1
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Bandyopadhyay K, Verma A, Pandey A, Walia R, Saha S. The crucial role of stability of intercalating agent for DNA binding studies in DMSO/water system. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 315:124265. [PMID: 38626674 DOI: 10.1016/j.saa.2024.124265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/02/2024] [Accepted: 04/06/2024] [Indexed: 04/18/2024]
Abstract
In recent years, extensive research has been directed towards understanding the interactions between various zinc complexes with DNA, specifically delving into their intercalation and binding behaviors. The binding of zinc complexes to DNA is particularly intriguing due to their distinctive intercalating capabilities. This study unveils a remarkable phenomenon observed with a specific Zn complex, ([B-Zn-N3], where B is a Schiff base ligand), during DNA intercalation investigations in the popular DMSO-Water binary solvent mixture. An unanticipated observation revealed time-dependent changes in the UV-visible absorption spectroscopic studies, coupled with the existence of an isosbestic point. This observation questions the stability of the intercalating agent itself during the intercalation process. The emergence of a decomposed product during the intercalation study has been confirmed through various analytical techniques, including CHN analysis, MALDI mass, XPS, Raman spectroscopy, and Powder XRD. The change in the chemical species on intercalation is further substantiated by theoretical studies, adding depth to our understanding of the intricate dynamics at play during DNA intercalation with the [B-Zn-N3] complex in the DMSO-Water system.
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Affiliation(s)
- Krishanu Bandyopadhyay
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Abhineet Verma
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Ankita Pandey
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Rajat Walia
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR
| | - Satyen Saha
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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2
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Mori K, Takezawa Y, Shionoya M. Metal-dependent base pairing of bifacial iminodiacetic acid-modified uracil bases for switching DNA hybridization partner. Chem Sci 2023; 14:1082-1088. [PMID: 36756334 PMCID: PMC9891364 DOI: 10.1039/d2sc06534g] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023] Open
Abstract
Dynamic control of DNA assembly by external stimuli has received increasing attention in recent years. Dynamic ligand exchange in metal complexes can be a central element in the structural and functional transformation of DNA assemblies. In this study, N,N-dicarboxymethyl-5-aminouracil (dcaU) nucleoside with an iminodiacetic acid (IDA) ligand at the 5-position of the uracil base has been developed as a bifacial nucleoside that can form both hydrogen-bonded and metal-mediated base pairs. Metal complexation study of dcaU nucleosides revealed their ability to form a 2:1 complex with a GdIII ion at the monomeric level. The characteristics of base pairing of dcaU nucleosides were then examined inside DNA duplexes. The results revealed that the formation of the metal-mediated dcaU-GdIII-dcaU pair significantly stabilized the DNA duplex containing one dcaU-dcaU mismatch (ΔT m = +16.1 °C). In contrast, a duplex containing a hydrogen-bonded dcaU-A pair was destabilized in the presence of GdIII (ΔT m = -3.5 °C). The GdIII-dependent base pairing of dcaU bases was applied to control the hybridization preference of DNA in response to metal ions. The hybridization partner of a dcaU-containing strand was reversibly exchanged by the addition and removal of GdIII ions. Since the incorporation of a single dcaU base can switch the hybridization behavior of DNA, the bifacial dcaU base would be a versatile building block for imparting metal responsiveness to DNA assemblies, allowing the rational design of dynamic DNA systems.
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Affiliation(s)
- Keita Mori
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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3
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Cao Y, Li W, Pei R. Exploring the catalytic mechanism of multivalent G-quadruplex/hemin DNAzymes by modulating the position and spatial orientation of connected G-quadruplexes. Anal Chim Acta 2022; 1221:340105. [DOI: 10.1016/j.aca.2022.340105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/06/2022] [Accepted: 06/18/2022] [Indexed: 11/15/2022]
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4
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Metal Ion-Directed Specific DNA Structures and Their Functions. Life (Basel) 2022; 12:life12050686. [PMID: 35629354 PMCID: PMC9145678 DOI: 10.3390/life12050686] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 11/17/2022] Open
Abstract
Various DNA structures, including specific metal ion complexes, have been designed based on the knowledge of canonical base pairing as well as general coordination chemistry. The role of metal ions in these studies is quite broad and diverse. Metal ions can be targets themselves in analytical applications, essential building blocks of certain DNA structures that one wishes to construct, or they can be responsible for signal generation, such as luminescence or redox. Using DNA conjugates with metal chelators, one can more freely design DNA complexes with diverse structures and functions by following the simple HSAB rule. In this short review, the authors summarize a part of their DNA chemistries involving specific metal ion coordination. It consists of three topics: (1) significant stabilization of DNA triple helix by silver ion; (2) metal ion-directed dynamic sequence edition through global conformational change by intramolecular complexation; and (3) reconstruction of luminescent lanthanide complexes on DNA and their analytical applications.
