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Nabi Afjadi M, Yazdanparast R, Barzegari E. The Impact of Terminal Peptide Extensions of Retinal Inosine 5´Monophosphate Dehydrogenase 1 Isoforms on their DNA-binding Activities. Protein J 2024; 43:592-602. [PMID: 38733555 DOI: 10.1007/s10930-024-10202-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
The main structural difference between the mutation-susceptible retinal isoforms of inosine 5´-monophosphate dehydrogenase-1 (IMPDH-1) with the canonical form resides in the C- and N-terminal peptide extensions with unknown structural/functional impacts. In this report, we aimed to experimentally evaluate the functional impact of these extensions on the specific/non-specific single-stranded DNA (ssDNA)-binding activities relative to those of the canonical form. Our in silico findings indicated the possible contribution of the C-terminal segment to the reduced flexibility of the Bateman domain of the enzyme. In addition, the in silico data indicated that the N-terminal tail acts by altering the distance between the tetramers in the concave octamer complex (the native form) of the enzyme. The overall impact of these predicted structural variations became evident, first, through higher Km values with respect to either of the substrates relative to the canonical isoform, as reported previously (Andashti et al. in Mol Cell Biochem 465(1):155-164, 2020). Secondary, the binding of the recombinant mouse retinal isoform IMPDH1 (603) to its specific Rhodopsin target gene was significantly augmented while its binding to non-specific ssDNA was lower than that of the canonical isoform. The DNA-binding activity of the other mouse retinal isoform, IMPDH1(546), to specific and non-specific ssDNA was lower than that of the canonical form most probably due to the in silico predicted rigidity created in the Bateman domain by the C-terminal peptide extension. Furthermore, the DNA binding to the Rhodopsin target gene by each of the IMPDH isoforms influenced in the presence of GTP (Guanosine triphosphate) and ATP (Adenosine triphosphate).
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Affiliation(s)
- Mohsen Nabi Afjadi
- Institute of Biochemistry and Biophysics, University of Tehran, P. O. Box 13145-1384, Tehran, Iran
| | - Razieh Yazdanparast
- Institute of Biochemistry and Biophysics, University of Tehran, P. O. Box 13145-1384, Tehran, Iran.
| | - Ebrahim Barzegari
- Institute of Biochemistry and Biophysics, University of Tehran, P. O. Box 13145-1384, Tehran, Iran
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2
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Gedeon A, Ayoub N, Brûlé S, Raynal B, Karimova G, Gelin M, Mechaly A, Haouz A, Labesse G, Munier‐Lehmann H. Insight into the role of the Bateman domain at the molecular and physiological levels through engineered IMP dehydrogenases. Protein Sci 2023; 32:e4703. [PMID: 37338125 PMCID: PMC10357500 DOI: 10.1002/pro.4703] [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: 03/03/2023] [Revised: 05/15/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023]
Abstract
Inosine 5'-monophosphate (IMP) dehydrogenase (IMPDH) is an ubiquitous enzyme that catalyzes the NAD+ -dependent oxidation of inosine 5'-monophosphate into xanthosine 5'-monophosphate. This enzyme is formed of two distinct domains, a core domain where the catalytic reaction occurs, and a less-conserved Bateman domain. Our previous studies gave rise to the classification of bacterial IMPDHs into two classes, according to their oligomeric and kinetic properties. MgATP is a common effector but cause to different effects when it binds within the Bateman domain: it is either an allosteric activator for Class I IMPDHs or a modulator of the oligomeric state for Class II IMPDHs. To get insight into the role of the Bateman domain in the dissimilar properties of the two classes, deleted variants of the Bateman domain and chimeras issued from the interchange of the Bateman domain between the three selected IMPDHs have been generated and characterized using an integrative structural biology approach. Biochemical, biophysical, structural, and physiological studies of these variants unveil the Bateman domain as being the carrier of the molecular behaviors of both classes.
