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Recombinant Fusion Proteins/biosynthesis
- Recombinant Fusion Proteins/genetics
- Software
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Affiliation(s)
- Nirpendra Singh
- Dr BR Ambedkar Center for Biomedical Research, University of Delhi, New Delhi 110 007, India
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Shanker S, Bandyopadhyay P. Determination of low-energy structures of a small RNA hairpin using Monte Carlo-based techniques. J Biosci 2012; 37:533-8. [PMID: 22750989 DOI: 10.1007/s12038-012-9209-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The energy landscape of RNA is known to be extremely rugged, and hence finding low-energy structures starting from a random structure is a challenging task for any optimization algorithm. In the current work, we have investigated the ability of one Monte Carlo-based optimization algorithm, Temperature Basin Paving, to explore the energy landscape of a small RNA T-loop hairpin. In this method, the history of the simulation is used to increase the probability of states less visited in the simulation. It has been found that using both energy and end-to-end distance as the biasing parameters in the simulation, the partially folded structure of the hairpin starting from random structures could be obtained.
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Affiliation(s)
- Sudhanshu Shanker
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110 067, India
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Islam MM, Suresh Kumar G. RNA-binding potential of protoberberine alkaloids: spectroscopic and calorimetric studies on the binding of berberine, palmatine, and coralyne to protonated RNA structures. DNA Cell Biol 2009; 28:637-50. [PMID: 19715476 DOI: 10.1089/dna.2009.0930] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Interaction of the protoberberine alkaloids berberine, palmatine, and coralyne with the two double-stranded RNA homopolymers of cytidine-guanosine (CG) and inosine-cytidine (IC) sequences in the protonated conformation was investigated using various biophysical techniques. All the three alkaloids bound polyC(+)G in a cooperative way. The binding of coralyne to both the polyribonucleotides was stronger than that of berberine and palmatine. Evidence for the intercalative binding of coralyne was revealed from fluorescence quenching studies. Isothermal titration calorimetry results suggested that the binding of berberine to both the polymers and palmatine to polyIC(+) was very weak while that of palmatine and coralyne to polyC(+)G and polyIC(+) was predominantly entropy driven. Circular dichroic results provided evidence for the perturbation of the RNA conformation with the bound coralyne in a more deeply intercalated position compared to berberine and palmatine as revealed by induced circular dichroism peaks. Taken together, the present study suggests that planarity of coralyne results in a more favorable and stronger binding to the double-stranded RNA conformations compared to berberine and palmatine that may potentiate its use in RNA-targeted drug design.
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Affiliation(s)
- M M Islam
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata 700032, India.
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Bhattacharyya D, Koripella SC, Mitra A, Rajendran VB, Sinha B. Theoretical analysis of noncanonical base pairing interactions in RNA molecules. J Biosci 2007; 32:809-25. [PMID: 17914224 DOI: 10.1007/s12038-007-0082-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Noncanonical base pairs in RNA have strong structural and functional implications but are currently not considered for secondary structure predictions. We present results of comparative ab initio studies of stabilities and interaction energies for the three standard and 24 selected unusual RNA base pairs reported in the literature. Hydrogen added models of isolated base pairs, with heavy atoms frozen in their 'away from equilibrium' geometries, built from coordinates extracted from NDB, were geometry optimized using HF/6-31G** basis set, both before and after unfreezing the heavy atoms. Interaction energies, including BSSE and deformation energy corrections, were calculated, compared with respective single point MP2 energies, and correlated with occurrence frequencies and with types and geometries of hydrogen bonding interactions. Systems having two or more N-H...O/N hydrogen bonds had reasonable interaction energies which correlated well with respective occurrence frequencies and highlighted the possibility of some of them playing important roles in improved secondary structure prediction methods. Several of the remaining base pairs with one N-H...O/N and/or one C-H...O/N interactions respectively, had poor interaction energies and negligible occurrences. High geometry variations on optimization of some of these were suggestive of their conformational switch like characteristics.
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Affiliation(s)
- Dhananjay Bhattacharyya
- Biophysics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700 064, India.
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Prathiba J, Malathi R. Group I introns and gnra tetraloops: remnants of ‘The RNA world’? Mol Biol Rep 2007; 35:239-49. [PMID: 17437184 DOI: 10.1007/s11033-007-9076-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2007] [Accepted: 02/26/2007] [Indexed: 10/23/2022]
Abstract
GNRA tetraloops, found in high frequency in natural RNAs, make loop-receptor interactions, stabilizing the tertiary structure of Group I introns, a class of small RNAs. Analyzing 230 Group I introns, to study the distribution and sequence pattern of the GNRA tetraloops, we suggest that these features reflect the ancestral nature of these catalytic molecules, in a prebiotic RNA world. The adenosine rich GNRA tetraloops would have interacted with each other through long range RNA-RNA interactions to form higher order structures forming potential sites that render the propensity for the short RNAs to bind to metal ions from the prebiotic pool, aiding them to act as metalloenzymes.
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Affiliation(s)
- J Prathiba
- Department of Genetics, Dr ALM PGIBMS, University of Madras, Taramani Campus, Chennai, 600 113, India
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