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5
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Sultana N, Kawahara T, Kuwahara Y, Ihara H, Takafuji M. Supramolecular assembly of glutamide attached terpyridine-lanthanide complex with enhanced chirality and high fluorescence quantum yield. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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6
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Wang L, Song B, Li Y, Gong L, Jiang X, Wang M, Lu S, Hao XQ, Xia Z, Zhang Y, Hla SW, Li X. Self-Assembly of Metallo-Supramolecules under Kinetic or Thermodynamic Control: Characterization of Positional Isomers Using Scanning Tunneling Spectroscopy. J Am Chem Soc 2020; 142:9809-9817. [PMID: 32311259 PMCID: PMC7375329 DOI: 10.1021/jacs.0c03459] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Coordination-driven self-assembly has been extensively employed to construct a variety of discrete structures as a bottom-up strategy. However, mechanistic understanding regarding whether self-assembly is under kinetic or thermodynamic control is less explored. To date, such mechanistic investigation has been limited to distinct, assembled structures. It still remains a formidable challenge to study the kinetic and thermodynamic behavior of self-assembly systems with multiple assembled isomers due to the lack of characterization methods. Herein, we use a stepwise strategy which combined self-recognition and self-assembly processes to construct giant metallo-supramolecules with 8 positional isomers in solution. With the help of ultrahigh-vacuum, low-temperature scanning tunneling microscopy and scanning tunneling spectroscopy, we were able to unambiguously differentiate 14 isomers on the substrate which correspond to 8 isomers in solution. Through measurement of 162 structures, the experimental probability of each isomer was obtained and compared with the theoretical probability. Such a comparison along with density functional theory (DFT) calculation suggested that although both kinetic and thermodynamic control existed in this self-assembly, the increased experimental probabilities of isomers compared to theoretical probabilities should be attributed to thermodynamic control.
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Affiliation(s)
- Lei Wang
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Bo Song
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Yiming Li
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Lele Gong
- Department of Materials Science and Engineering, University of North Texas, Denton, Texas 76203, United States
| | - Xin Jiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, Jilin 130012, China
| | - Ming Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, Jilin 130012, China
| | - Shuai Lu
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
- College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xin-Qi Hao
- College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Zhenhai Xia
- Department of Materials Science and Engineering, University of North Texas, Denton, Texas 76203, United States
| | - Yuan Zhang
- Nanoscience and Technology Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
- Department of Physics, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Saw Wai Hla
- Nanoscience and Technology Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Xiaopeng Li
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
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7
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Takafuji M, Kawahara T, Sultana N, Ryu N, Yoshida K, Kuwahara Y, Oda R, Ihara H. Extreme enhancement of secondary chirality through coordination-driven steric changes of terpyridyl ligand in glutamide-based molecular gels. RSC Adv 2020; 10:29627-29632. [PMID: 35518247 PMCID: PMC9056163 DOI: 10.1039/d0ra05057a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/03/2020] [Indexed: 01/01/2023] Open
Abstract
Aggregation-induced chirality is potentially useful in sensor technology applications. Herein we show extreme enhancement of secondary chirality through coordination-driven steric changes of terpyridyl ligand in molecular gels. The secondary chirality reflecting on enhancement of chiral signals (i.e., circular dichroism (CD) and circularly polarised luminescence (CPL)) of the molecular gels formed from glutamide-attached terpyridine (G-tpy) is extremely enhanced by the coordination of its terpyridyl groups to metal ions such as Cu2+, Zn2+ and Ru2+, which is due to dramatic changes in the stacked structure of the chromophore groups through the formation of metal ion complex. Metal-free terpyridine exists in a non-planar geometry, which suppress π–π stacking interactions among aggregates. The planarity of the terpyridyl group is improved through metal-ion complexation, which induces the metal-ion-coordinated terpyridyl groups to stack. The thermal stabilities of the CD signals are strongly affected by the metal-ion species. CPL signal is generated in the molecular gel formed from G-tpy–Zn2+ complex accompanied by chelation-enhanced fluorescence. It is expected that large and sensitive coordination-driven secondary chirality signals (CD and CPL) are useful for sensing guest molecules and the surrounding environment. Dramatic changes of secondary chirality reflecting on enhancement of chiral signals (i.e., CD and CPL) is induced through coordination-derived steric changes of terpyridyl ligand attached on glutamide-based molecular gels.![]()