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Affiliation(s)
- Antoine Gedeon
- Institut Pasteur, Université Paris Cité, Unité de Chimie et Biocatalyse, CNRS UMR3523ParisFrance
- Present address:
Institut Pasteur, Université Paris Cité, Unité de Microbiologie Structurale, CNRS UMR3525ParisFrance
| | - Nour Ayoub
- Institut Pasteur, Université Paris Cité, Unité de Chimie et Biocatalyse, CNRS UMR3523ParisFrance
- Present address:
Institut Pasteur, Université Paris Cité, Plate‐Forme de Criblage Chémogénomique et Biologique, CNRS UMR3523ParisFrance
| | - Sébastien Brûlé
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Biophysique Moléculaire, C2RT, CNRS UMR3528ParisFrance
| | - Bertrand Raynal
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Biophysique Moléculaire, C2RT, CNRS UMR3528ParisFrance
| | - Gouzel Karimova
- Institut Pasteur, Université Paris Cité, Unité de Biochimie des Interactions Macromoléculaires, CNRS UMR3528ParisFrance
| | - Muriel Gelin
- Centre de Biologie StructuraleUniversité Montpellier, INSERM, CNRSMontpellierFrance
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Cristallographie, C2RT, CNRS UMR3528ParisFrance
| | - Ahmed Haouz
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Cristallographie, C2RT, CNRS UMR3528ParisFrance
| | - Gilles Labesse
- Centre de Biologie StructuraleUniversité Montpellier, INSERM, CNRSMontpellierFrance
| | - Hélène Munier‐Lehmann
- Institut Pasteur, Université Paris Cité, Unité de Chimie et Biocatalyse, CNRS UMR3523ParisFrance
- Present address:
Institut Pasteur, Université Paris Cité, Plate‐Forme de Criblage Chémogénomique et Biologique, CNRS UMR3523ParisFrance
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3
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IMPDH dysregulation in disease: a mini review. Biochem Soc Trans 2022; 50:71-82. [PMID: 35191957 PMCID: PMC9022972 DOI: 10.1042/bst20210446] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 12/20/2022]
Abstract
Inosine-5′-monophosphate dehydrogenase (IMPDH) is a highly conserved enzyme in purine metabolism that is tightly regulated on multiple levels. IMPDH has a critical role in purine biosynthesis, where it regulates flux at the branch point between adenine and guanine nucleotide synthesis, but it also has a role in transcription regulation and other moonlighting functions have been described. Vertebrates have two isoforms, IMPDH1 and IMPDH2, and point mutations in each are linked to human disease. Mutations in IMPDH2 in humans are associated with neurodevelopmental disease, but the effects of mutations at the enzyme level have not yet been characterized. Mutations in IMPDH1 lead to retinal degeneration in humans, and recent studies have characterized how they cause functional defects in regulation. IMPDH1 is expressed as two unique splice variants in the retina, a tissue with very high and specific demands for purine nucleotides. Recent studies have revealed functional differences among splice variants, demonstrating that retinal variants up-regulate guanine nucleotide synthesis by reducing sensitivity to feedback inhibition by downstream products. A better understanding of the role of IMPDH1 in the retina and the characterization of an animal disease model will be critical for determining the molecular mechanism of IMPDH1-associated blindness.
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Calise SJ, Chan EKL. Anti-rods/rings autoantibody and IMPDH filaments: an update after fifteen years of discovery. Autoimmun Rev 2020; 19:102643. [PMID: 32805424 DOI: 10.1016/j.autrev.2020.102643] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 03/27/2020] [Indexed: 02/07/2023]
Abstract
Autoantibodies to unknown subcellular rod and ring-shaped structures were first discovered in sera from hepatitis C patients in 2005. Early studies showed a strong association between these anti-rods/rings antibodies (anti-RR) and the standard of care interferon-α plus ribavirin combination therapy (IFN/RBV), suggesting that anti-RR are drug-induced autoantibodies. In the context of hepatitis C, anti-RR have been linked with relapse from or lack of response to IFN/RBV in some patient cohorts. However, examples of anti-RR in other diseases and healthy individuals have also been reported over the years, although anti-RR remains a rare autoantibody response in general. The advent of new direct-acting antiviral drugs for chronic hepatitis C and studies of anti-RR from different parts of the world are also beginning to change the perception of anti-RR. The nucleotide biosynthetic enzyme inosine monophosphate dehydrogenase (IMPDH) has been identified as the major autoantigen recognized by anti-RR. Coincidentally, the assembly of IMPDH into micron-scale rod and ring-shaped structures was discovered around the same time as anti-RR. Knowledge of the fundamental biological properties and cellular functions of these structures, referred to as "IMPDH filaments" by cell biologists, has advanced in parallel to anti-RR antibodies. Recent studies have revealed that IMPDH filament assembly is a mechanism to prevent feedback inhibition of IMPDH and is therefore important for the increased nucleotide production required in hyperproliferating cells, like activated T cells. Fifteen years later, we review the history and current knowledge in both the anti-RR autoantibody and IMPDH filament fields. TAKE-HOME MESSAGE: Anti-rods/rings are recognized as an example of a drug-induced autoantibody in hepatitis C patients treated with interferon and ribavirin, although new studies suggest anti-rods/rings may be detected in other contexts and may depend on unknown environmental or genetic factors in different populations. Recent data suggest that the assembly of IMPDH into rod and ring structures, the targets of anti-rods/rings autoantibody, is a mechanism for hyperproliferating cells, like activated T cells, to maintain increased guanine nucleotide levels to support rapid cell division.
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Affiliation(s)
- S John Calise
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424, USA.
| | - Edward K L Chan
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424, USA.
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Manna S, Srivatsan SG. Fluorescence-based tools to probe G-quadruplexes in cell-free and cellular environments. RSC Adv 2018; 8:25673-25694. [PMID: 30210793 PMCID: PMC6130854 DOI: 10.1039/c8ra03708f] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/08/2018] [Indexed: 12/26/2022] Open
Abstract
Biophysical and biochemical investigations provide compelling evidence connecting the four-stranded G-quadruplex (GQ) structure with its role in regulating multiple cellular processes. Hence, modulating the function of GQs by using small molecule binders is being actively pursued as a strategy to develop new chemotherapeutic agents. However, sequence diversity and structural polymorphism of GQs have posed immense challenges in terms of understanding what conformation a G-rich sequence adopts inside the cell and how to specifically target a GQ motif amidst several other GQ-forming sequences. In this context, here we review recent developments in the applications of biophysical tools that use fluorescence readout to probe the GQ structure and recognition in cell-free and cellular environments. First, we provide a detailed discussion on the utility of covalently labeled environment-sensitive fluorescent nucleoside analogs in assessing the subtle difference in GQ structures and their ligand binding abilities. Furthermore, a detailed discussion on structure-specific antibodies and small molecule probes used to visualize and confirm the existence of DNA and RNA GQs in cells is provided. We also highlight the open challenges in the study of tetraplexes (GQ and i-motif structures) and how addressing these challenges by developing new tools and techniques will have a profound impact on tetraplex-directed therapeutic strategies.
