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Dekker JG, Klaver B, Berkhout B, Das AT. HIV-1 3'-Polypurine Tract Mutations Confer Dolutegravir Resistance by Switching to an Integration-Independent Replication Mechanism via 1-LTR Circles. J Virol 2023; 97:e0036123. [PMID: 37125907 PMCID: PMC10231180 DOI: 10.1128/jvi.00361-23] [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: 03/07/2023] [Accepted: 04/07/2023] [Indexed: 05/02/2023] Open
Abstract
Several recent studies indicate that mutations in the human immunodeficiency virus type 1 (HIV-1) 3'polypurine tract (3'PPT) motif can reduce sensitivity to the integrase inhibitor dolutegravir (DTG). Using an in vivo systematic evolution of ligands by exponential enrichment (SELEX) approach, we discovered that multiple different mutations in this viral RNA element can confer DTG resistance, suggesting that the inactivation of this critical reverse transcription element causes resistance. An analysis of the viral DNA products formed upon infection by these 3'PPT mutants revealed that they replicate without integration into the host cell genome, concomitant with an increased production of 1-LTR circles. As the replication of these virus variants is activated by the human T-lymphotropic virus 1 (HTLV-1) Tax protein, a factor that reverses epigenetic silencing of episomal HIV DNA, these data indicate that the 3'PPT-mutated viruses escape from the integrase inhibitor DTG by switching to an integration-independent replication mechanism. IMPORTANCE The integrase inhibitor DTG is a potent inhibitor of HIV replication and is currently recommended in drug regimens for people living with HIV. Whereas HIV normally escapes from antiviral drugs by the acquisition of specific mutations in the gene that encodes the targeted enzyme, mutational inactivation of the viral 3'PPT sequence, an RNA element that has a crucial role in the viral reverse transcription process, was found to allow HIV replication in the presence of DTG in cell culture experiments. While the integration of the viral DNA into the cellular genome is considered one of the hallmarks of retroviruses, including HIV, 3'PPT inactivation caused integration-independent replication, which can explain the reduced DTG sensitivity. Whether this exotic escape route can also contribute to viral escape in HIV-infected persons remains to be determined, but our results indicate that screening for 3'PPT mutations in patients that fail on DTG therapy should be considered.
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Affiliation(s)
- José G. Dekker
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Bep Klaver
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Ben Berkhout
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Atze T. Das
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
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2
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Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Gorb LG. Genome sequence analysis suggests coevolution of the DIS, SD, and Psi hairpins in HIV-1 genomes. Virus Res 2022; 321:198910. [PMID: 36070810 DOI: 10.1016/j.virusres.2022.198910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 12/24/2022]
Abstract
HIV-1 RNA dimerization is a critical step in viral life cycle. It is a prerequisite for genome packaging and plays an important role in reverse transcription and recombination. Dimerization is promoted by the DIS (dimerization initiation site) hairpin located in the 5' leader of HIV-1 genome. Despite the high genetic diversity in HIV-1 group M, only five apical loops (AAGCGCGCA, AAGUGCGCA, AAGUGCACA, AGGUGCACA and AGUGCAC) are commonly found in DIS hairpins. We refer to the parent DISes with these apical loops as DISLai, DISTrans, DISF, DISMal, and DISC, respectively. Based on identity or similarity of DIS hairpins to parent DISes, we distributed HIV-1 M genomes into five dimerization groups. Comparison of the primary and secondary structures of DIS, SD and Psi hairpins in about 3000 HIV-1 M genomes showed that the mutation frequencies at particular nucleotide positions of these hairpins differ among the dimerization groups, and DISF may be an origin of other parent DISes. We found that DIS, SD and Psi hairpins have hundreds of variants, only some of them occurring rather frequently. The lower part of DIS hairpin with G x AGG internal loop is highly conserved in both HIV-1 and SIV genomes. We supposed that the G-quadruplex, located 56 nts downstream of the Gag start codon, may participate in switching of HIV-1 leader RNA from BMH (branched multiple hairpins) to LDI (long distance interaction) conformation.
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Affiliation(s)
- Margarita I Zarudnaya
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine
| | - Andriy L Potyahaylo
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine
| | - Iryna M Kolomiets
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine
| | - Leonid G Gorb
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine.