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Affiliation(s)
- Makoto Takafuji
- Department of Applied Chemistry and Biochemistry
- Kumamoto University
- Kumamoto 860-8555
- Japan
| | - Tomoki Kawahara
- Department of Applied Chemistry and Biochemistry
- Kumamoto University
- Kumamoto 860-8555
- Japan
| | - Nahid Sultana
- Department of Applied Chemistry and Biochemistry
- Kumamoto University
- Kumamoto 860-8555
- Japan
| | - Naoya Ryu
- Materials Development Department
- Kumamoto Industrial Research Institute
- Kumamoto 862-0901
- Japan
| | - Kyohei Yoshida
- Institut de Chimie & Biologie des Membranes & des Nano-objets (UMR5248 CBMN)
- CNRS
- Université de Bordeaux
- Institut Polytechnique Bordeaux
- 33607 Pessac
| | - Yutaka Kuwahara
- Department of Applied Chemistry and Biochemistry
- Kumamoto University
- Kumamoto 860-8555
- Japan
| | - Reiko Oda
- Institut de Chimie & Biologie des Membranes & des Nano-objets (UMR5248 CBMN)
- CNRS
- Université de Bordeaux
- Institut Polytechnique Bordeaux
- 33607 Pessac
| | - Hirotaka Ihara
- Department of Applied Chemistry and Biochemistry
- Kumamoto University
- Kumamoto 860-8555
- Japan
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8
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Takezawa Y, Nakama T, Shionoya M. Enzymatic Synthesis of Cu(II)-Responsive Deoxyribozymes through Polymerase Incorporation of Artificial Ligand-Type Nucleotides. J Am Chem Soc 2019; 141:19342-19350. [PMID: 31731834 DOI: 10.1021/jacs.9b08955] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metal-mediated artificial base pairs, consisting of ligand-type nucleotides and a bridging metal ion, have shown promise as functional units to develop stimuli-responsive DNA materials. Although a variety of metal-mediated base pairs have been constructed with artificial ligand-type nucleotides and various metal ions, the application of such metal-mediated base pairs has been relatively poorly explored mainly due to the cumbersome chemical synthesis of artificial DNA strands. Herein we report a facile enzymatic method to synthesize DNA strands containing a ligand-type hydroxypyridone (H) nucleotide, which forms a CuII-mediated base pair (H-CuII-H). A two-step primer extension reaction using two commercially available polymerases enabled the incorporation of a H nucleotide at an internal position of oligonucleotides. The polymerase synthesis was subsequently applied to the development of metal-responsive deoxyribozymes (DNAzymes), whose catalytic activity was regulated by the formation of a single H-CuII-H base pair in its stem region. The DNAzyme activity was reversibly switched by the alternate addition and the removal of CuII ions. Furthermore, metal-dependent orthogonal activation of a CuII-responsive H-DNAzyme and a HgII-responsive T-DNAzyme was experimentally demonstrated by utilizing both H-CuII-H as well as widely explored T-HgII-T base pairs. These results suggest that the incorporation of H-CuII-H base pairs would facilitate the rational design of metal-responsive functional DNAs. Accordingly, the facile enzymatic synthesis of artificial ligand-bearing DNAs developed in this study would significantly expand the toolbox of DNA-based supramolecular chemistry and DNA nanotechnology.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Takahiro Nakama
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
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9
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Kitamura Y, Nagai K, Furuzono T, Katsuda Y, Ihara T. Cooperative recognition of a repetitive sequence through consecutive formation of triplex and duplex structures. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:97-108. [PMID: 31638471 DOI: 10.1080/15257770.2019.1679833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Cooperative recognition of a repetitive sequence was performed with a short single DNA strand consisting of duplex- and triplex-forming regions modified with a ligand (benzoquinoquinoxaline) to stabilize a triplex structure. The former region was complementary with one unit of a repetitive sequence and the latter had a sequence that can bind with a cognate duplex formed by another DNA molecule bound on an adjacent site. The DNA binding to one unit of the repetitive sequence is expected to facilitate the second binding to an adjacent unit through cooperative triplex formation. The cooperativity was confirmed by evaluation of thermal stabilities of the complexes with a series of model repetitive sequences.