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Affiliation(s)
- Sudeshna Manna
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), PuneDr. Homi Bhabha RoadPune 411008India
| | - Seergazhi G. Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), PuneDr. Homi Bhabha RoadPune 411008India
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6
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Gouda AS, Amine MS, Pedersen EB. Improved i-motif thermal stability by insertion of anthraquinone monomers. Org Biomol Chem 2018; 15:6613-6621. [PMID: 28752173 DOI: 10.1039/c7ob01393k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In order to gain insight into how to improve thermal stability of i-motifs when used in the context of biomedical and nanotechnological applications, novel anthraquinone-modified i-motifs were synthesized by insertion of 1,8-, 1,4-, 1,5- and 2,6-disubstituted anthraquinone monomers into the TAA loops of a 22mer cytosine-rich human telomeric DNA sequence. The influence of the four anthraquinone linkers on the i-motif thermal stability was investigated at 295 nm and pH 5.5. Anthraquinone monomers modulate the i-motif stability in a position-depending manner and the modulation also depends on the substitution pattern of the anthraquinone. The insertion of anthraquinone was found to stabilize the i-motif structure when replacing any one of the positions of the central TAA loop and the thermal stabilities were typically higher than those previously found for i-motifs containing pyrene-modified uracilyl unlocked nucleic acid monomers or twisted intercalating nucleic acid. The 2,6-disubstituted anthraquinone linker replacing T10 enabled a significant increase of i-motif thermal melting by 8.2 °C. A substantial increase of 5.0 °C in i-motif thermal melting was recorded when both A6 and T16 were modified with a double replacement by the 2,6-isomer into the TAA loops in the outer regions. The largest destabilization is observed for the 1,5-disubstituted anthraquinone linker upon the replacement of A18. CD curves of anthraquinone-modified variants imply no structural changes in all cases under potassium buffer conditions compared with those of the native i-motif. Molecular modeling studies explained the increased thermal stabilities of anthraquinone-modified i-motifs.
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Affiliation(s)
- Alaa S Gouda
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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7
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Kshirsagar R, Khan K, Joshi MV, Hosur RV, Muniyappa K. Probing the Potential Role of Non-B DNA Structures at Yeast Meiosis-Specific DNA Double-Strand Breaks. Biophys J 2017; 112:2056-2074. [PMID: 28538144 DOI: 10.1016/j.bpj.2017.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 04/13/2017] [Accepted: 04/19/2017] [Indexed: 12/29/2022] Open
Abstract
A plethora of evidence suggests that different types of DNA quadruplexes are widely present in the genome of all organisms. The existence of a growing number of proteins that selectively bind and/or process these structures underscores their biological relevance. Moreover, G-quadruplex DNA has been implicated in the alignment of four sister chromatids by forming parallel guanine quadruplexes during meiosis; however, the underlying mechanism is not well defined. Here we show that a G/C-rich motif associated with a meiosis-specific DNA double-strand break (DSB) in Saccharomyces cerevisiae folds into G-quadruplex, and the C-rich sequence complementary to the G-rich sequence forms an i-motif. The presence of G-quadruplex or i-motif structures upstream of the green fluorescent protein-coding sequence markedly reduces the levels of gfp mRNA expression in S. cerevisiae cells, with a concomitant decrease in green fluorescent protein abundance, and blocks primer extension by DNA polymerase, thereby demonstrating the functional significance of these structures. Surprisingly, although S. cerevisiae Hop1, a component of synaptonemal complex axial/lateral elements, exhibits strong affinity to G-quadruplex DNA, it displays a much weaker affinity for the i-motif structure. However, the Hop1 C-terminal but not the N-terminal domain possesses strong i-motif binding activity, implying that the C-terminal domain has a distinct substrate specificity. Additionally, we found that Hop1 promotes intermolecular pairing between G/C-rich DNA segments associated with a meiosis-specific DSB site. Our results support the idea that the G/C-rich motifs associated with meiosis-specific DSBs fold into intramolecular G-quadruplex and i-motif structures, both in vitro and in vivo, thus revealing an important link between non-B form DNA structures and Hop1 in meiotic chromosome synapsis and recombination.