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3
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Satish S, Dey A, Tharmavaram M, Khatri N, Rawtani D. Risk assessment of selected pharmaceuticals on wildlife with nanomaterials based aptasensors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 836:155622. [PMID: 35508236 DOI: 10.1016/j.scitotenv.2022.155622] [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: 03/04/2022] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/14/2023]
Abstract
Pharmaceuticals have improved human and veterinary health tremendously over the years. But the implications of the presence of pharmaceuticals in the environment on terrestrial, avian, and aquatic organisms are still not fully comprehended. The bioaccumulation and biomagnifications of these chemicals through the food chain have long-term effects on the wildlife. The detection and quantification of such pharmaceutical residues in the environment is a tedious process and quicker methods are needed. Aptasensors are one such quick and reliable method for the identification of pharmaceutical residues in the wildlife. Aptasensors are a class of biosensors that work on the principles of biological recognition of elements. The aptamers are unique biological recognition elements with high specificity and affinity to various targets. Their efficiency makes them a very promising candidate for such sensitive research. In this review, the pharmaceutical threats to wildlife and their detection techniques using aptasensors have been discussed.
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Affiliation(s)
- Swathi Satish
- School of Pharmacy, National Forensic Sciences University, Sector 9, Near Police Bhawan, Gandhinagar, Gujarat, India
| | - Aayush Dey
- School of Doctoral Studies & Research (SDSR), National Forensic Sciences University, Sector 9, Near Police Bhawan, Gandhinagar, Gujarat, India
| | - Maithri Tharmavaram
- School of Pharmacy, National Forensic Sciences University, Sector 9, Near Police Bhawan, Gandhinagar, Gujarat, India
| | - Nitasha Khatri
- Gujarat Environment Management Institute, Department of Forest and Environment, Sector 10B, Jivraj Mehta Bhavan, Gandhinagar, Gujarat, India
| | - Deepak Rawtani
- School of Pharmacy, National Forensic Sciences University, Sector 9, Near Police Bhawan, Gandhinagar, Gujarat, India.
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4
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Xu Y, Jiang X, Zhou Y, Ma M, Wang M, Ying B. Systematic Evolution of Ligands by Exponential Enrichment Technologies and Aptamer-Based Applications: Recent Progress and Challenges in Precision Medicine of Infectious Diseases. Front Bioeng Biotechnol 2021; 9:704077. [PMID: 34447741 PMCID: PMC8383106 DOI: 10.3389/fbioe.2021.704077] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/26/2021] [Indexed: 02/05/2023] Open
Abstract
Infectious diseases are considered as a pressing challenge to global public health. Accurate and rapid diagnostics tools for early recognition of the pathogen, as well as individualized precision therapy are essential for controlling the spread of infectious diseases. Aptamers, which were screened by systematic evolution of ligands by exponential enrichment (SELEX), can bind to targets with high affinity and specificity so that have exciting potential in both diagnosis and treatment of infectious diseases. In this review, we provide a comprehensive overview of the latest development of SELEX technology and focus on the applications of aptamer-based technologies in infectious diseases, such as targeted drug-delivery, treatments and biosensors for diagnosing. The challenges and the future development in this field of clinical application will also be discussed.
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Affiliation(s)
- Yixin Xu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Xin Jiang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yanhong Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Ming Ma
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,The First People's Hospital of Shuangliu District, Chengdu/West China (Airport)Hospital Sichuan University, Chengdu, China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
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5
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Odeh F, Nsairat H, Alshaer W, Ismail MA, Esawi E, Qaqish B, Bawab AA, Ismail SI. Aptamers Chemistry: Chemical Modifications and Conjugation Strategies. Molecules 2019; 25:E3. [PMID: 31861277 PMCID: PMC6982925 DOI: 10.3390/molecules25010003] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/14/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022] Open
Abstract
Soon after they were first described in 1990, aptamers were largely recognized as a new class of biological ligands that can rival antibodies in various analytical, diagnostic, and therapeutic applications. Aptamers are short single-stranded RNA or DNA oligonucleotides capable of folding into complex 3D structures, enabling them to bind to a large variety of targets ranging from small ions to an entire organism. Their high binding specificity and affinity make them comparable to antibodies, but they are superior regarding a longer shelf life, simple production and chemical modification, in addition to low toxicity and immunogenicity. In the past three decades, aptamers have been used in a plethora of therapeutics and drug delivery systems that involve innovative delivery mechanisms and carrying various types of drug cargos. However, the successful translation of aptamer research from bench to bedside has been challenged by several limitations that slow down the realization of promising aptamer applications as therapeutics at the clinical level. The main limitations include the susceptibility to degradation by nucleases, fast renal clearance, low thermal stability, and the limited functional group diversity. The solution to overcome such limitations lies in the chemistry of aptamers. The current review will focus on the recent arts of aptamer chemistry that have been evolved to refine the pharmacological properties of aptamers. Moreover, this review will analyze the advantages and disadvantages of such chemical modifications and how they impact the pharmacological properties of aptamers. Finally, this review will summarize the conjugation strategies of aptamers to nanocarriers for developing targeted drug delivery systems.