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Affiliation(s)
- Yusuke Kitamura
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Koki Nagai
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Tomohiro Furuzono
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Yousuke Katsuda
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Toshihiro Ihara
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
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10
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Singh S, Singh MK, Das P. Visual detection of cyclobutane pyrimidine dimer DNA damage lesions by Hg 2+ and carbon dots. Anal Chim Acta 2018. [PMID: 29534804 DOI: 10.1016/j.aca.2018.02.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cyclobutane pyrimidine dimmers (CPDs) and 6-4-[pyrimidine-2'-one] pyrimidine (6-4 PP) are major UV induced DNA damage lesions formed from solar radiation and other sources. CPD lesions are presumably mutagenic and carcinogenic that inhibit polymerases and interfere in DNA replication. An easy and cost effective way for visual detection of these lesions by using fluorescence based method is shown here. Artificial UVA and UVB lights were used for the generation of CPD and 6-4 PPs in selected DNA samples. Binding of Hg2+ ions with DNA before and after induction of CPD and 6-4 PP lesions was evaluated in the presence of highly fluorescent blue emitting carbon dots (CDs). Induction of CPD and 6-4 PPs in DNA causes distortion of DNA structure which hinders the binding of Hg2+ ions to DNA nucleobases. Quenching of fluorescence intensity of CDs by unbound Hg2+ ions was found to be proportional to the amount of CPD and 6-4 PP lesions induced by UV irradiation of DNA samples that offer a biosensing platform for the sensitive detection of CPD lesions in DNA. The fluorescent quenching was visually detectable using hand held UV light without the intervention of any equipment.
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Affiliation(s)
- Seema Singh
- Department of Chemistry, Indian Institute of Technology Patna, Patna, 801106, Bihar, India
| | - Manoj K Singh
- Atomic and Molecular Physics Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Prolay Das
- Department of Chemistry, Indian Institute of Technology Patna, Patna, 801106, Bihar, India.
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11
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van Veelen HPJ, Falcao Salles J, Tieleman BI. Multi-level comparisons of cloacal, skin, feather and nest-associated microbiota suggest considerable influence of horizontal acquisition on the microbiota assembly of sympatric woodlarks and skylarks. MICROBIOME 2017; 5:156. [PMID: 29191217 PMCID: PMC5709917 DOI: 10.1186/s40168-017-0371-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 11/09/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND Working toward a general framework to understand the role of microbiota in animal biology requires the characterisation of animal-associated microbial communities and identification of the evolutionary and ecological factors shaping their variation. In this study, we described the microbiota in the cloaca, brood patch skin and feathers of two species of birds and the microbial communities in their nest environment. We compared patterns of resemblance between these microbial communities at different levels of biological organisation (species, individual, body part) and investigated the phylogenetic structure to deduce potential microbial community assembly processes. RESULTS Using 16S rRNA gene amplicon data of woodlarks (Lullula arborea) and skylarks (Alauda arvensis), we demonstrated that bird- and nest-associated microbiota showed substantial OTU co-occurrences and shared dominant taxonomic groups, despite variation in OTU richness, diversity and composition. Comparing host species, we uncovered that sympatric woodlarks and skylarks harboured similar microbiota, dominated by Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria. Yet, compared with the nest microbiota that showed little variation, each species' bird-associated microbiota displayed substantial variation. The latter could be partly (~ 20%) explained by significant inter-individual differences. The various communities of the bird's body (cloaca, brood patch skin and feathers) appeared connected with each other and with the nest microbiota (nest lining material and surface soil). Communities were more similar when the contact between niches was frequent or intense. Finally, bird microbiota showed significant phylogenetic clustering at the tips, but not at deeper branches of the phylogeny. CONCLUSIONS Our interspecific comparison suggested that the environment is more important than phylogeny in shaping the bird-associated microbiotas. In addition, variation among individuals and among body parts suggested that intrinsic or behavioural differences among females and spatial heterogeneity among territories contributed to the microbiome variation of larks. Modest but significant phylogenetic clustering of cloacal, skin and feather microbiotas suggested weak habitat filtering in these niches. We propose that lark microbiota may be primarily, but not exclusively, shaped by horizontal acquisition from the regional bacterial pool at the breeding site. More generally, we hypothesise that the extent of ecological niche-sharing by avian (or other vertebrate) hosts may predict the convergence of their microbiota.