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Affiliation(s)
- Rucha Kshirsagar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Krishnendu Khan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Mamata V Joshi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Ramakrishna V Hosur
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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8
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Xu B, Devi G, Shao F. Regulation of telomeric i-motif stability by 5-methylcytosine and 5-hydroxymethylcytosine modification. Org Biomol Chem 2016; 13:5646-51. [PMID: 25886653 DOI: 10.1039/c4ob02646b] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The two important epigenetic markers in the human genome, 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC), are involved in gene regulation processes. As a major epigenetic target, cytosines in a C-rich DNA sequence were substituted with mC and hmC to investigate the thermal stability and pH sensitivity of the corresponding i-motifs. Circular Dichroism (CD) studies indicate the formation of i-motifs at acidic pH (<6.5) for mC- and hmC-modified DNA sequences. Thermal denaturation results suggest that DNA i-motifs are stabilized when modified with one or two mCs. However, hypermethylation with mC and single modification with hmC cause destabilization of the structure. A biomimetic crowding agent does not alter the stability effect trends resulting from mC and hmC modifications, though the corresponding i-motifs show elevated melting temperatures without significant changes in pKa values.
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Affiliation(s)
- Baochang Xu
- Division of Chemistry and Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore 637371.
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9
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Devi G, He L, Xu B, Li T, Shao F. In-stem thiazole orange reveals the same triplex intermediate for pH and thermal unfolding of i-motifs. Chem Commun (Camb) 2016; 52:7261-4. [DOI: 10.1039/c6cc01643j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The unfolding pathway of human telomeric i-motifs was monitored by both monomer and exciplex fluorescence of in-stem thiazole orange. A uniform triplex intermediate was determined upon unfolding i-motifs against either pH or thermal denaturation.
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Affiliation(s)
- Gitali Devi
- Division of Chemistry and Biological Chemistry
- School of Physical and Mathematical Sciences
- Nanyang Technological University
- Singapore 637371
- Singapore
| | - Lei He
- Division of Chemistry and Biological Chemistry
- School of Physical and Mathematical Sciences
- Nanyang Technological University
- Singapore 637371
- Singapore
| | - Baochang Xu
- Division of Chemistry and Biological Chemistry
- School of Physical and Mathematical Sciences
- Nanyang Technological University
- Singapore 637371
- Singapore
| | - Tianhu Li
- Division of Chemistry and Biological Chemistry
- School of Physical and Mathematical Sciences
- Nanyang Technological University
- Singapore 637371
- Singapore
| | - Fangwei Shao
- Division of Chemistry and Biological Chemistry
- School of Physical and Mathematical Sciences
- Nanyang Technological University
- Singapore 637371
- Singapore
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10
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Day HA, Pavlou P, Waller ZAE. i-Motif DNA: structure, stability and targeting with ligands. Bioorg Med Chem 2014; 22:4407-18. [PMID: 24957878 DOI: 10.1016/j.bmc.2014.05.047] [Citation(s) in RCA: 270] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/09/2014] [Accepted: 05/22/2014] [Indexed: 10/25/2022]
Abstract
i-Motifs are four-stranded DNA secondary structures which can form in sequences rich in cytosine. Stabilised by acidic conditions, they are comprised of two parallel-stranded DNA duplexes held together in an antiparallel orientation by intercalated, cytosine-cytosine(+) base pairs. By virtue of their pH dependent folding, i-motif forming DNA sequences have been used extensively as pH switches for applications in nanotechnology. Initially, i-motifs were thought to be unstable at physiological pH, which precluded substantial biological investigation. However, recent advances have shown that this is not always the case and that i-motif stability is highly dependent on factors such as sequence and environmental conditions. In this review, we discuss some of the different i-motif structures investigated to date and the factors which affect their topology, stability and dynamics. Ligands which can interact with these structures are necessary to aid investigations into the potential biological functions of i-motif DNA and herein we review the existing i-motif ligands and give our perspective on the associated challenges with targeting this structure.
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Affiliation(s)
- Henry A Day
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Pavlos Pavlou
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Zoë A E Waller
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK.
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11
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El-Sayed AA, Pedersen EB, Khaireldin NA. Studying the influence of the pyrene intercalator TINA on the stability of DNA i-motifs. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2014; 31:872-9. [PMID: 23215550 DOI: 10.1080/15257770.2012.742199] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Certain cytosine-rich (C-rich) DNA sequences can fold into secondary structures as four-stranded i-motifs with hemiprotonated base pairs. Here we synthesized C-rich TINA-intercalating oligonucleotides by inserting a nonnucleotide pyrene moiety between two C-rich regions. The stability of their i-motif structures was studied by using UV melting temperature measurements and circular dichroism spectra at different pH values under noncrowding and crowding conditions (20% poly(ethylene glycol)). When TINA ((R)-3-((4-(1-pyrenylethynyl)benzyl)oxy) propane-1,2-diol) is inserted, the oligonucleotides could form an i-motif at a higher pH than observed for the corresponding wildtype oligonucleotide.
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Affiliation(s)
- Ahmed A El-Sayed
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
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12
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Benabou S, Aviñó A, Eritja R, González C, Gargallo R. Fundamental aspects of the nucleic acid i-motif structures. RSC Adv 2014. [DOI: 10.1039/c4ra02129k] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The latest research on fundamental aspects of i-motif structures is reviewed with special attention to their hypothetical rolein vivo.