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Affiliation(s)
- Fadwa Odeh
- Faculty of Science, The University of Jordan, Amman 11942, Jordan; (F.O.); (H.N.); (A.A.B.)
- Hamdi Mango Center for Scientific Research, The University of Jordan, Amman 11942, Jordan
| | - Hamdi Nsairat
- Faculty of Science, The University of Jordan, Amman 11942, Jordan; (F.O.); (H.N.); (A.A.B.)
| | - Walhan Alshaer
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan
| | - Mohammad A. Ismail
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
| | - Ezaldeen Esawi
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
| | - Baraa Qaqish
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
| | - Abeer Al Bawab
- Faculty of Science, The University of Jordan, Amman 11942, Jordan; (F.O.); (H.N.); (A.A.B.)
- Hamdi Mango Center for Scientific Research, The University of Jordan, Amman 11942, Jordan
| | - Said I. Ismail
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
- Qatar Genome Project, Qatar Foundation, Doha 5825, Qatar
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Kumar S, Jain S, Dilbaghi N, Ahluwalia AS, Hassan AA, Kim KH. Advanced Selection Methodologies for DNAzymes in Sensing and Healthcare Applications. Trends Biochem Sci 2018; 44:190-213. [PMID: 30559045 DOI: 10.1016/j.tibs.2018.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 02/07/2023]
Abstract
DNAzymes have been widely explored owing to their excellent catalytic activity in a broad range of applications, notably in sensing and biomedical devices. These newly discovered applications have built high hopes for designing novel catalytic DNAzymes. However, the selection of efficient DNAzymes is a challenging process but one that is of crucial importance. Initially, systemic evolution of ligands by exponential enrichment (SELEX) was a labor-intensive and time-consuming process, but recent advances have accelerated the automated generation of DNAzyme molecules. This review summarizes recent advances in SELEX that improve the affinity and specificity of DNAzymes. The thriving generation of new DNAzymes is expected to open the door to several healthcare applications. Therefore, a significant portion of this review is dedicated to various biological applications of DNAzymes, such as sensing, therapeutics, and nanodevices. In addition, discussion is further extended to the barriers encountered for the real-life application of these DNAzymes to provide a foundation for future research.
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Affiliation(s)
- Sandeep Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India; Department of Civil Engineering, College of Engineering, University of Nebraska at Lincoln, PO Box 886105, Lincoln, NE 68588-6105, USA.
| | - Shikha Jain
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India
| | - Neeraj Dilbaghi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India
| | | | - Ashraf Aly Hassan
- Department of Civil Engineering, College of Engineering, University of Nebraska at Lincoln, PO Box 886105, Lincoln, NE 68588-6105, USA
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, Republic of Korea.
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7
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Bayat P, Nosrati R, Alibolandi M, Rafatpanah H, Abnous K, Khedri M, Ramezani M. SELEX methods on the road to protein targeting with nucleic acid aptamers. Biochimie 2018; 154:132-155. [PMID: 30193856 DOI: 10.1016/j.biochi.2018.09.001] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/02/2018] [Indexed: 12/14/2022]
Abstract
Systematic evolution of ligand by exponential enrichment (SELEX) is an efficient method used to isolate high-affinity single stranded oligonucleotides from a large random sequence pool. These SELEX-derived oligonucleotides named aptamer, can be selected against a broad spectrum of target molecules including proteins, cells, microorganisms and chemical compounds. Like antibodies, aptamers have a great potential in interacting with and binding to their targets through structural recognition and are therefore called "chemical antibodies". However, aptamers offer advantages over antibodies including smaller size, better tissue penetration, higher thermal stability, lower immunogenicity, easier production, lower cost of synthesis and facilitated conjugation or modification with different functional moieties. Thus, aptamers represent an attractive substitution for protein antibodies in the fields of biomarker discovery, diagnosis, imaging and targeted therapy. Enormous interest in aptamer technology triggered the development of SELEX that has underwent numerous modifications since its introduction in 1990. This review will discuss the recent advances in SELEX methods and their advantages and limitations. Aptamer applications are also briefly outlined in this review.