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Affiliation(s)
- H Pieter J van Veelen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. box 11103, 9700 CC, Groningen, The Netherlands.
| | - Joana Falcao Salles
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. box 11103, 9700 CC, Groningen, The Netherlands
| | - B Irene Tieleman
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. box 11103, 9700 CC, Groningen, The Netherlands
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12
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DNA incorporation of a trans-chelating bis-pyridyl ligand for square-planar coordinated metal cations. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Li W, Li Y, Liu Z, Lin B, Yi H, Xu F, Nie Z, Yao S. Insight into G-quadruplex-hemin DNAzyme/RNAzyme: adjacent adenine as the intramolecular species for remarkable enhancement of enzymatic activity. Nucleic Acids Res 2016; 44:7373-84. [PMID: 27422869 PMCID: PMC5009756 DOI: 10.1093/nar/gkw634] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/29/2016] [Indexed: 01/15/2023] Open
Abstract
G-quadruplex (G4) with stacked G-tetrads structure is able to bind hemin (iron (III)-protoporphyrin IX) to form a unique type of DNAzyme/RNAzyme with peroxidase-mimicking activity, which has been widely employed in multidisciplinary fields. However, its further applications are hampered by its relatively weak activity compared with protein enzymes. Herein, we report a unique intramolecular enhancement effect of the adjacent adenine (EnEAA) at 3' end of G4 core sequences that significantly improves the activity of G4 DNAzymes. Through detailed investigations of the EnEAA, the added 3' adenine was proved to accelerate the compound I formation in catalytic cycle and thus improve the G4 DNAzyme activity. EnEAA was found to be highly dependent on the unprotonated state of the N1 of adenine, substantiating that adenine might function as a general acid-base catalyst. Further adenine analogs analysis supported that both N1 and exocyclic 6-amino groups in adenine played key role in the catalysis. Moreover, we proved that EnEAA was generally applicable for various parallel G-quadruplex structures and even G4 RNAzyme. Our studies implied that adenine might act analogously as the distal histidine in protein peroxidases, which shed light on the fundamental understanding and rational design of G4 DNAzyme/RNAzyme catalysts with enhanced functions.
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Affiliation(s)
- Wang Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Yong Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Zhuoliang Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Bin Lin
- Department of Medicinal Chemistry, School of Pharmaceutical Engineering & Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China
| | - Haibo Yi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Feng Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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14
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Joo JH, Lee JS. Divalent metal ion-mediated assembly of spherical nucleic acids: the case study of Cu2+. Phys Chem Chem Phys 2015; 17:30292-9. [DOI: 10.1039/c5cp05202e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A new strategy for reversibly assembling spherical nucleic acids (SNAs) is demonstrated based on the coordinative binding of divalent metal ions, particularly Cu2+, to nucleobases.
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Affiliation(s)
- Jang Ho Joo
- Department of Materials Science and Engineering
- Korea University
- Seoul
- 02841 Republic of Korea
| | - Jae-Seung Lee
- Department of Materials Science and Engineering
- Korea University
- Seoul
- 02841 Republic of Korea
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