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Affiliation(s)
- S. Benabou
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
| | - A. Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - R. Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - C. González
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- E-28006 Madrid, Spain
| | - R. Gargallo
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
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Wu S, Wang X, Ye X, Zhang G. pH-Induced conformational change and dimerization of DNA chains investigated by analytical ultracentrifugation. J Phys Chem B 2013; 117:11541-7. [PMID: 24010411 DOI: 10.1021/jp405561f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
pH-induced conformational change of i-motif DNA has been studied by analytical ultracentrifugation. As pH increases, the hydrodynamic radius of individual DNA chains in aqueous solutions prepared by being heat-treated suddenly increases while the molar mass is constant, indicating that the conformation changes from an i-motif to a random coil. When DNA concentrations are higher than 1.0 μM, relatively stable dimers are formed as pH sharply decreases from 7.5 to 4.5. Moreover, the weight percentage of the dimers increases with the initial DNA concentration. The study can help to understand the functions of the telomeres containing repeated cytosine-rich sequences and to develop DNA-based devices.
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Affiliation(s)
- Sha Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China , Hefei, Anhui 230026, China
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Affiliation(s)
- Yuhao Du
- College of Chemistry and Molecular Sciences; Wuhan University; Hubei; Wuhan; 430072; P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences; Wuhan University; Hubei; Wuhan; 430072; P. R. China
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15
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Hedstrom L. The dynamic determinants of reaction specificity in the IMPDH/GMPR family of (β/α)(8) barrel enzymes. Crit Rev Biochem Mol Biol 2012; 47:250-63. [PMID: 22332716 DOI: 10.3109/10409238.2012.656843] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The inosine monophosphate dehydrogenase (IMPDH)/guanosine monophosphate reductase (GMPR) family of (β/α)(8) enzymes presents an excellent opportunity to investigate how subtle changes in enzyme structure change reaction specificity. IMPDH and GMPR bind the same ligands with similar affinities and share a common set of catalytic residues. Both enzymes catalyze a hydride transfer reaction involving a nicotinamide cofactor hydride, and both reactions proceed via the same covalent intermediate. In the case of IMPDH, this intermediate reacts with water, while in GMPR it reacts with ammonia. In both cases, the two chemical transformations are separated by a conformational change. In IMPDH, the conformational change involves a mobile protein flap while in GMPR, the cofactor moves. Thus reaction specificity is controlled by differences in dynamics, which in turn are controlled by residues outside the active site. These findings have some intriguing implications for the evolution of the IMPDH/GMPR family.
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Affiliation(s)
- Lizbeth Hedstrom
- Departments of Biology and Chemistry, Brandeis University, Waltham, MA 02454, USA.
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16
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McGrew DA, Hedstrom L. Towards a Pathological Mechanism for IMPDH1-Linked Retinitis Pigmentosa. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 723:539-45. [DOI: 10.1007/978-1-4614-0631-0_68] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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17
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Lee IJ, Kim BH. Monitoring i-motif transitions through the exciplex emission of a fluorescent probe incorporating two PyA units. Chem Commun (Camb) 2012; 48:2074-6. [DOI: 10.1039/c1cc16497j] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Specific biotinylation of IMP dehydrogenase. Bioorg Med Chem Lett 2011; 21:1363-5. [DOI: 10.1016/j.bmcl.2011.01.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 01/07/2011] [Accepted: 01/11/2011] [Indexed: 11/22/2022]
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19
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Pasternak A, Wengel J. Modulation of i-motif thermodynamic stability by the introduction of UNA (unlocked nucleic acid) monomers. Bioorg Med Chem Lett 2010; 21:752-5. [PMID: 21185179 DOI: 10.1016/j.bmcl.2010.11.106] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 11/22/2010] [Accepted: 11/23/2010] [Indexed: 02/04/2023]
Abstract
The influence of acyclic RNA derivatives, UNA (unlocked nucleic acid) monomers, on i-DNA thermodynamic stability has been investigated. The 22nt human telomeric fragment was chosen as the model sequence for stability studies. UNA monomers modulate i-motif stability in a position-depending manner. The largest destabilization is observed for position C14, while UNA placed in position A12 causes significant increase of i-DNA thermodynamic stability. CD curves of UNA-modified variants imply no structural changes relative to the native i-motif.
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Affiliation(s)
- Anna Pasternak
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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20
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IMP dehydrogenase is recruited to the transcription complex through serine 2 phosphorylation of RNA polymerase II. Biochem Biophys Res Commun 2010; 392:588-92. [DOI: 10.1016/j.bbrc.2010.01.079] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Accepted: 01/18/2010] [Indexed: 11/21/2022]
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21
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Zhou J, Wei C, Jia G, Wang X, Feng Z, Li C. Formation of i-motif structure at neutral and slightly alkaline pH. MOLECULAR BIOSYSTEMS 2009; 6:580-6. [PMID: 20174686 DOI: 10.1039/b919600e] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
It is well known that oligonucleotides containing tracts cytosines can form i-motif structures under acidic conditions (pH < 7). However, whether i-motif can be formed under normal physiological cellular conditions (pH 7.0-7.5) is yet no conclusive proof. In the present work, using circular dichroism (CD), UV absorption spectroscopies and native polyacrylamide gel electrophoresis (PAGE), we provided the compelling evidence for the formation of i-motif structures by four cytosine clusters, [C(3)TA(2)](3)C(3) (HT), [C(4)G](3)C(4)TA (RET), C(2)T(3)C(2)T(4)C(2)T(3)C(2) (CTC) and GC(2)GC(3)A(4)C(6)G (Rb), at neutral and slightly alkaline pH at 4 degrees C. Furthermore, for HT, we also supplied the evidence for the formation of i-motif structure by fluorescence resonance energy transfer (FRET) and investigated its folding kinetics. The formation time constants obtained by CD and fluorescence experiments are 214 and 493 s, respectively, indicating that HT can slowly form i-motif structure at pH 7.0 and 4 degrees C. This work implies that i-motif structures may possible form in vivo.