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Affiliation(s)
- Payam Bayat
- Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rahim Nosrati
- Cellular and Molecular Research Center, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Houshang Rafatpanah
- Inflammation and Inflammatory Diseases Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mostafa Khedri
- Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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8
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Bayne CF, Widawski ME, Gao F, Masab MH, Chattopadhyay M, Murawski AM, Sansevere RM, Lerner BD, Castillo RJ, Griesman T, Fu J, Hibben JK, Garcia-Perez AD, Simon AE, Kushner DB. SELEX and SHAPE reveal that sequence motifs and an extended hairpin in the 5' portion of Turnip crinkle virus satellite RNA C mediate fitness in plants. Virology 2018; 520:137-152. [PMID: 29864677 DOI: 10.1016/j.virol.2018.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/06/2018] [Accepted: 05/12/2018] [Indexed: 11/19/2022]
Abstract
Noncoding RNAs use their sequence and/or structure to mediate function(s). The 5' portion (166 nt) of the 356-nt noncoding satellite RNA C (satC) of Turnip crinkle virus (TCV) was previously modeled to contain a central region with two stem-loops (H6 and H7) and a large connecting hairpin (H2). We now report that in vivo functional selection (SELEX) experiments assessing sequence/structure requirements in H2, H6, and H7 reveal that H6 loop sequence motifs were recovered at nonrandom rates and only some residues are proposed to base-pair with accessible complementary sequences within the 5' central region. In vitro SHAPE of SELEX winners indicates that the central region is heavily base-paired, such that along with the lower stem and H2 region, one extensive hairpin exists composing the entire 5' region. As these SELEX winners are highly fit, these characteristics facilitate satRNA amplification in association with TCV in plants.
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Affiliation(s)
- Charlie F Bayne
- Department of Biology, Dickinson College, Carlisle, PA 17013, USA
| | - Max E Widawski
- Department of Biology, Dickinson College, Carlisle, PA 17013, USA
| | - Feng Gao
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Mohammed H Masab
- Department of Biology, Dickinson College, Carlisle, PA 17013, USA
| | - Maitreyi Chattopadhyay
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | | | | | - Bryan D Lerner
- Department of Biology, Dickinson College, Carlisle, PA 17013, USA
| | | | - Trevor Griesman
- Department of Biology, Dickinson College, Carlisle, PA 17013, USA
| | - Jiantao Fu
- Department of Biology, Dickinson College, Carlisle, PA 17013, USA
| | | | | | - Anne E Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - David B Kushner
- Department of Biology, Dickinson College, Carlisle, PA 17013, USA.
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Klaver B, van der Velden Y, van Hemert F, van der Kuyl AC, Berkhout B. HIV-1 tolerates changes in A-count in a small segment of the pol gene. Retrovirology 2017; 14:43. [PMID: 28870251 PMCID: PMC5583962 DOI: 10.1186/s12977-017-0367-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 08/30/2017] [Indexed: 11/21/2022] Open
Abstract
Background The HIV-1 RNA genome has a biased nucleotide composition with a surplus of As. Several hypotheses have been put forward to explain this striking phenomenon, but the A-count of the HIV-1 genome has thus far not been systematically manipulated. The reason for this reservation is the likelihood that known and unknown sequence motifs will be affected by such a massive mutational approach, thus resulting in replication-impaired virus mutants. We present the first attempt to increase and decrease the A-count in a relatively small polymerase (pol) gene segment of HIV-1 RNA. Results To minimize the mutational impact, a new mutational approach was developed that is inspired by natural sequence variation as present in HIV-1 isolates. This phylogeny-instructed mutagenesis allowed us to create replication-competent HIV-1 mutants with a significantly increased or decreased local A-count. The local A-count of the wild-type (wt) virus (40.2%) was further increased to 46.9% or reduced to 31.7 and 26.3%. These HIV-1 variants replicate efficiently in vitro, despite the fact that the pol changes cause a quite profound move in HIV–SIV sequence space. Conclusions Extrapolating these results to the complete 9 kb RNA genome, we may cautiously suggest that the A-rich signature does not have to be maintained. This survey also provided clues that silent codon changes, in particular from G-to-A, determine the subtype-specific sequence signatures.
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Affiliation(s)
- Bep Klaver
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Yme van der Velden
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Formijn van Hemert
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
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10
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A Phylogenetic Survey on the Structure of the HIV-1 Leader RNA Domain That Encodes the Splice Donor Signal. Viruses 2016; 8:v8070200. [PMID: 27455303 PMCID: PMC4974535 DOI: 10.3390/v8070200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/29/2016] [Accepted: 07/01/2016] [Indexed: 11/16/2022] Open
Abstract
RNA splicing is a critical step in the human immunodeficiency virus type 1 (HIV-1) replication cycle because it controls the expression of the complex viral proteome. The major 5′ splice site (5′ss) that is positioned in the untranslated leader of the HIV-1 RNA transcript is of particular interest because it is used for the production of the more than 40 differentially spliced subgenomic mRNAs. HIV-1 splicing needs to be balanced tightly to ensure the proper levels of all viral proteins, including the Gag-Pol proteins that are translated from the unspliced RNA. We previously presented evidence that the major 5′ss is regulated by a repressive local RNA structure, the splice donor (SD) hairpin, that masks the 11 nucleotides (nts) of the 5′ss signal for recognition by U1 small nuclear RNA (snRNA) of the spliceosome machinery. A strikingly different multiple-hairpin RNA conformation was recently proposed for this part of the HIV-1 leader RNA. We therefore inspected the sequence of natural HIV-1 isolates in search for support, in the form of base pair (bp) co-variations, for the different RNA conformations.
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11
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van Bel N, Ghabri A, Das AT, Berkhout B. The HIV-1 leader RNA is exquisitely sensitive to structural changes. Virology 2015; 483:236-52. [DOI: 10.1016/j.virol.2015.03.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 03/05/2015] [Accepted: 03/27/2015] [Indexed: 01/14/2023]
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12
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Xu Z, Wu J, Feng F, Zhang X, Ma X, Tang M, Huang Y, Zhang Y, Cao Y, Cao W, He R, Gao Y, Liu Q. Isolation of novel sequences targeting highly variable viral protein hemagglutinin. MethodsX 2015; 2:64-71. [PMID: 26150973 PMCID: PMC4487337 DOI: 10.1016/j.mex.2015.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Accepted: 02/12/2015] [Indexed: 11/19/2022] Open
Abstract
Rapid evolution is a hallmark of the viral kingdom and a major concern for developing universal vaccines. The isolation of substantial numbers of viral sequence variants at highly variable viral protein domains remains a major challenge. We previously developed a combinatorial method for the isolation of novel sequences to cope with rapid viral variations at the G-H loop of Foot and Mouth Disease virus VP1 protein [1]. Here we present a modification of that method in its application in the randomization of the hemagglutinin gene from a H5N2 virus, namely: removal of potentially stressful region which harbored a stretch of basic amino acids to increase the success rates of gene cloning, and to streamline the process of future engineering of novel viral variants. clustered randomization in a full-length gene, as the positive rate for partial gene fragment libraries was extremely low before enrichment in the previous FMDV studies. the use of fusion partner was avoided, which was used previously for protein expression, stabilization of clones and reduction of stresses on host cells. the use of Poisson distribution is proposed to approximate sequencing output to achieve cost effectiveness.
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Affiliation(s)
- Zhiwu Xu
- MOE Key Laboratory of Aquatic Product Safety, State Key Laboratory of Biocontrol, Biotechnology Research Center, The School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jieyu Wu
- MOE Key Laboratory of Aquatic Product Safety, State Key Laboratory of Biocontrol, Biotechnology Research Center, The School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Fan Feng
- MOE Key Laboratory of Aquatic Product Safety, State Key Laboratory of Biocontrol, Biotechnology Research Center, The School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiaoxiao Zhang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaoqian Ma
- MOE Key Laboratory of Aquatic Product Safety, State Key Laboratory of Biocontrol, Biotechnology Research Center, The School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Man Tang
- MOE Key Laboratory of Aquatic Product Safety, State Key Laboratory of Biocontrol, Biotechnology Research Center, The School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yan Huang
- MOE Key Laboratory of Aquatic Product Safety, State Key Laboratory of Biocontrol, Biotechnology Research Center, The School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ying Zhang
- Guangzhou Center for Disease Control and Prevention, Guangzhou 510440, China
| | - Yongchang Cao
- MOE Key Laboratory of Aquatic Product Safety, State Key Laboratory of Biocontrol, Biotechnology Research Center, The School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Weiguo Cao
- MOE Key Laboratory of Aquatic Product Safety, State Key Laboratory of Biocontrol, Biotechnology Research Center, The School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Ran He
- MOE Key Laboratory of Aquatic Product Safety, State Key Laboratory of Biocontrol, Biotechnology Research Center, The School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Corresponding authors at: MOE Key Laboratory of Aquatic Product Safety, State Key Laboratory of Biocontrol, Biotechnology Research Center, The School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China. Tel.: +86 020 84110296; fax: +86 020 84036551.