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Affiliation(s)
- Jun Zhou
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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Affiliation(s)
- Lizbeth Hedstrom
- Department of Biology, Brandeis University, MS009, 415 South Street, Waltham, Massachusetts 02454, USA.
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Mortimer SE, Xu D, McGrew D, Hamaguchi N, Lim HC, Bowne SJ, Daiger SP, Hedstrom L. IMP dehydrogenase type 1 associates with polyribosomes translating rhodopsin mRNA. J Biol Chem 2008; 283:36354-60. [PMID: 18974094 PMCID: PMC2605994 DOI: 10.1074/jbc.m806143200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Revised: 10/29/2008] [Indexed: 01/28/2023] Open
Abstract
IMP dehydrogenase (IMPDH) catalyzes the pivotal step in guanine nucleotide biosynthesis. Here we show that both IMPDH type 1 (IMPDH1) and IMPDH type 2 are associated with polyribosomes, suggesting that these housekeeping proteins have an unanticipated role in translation regulation. This interaction is mediated by the subdomain, a region of disputed function that is the site of mutations that cause retinal degeneration. The retinal isoforms of IMPDH1 also associate with polyribosomes. The most common disease-causing mutation, D226N, disrupts the polyribosome association of at least one retinal IMPDH1 isoform. Finally, we find that IMPDH1 is associated with polyribosomes containing rhodopsin mRNA. Because any perturbation of rhodopsin expression can trigger apoptosis in photoreceptor cells, these observations suggest a likely pathological mechanism for IMPDH1-mediated hereditary blindness. We propose that IMPDH coordinates the translation of a set of mRNAs, perhaps by modulating localization or degradation.
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Affiliation(s)
- Sarah E Mortimer
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454-9110, USA
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Kumar N, Nielsen JT, Maiti S, Petersen M. i-Motif formation with locked nucleic acid (LNA). Angew Chem Int Ed Engl 2008; 46:9220-2. [PMID: 17969212 DOI: 10.1002/anie.200701667] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Niti Kumar
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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Fenna CP, Wilkinson VJ, Arnold JRP, Cosstick R, Fisher J. The effect of 2′-fluorine substitutions on DNA i-motif conformation and stability. Chem Commun (Camb) 2008:3567-9. [DOI: 10.1039/b804833a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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26
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Kumar N, Nielsen J, Maiti S, Petersen M. i-Motif Formation with Locked Nucleic Acid (LNA). Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200701667] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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. SRJ, . MC, . AKG. Molecular Cloning, Expression and Analysis of Antheraea mylitta Cypovirus Genome Segments 8 and 11. ACTA ACUST UNITED AC 2007. [DOI: 10.3923/ijv.2007.60.72] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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28
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Dobie F, Berg A, Boitz JM, Jardim A. Kinetic characterization of inosine monophosphate dehydrogenase of Leishmania donovani. Mol Biochem Parasitol 2006; 152:11-21. [PMID: 17173987 DOI: 10.1016/j.molbiopara.2006.11.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2006] [Revised: 11/08/2006] [Accepted: 11/14/2006] [Indexed: 11/27/2022]
Abstract
Trypanosomatid protozoan pathogens are purine auxotrophs that are highly dependent on the enzyme inosine monophosphate dehydrogenase (IMPDH) for the synthesis of guanylate nucleotides. Enzymatic characterization of the Leishmania donovani IMPDH (LdIMPDH) overexpressed in E. coli revealed that this enzyme was highly specific for the substrates IMP and NAD(+) with K(m)(app) values of 33 and 390 microM, respectively. In contrast to other IMPDHs, LdIMPDH exhibits no substrate inhibition in high concentrations of NAD(+). Kinetic studies revealed that XMP and GMP were inhibitors with K(i) values of approximately 26 and 210 microM, respectively, suggesting that these nucleotides may regulate LdIMPDH activity. Mycophenolic acid was also a potent inhibitor of L. donovani IMPDH with a K(i) value of approximately 25 nM. Confocal immunofluorescence microscopy and subcellular fractionation localized LdIMPDH to the glycosome. Protein-protein interaction assays revealed that LdIMPDH associated tightly with glycosomal protein sorting receptor LdPEX5.
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Affiliation(s)
- Fredrick Dobie
- Institute of Parasitology, Macdonald Campus of McGill University, 21, 111 Lakeshore Road, Ste. Anne-de-Bellevue, Quebec, Canada H9X 3V9
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Bowne SJ, Liu Q, Sullivan LS, Zhu J, Spellicy CJ, Rickman CB, Pierce EA, Daiger SP. Why do mutations in the ubiquitously expressed housekeeping gene IMPDH1 cause retina-specific photoreceptor degeneration? Invest Ophthalmol Vis Sci 2006; 47:3754-65. [PMID: 16936083 PMCID: PMC2581456 DOI: 10.1167/iovs.06-0207] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE The purpose of this study was to investigate retinal inosine monophosphate dehydrogenase 1 (IMPDH1) transcripts and proteins to gain an understanding of how mutations in IMPDH1 lead to retinal disease. Mutations in IMPDH1 cause the RP10 form of autosomal dominant retinitis pigmentosa (adRP) and are a rare cause of dominant Leber congenital amaurosis (LCA). IMPDH1 is a highly conserved, widely expressed housekeeping gene, the product of which catalyzes the rate-limiting step of de novo guanine synthesis. Despite its conservation and ubiquity, the clinical consequences of missense mutations in IMPDH1 are limited to the retina, and the disease mechanism is currently unknown. METHODS A variety of methods were used to address the unique features of IMPDH1 in the retina, including Northern blot analysis, serial analysis of gene expression (SAGE), immunohistochemistry, transcript sequencing, and Western blot analysis. RESULTS Results of the experiments showed that IMPDH1 levels are higher in the retina than in any other tissue tested. Specifically, IMPDH1 is found predominately in the inner segment and synaptic terminals of retinal photoreceptors. The predominant transcripts of IMPDH1 in human retina are the result of alternate splicing and alternate start sites of translation. They are significantly different from those in other tissues, and these variant transcripts encode distinct proteins. Further, the proportions of IMPDH1 transcripts and proteins in human retina are different from those in mouse retina. CONCLUSIONS Identification of unique retinal isoforms supports the existence of a novel IMPDH1 function in the retina, one that is probably altered by disease-causing mutations. This alone, or coupled with the high levels of IMPDH1 in the retina, may explain the retina-specific phenotype associated with IMPDH1 mutations. Elucidating the functional properties of these unique, human retinal isoforms is crucial to understanding the pathophysiology of IMPDH1 mutations.
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Affiliation(s)
- Sara J. Bowne
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center Houston, Houston, Texas
| | - Qin Liu
- F. M. Kirby Center for Molecular Ophthalmology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - Lori S. Sullivan
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center Houston, Houston, Texas
| | - Jingya Zhu
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center Houston, Houston, Texas
| | - Catherine J. Spellicy
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center Houston, Houston, Texas
| | - Catherine Bowes Rickman
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina
| | - Eric A. Pierce
- F. M. Kirby Center for Molecular Ophthalmology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - Stephen P. Daiger
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center Houston, Houston, Texas
- Department of Ophthalmology and Visual Science, The University of Texas Health Science Center Houston, Houston, Texas
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Mortimer S, Hedstrom L. Autosomal dominant retinitis pigmentosa mutations in inosine 5'-monophosphate dehydrogenase type I disrupt nucleic acid binding. Biochem J 2005; 390:41-7. [PMID: 15882147 PMCID: PMC1184561 DOI: 10.1042/bj20042051] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Two mutations of IMPDH1 (inosine 5'-monophosphate dehydrogenase type I), R224P and D226N, have recently been found to cause adRP (autosomal dominant retinitis pigmentosa). IMPDH1 catalyses the rate-limiting step in guanine nucleotide biosynthesis and also binds single-stranded nucleic acids. In the present paper, we report the biochemical characterization of the adRP-linked mutations, R224P and D226N, and a potentially pathogenic mutation, V268I. The adRP-linked mutations have no effect on enzyme activity, protein stability or protein aggregation. These results suggest strongly that the mutations do not affect enzyme activity in vivo and thus do not perturb the guanine nucleotide pool. The R224P mutation changes the distribution of enzyme between the nucleus and cytoplasm. This effect was not observed with the D226N mutation, so the relevance of this observation to disease is unclear. In contrast, both mutations decrease the affinity of nucleic acid binding and both fail to co-immunoprecipitate RNA. These observations suggest that nucleic acid binding provides a functional assay for adRP pathogenicity. The putative adRP-linked mutation V268I also disrupts nucleic acid binding, which suggests that this mutation is indeed pathogenic.
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Affiliation(s)
- Sarah E. Mortimer
- Department of Biochemistry, Brandeis University, 415 South St., Waltham MA 02454-9110, U.S.A
| | - Lizbeth Hedstrom
- Department of Biochemistry, Brandeis University, 415 South St., Waltham MA 02454-9110, U.S.A
- To whom correspondence should be addressed (email )
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31
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Zhao Y, Zeng ZX, Kan ZY, Hao YH, Tan Z. The Folding and Unfolding Kinetics of the i-Motif Structure Formed by the C-Rich Strand of Human Telomere DNA. Chembiochem 2005; 6:1957-60. [PMID: 16206324 DOI: 10.1002/cbic.200500175] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yong Zhao
- Laboratory of Biochemistry and Biophysics, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
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32
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Esmaili N, Leroy JL. i-motif solution structure and dynamics of the d(AACCCC) and d(CCCCAA) tetrahymena telomeric repeats. Nucleic Acids Res 2005; 33:213-24. [PMID: 15647504 PMCID: PMC546148 DOI: 10.1093/nar/gki160] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Using NMR methods, we have resolved the i-motif structures formed by d(AACCCC) and by d(CCCCAA), two versions of the DNA sequence repeated in the telomeric regions of the C-rich strand of tetrahymena chromosomes. Both oligonucleotides form fully symmetrical i-motif tetramers built by intercalation of two hemiprotonated duplexes containing four C*C+ pairs. The structures are extremely stable. In the tetramer of d(AACCCC), the outermost C*C+ pairs are formed by the cytidines of the 5' ends of the cytidine tracts. A2 forms an A2*A2 (H6trans-N7) pair stacked to C3*C3+ and cross-strand stacked to A1. At 0 degrees C, the lifetimes of the hemiprotonated pairs range from 1 ms for the outermost pair to approximately 1 h for the innermost pairs. The tetramer of d(CCCCAA) adopts two distinct intercalation topologies in slow conformational exchange. One, whose outermost C*C+ pairs are built by the cytidines of the 5' end and the other by those of the 3' end. In both topologies, the adenosine bases are fairly well stacked to the adjacent C*C+ pairs. They are not paired but form symmetrical pseudo-pairs with their H6cis amino proton and N1 nitrogen pointing towards each other.
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Affiliation(s)
| | - Jean Louis Leroy
- To whom correspondence should be addressed. Tel: +33 169 823630; Fax: +33 169 823784;
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33
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McLean JE, Hamaguchi N, Belenky P, Mortimer SE, Stanton M, Hedstrom L. Inosine 5'-monophosphate dehydrogenase binds nucleic acids in vitro and in vivo. Biochem J 2004; 379:243-51. [PMID: 14766016 PMCID: PMC1224093 DOI: 10.1042/bj20031585] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2003] [Accepted: 02/06/2004] [Indexed: 11/17/2022]
Abstract
Inosine 5'-monophosphate dehydrogenase (IMPDH) is the rate-limiting enzyme in the de novo biosynthesis of guanine nucleotides. In addition to the catalytic domain, IMPDH contains a subdomain of unknown function composed of two cystathione beta-synthase domains. Our results, using three different assays, show that IMPDHs from Tritrichomonas foetus, Escherichia coli, and both human isoforms bind single-stranded nucleic acids with nanomolar affinity via the subdomain. Approx. 100 nucleotides are bound per IMPDH tetramer. Deletion of the subdomain decreases affinity 10-fold and decreases site size to 60 nucleotides, whereas substitution of conserved Arg/Lys residues in the subdomain with Glu decreases affinity by 20-fold. IMPDH is found in the nucleus of human cells, as might be expected for a nucleic-acid-binding protein. Lastly, immunoprecipitation experiments show that IMPDH binds both RNA and DNA in vivo. These experiments indicate that IMPDH has a previously unappreciated role in replication, transcription or translation that is mediated by the subdomain.
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Affiliation(s)
- Jeremy E McLean
- Program in Biophysics and Structural Biology, Brandeis University, MS 009, 415 South St., Waltham, MA 02454, USA
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Abstract
The i-motif is a four-stranded structure built by intercalation in head-to-tail orientation of two parallel duplexes associated by hemi-protonated C.C(+) pairs. Using NMR methods, we investigated the structure, the base-pair opening kinetics and the internal motions of three i-motif tetramers: [d(5mCCTCnTCC)](4) (n=1, 2, 3). These tetramers cannot accommodate the intercalation of two T.T pairs in face-to-face orientation. They are built by intercalation of two symmetrical duplexes whose contacting T3/TM thymidine bases (M=5, 6, 7) are either base-paired or unstacked. The arrangement of the unstacked/paired thymidine bases of the two T/T groups results in the formation of two different conformations. One, fully symmetric, whose thymidine bases T3 and TM are unstacked and base-paired respectively. The other is the asymmetric assembly of two duplexes: one where both thymidine bases are unstacked and the other with two T.T pairs. The proportion of the symmetric conformer increases from a value beyond the detection threshold for n=1, to 19% for n=2 and up to more than 95% for n=3. The exchange cross-peaks connecting together the intercalated duplexes of [d(5mCCTCTCC)](4) and [d(5mCCTCCTCC)](4) reveal a structural interconversion induced by the simultaneous opening/closing of the contacting T3/TM thymidine bases. In [d(5mCCTCCTCC)](4) the motion of the T3/T6 groups triggers the interconversion of the symmetric and asymmetric conformations. In [d(5mCCTCTCC)](4) the intercalated duplexes exchange their structures in an apparently concerted motion, suggesting the simultaneous opening/closing of two distant T3/T5* and T5/T3* switching groups. The spectrum of [d(5mCCTCCCTCC)](4) is fully symmetric and, for this reason, its spectrum gives no indication for duplex interconversion. Nevertheless, the imino proton exchange kinetics argues for a switching motion of the T3/T7 group. Duplex interconversion is not detectable in that case, due to the tetramer symmetry. The origin of the structural conflict hindering the intercalation of two T.T pairs into the i-motif is discussed.
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Affiliation(s)
- Jean Louis Leroy
- Laboratoire de RMN à Haut Champ, Centre National de la Recherche Scientifique, Institut de Chimie des Substances Naturelles, Ave de la Terrasse Bat 27, 91198 Gif-sur-Yvette, France
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Current Awareness on Yeast. Yeast 2003. [DOI: 10.1002/yea.940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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