| | - Ye Gao
- MOE Key Laboratory of Aquatic Product Safety, State Key Laboratory of Biocontrol, Biotechnology Research Center, The School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
- Corresponding authors at: MOE Key Laboratory of Aquatic Product Safety, State Key Laboratory of Biocontrol, Biotechnology Research Center, The School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China. Tel.: +86 020 84110296; fax: +86 020 84036551.
| | - Qiuyun Liu
- MOE Key Laboratory of Aquatic Product Safety, State Key Laboratory of Biocontrol, Biotechnology Research Center, The School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Corresponding authors at: MOE Key Laboratory of Aquatic Product Safety, State Key Laboratory of Biocontrol, Biotechnology Research Center, The School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China. Tel.: +86 020 84110296; fax: +86 020 84036551.
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13
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Darmostuk M, Rimpelova S, Gbelcova H, Ruml T. Current approaches in SELEX: An update to aptamer selection technology. Biotechnol Adv 2015; 33:1141-61. [PMID: 25708387 DOI: 10.1016/j.biotechadv.2015.02.008] [Citation(s) in RCA: 406] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 01/26/2015] [Accepted: 02/13/2015] [Indexed: 12/21/2022]
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) is a well-established and efficient technology for the generation of oligonucleotides with a high target affinity. These SELEX-derived single stranded DNA and RNA molecules, called aptamers, were selected against various targets, such as proteins, cells, microorganisms, chemical compounds etc. They have a great potential in the use as novel antibodies, in cancer theragnostics and in biomedical research. Vast interest in aptamers stimulated continuous development of SELEX, which underwent numerous modifications since its first application in 1990. Novel modifications made the selection process more efficient, cost-effective and significantly less time-consuming. This article brings a comprehensive and up-to-date review of recent advances in SELEX methods and pinpoints advantages, main obstacles and limitations. The post-SELEX strategies and examples of application are also briefly outlined in this review.
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Affiliation(s)
- Mariia Darmostuk
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic.
| | - Silvie Rimpelova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic.
| | - Helena Gbelcova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic; Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, Bratislava 811 08, Slovak Republic.
| | - Tomas Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic.
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14
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Barman J. Targeting cancer cells using aptamers: cell-SELEX approach and recent advancements. RSC Adv 2015. [DOI: 10.1039/c4ra12407c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aptamers are short single stranded nucleic acid based therapeutic and diagnostic molecules which can be isolated from a random pool of oligonucleotides by Systematic Evolution of Ligands by EXponential Enrichment (SELEX).
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Affiliation(s)
- Jharna Barman
- Agricultural and Ecological Research Unit
- Biological Science Division
- Indian Statistical Institute
- Kolkata
- India
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15
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van Bel N, Das AT, Cornelissen M, Abbink TEM, Berkhout B. A short sequence motif in the 5' leader of the HIV-1 genome modulates extended RNA dimer formation and virus replication. J Biol Chem 2014; 289:35061-74. [PMID: 25368321 DOI: 10.1074/jbc.m114.621425] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 5' leader of the HIV-1 RNA genome encodes signals that control various steps in the replication cycle, including the dimerization initiation signal (DIS) that triggers RNA dimerization. The DIS folds a hairpin structure with a palindromic sequence in the loop that allows RNA dimerization via intermolecular kissing loop (KL) base pairing. The KL dimer can be stabilized by including the DIS stem nucleotides in the intermolecular base pairing, forming an extended dimer (ED). The role of the ED RNA dimer in HIV-1 replication has hardly been addressed because of technical challenges. We analyzed a set of leader mutants with a stabilized DIS hairpin for in vitro RNA dimerization and virus replication in T cells. In agreement with previous observations, DIS hairpin stability modulated KL and ED dimerization. An unexpected previous finding was that mutation of three nucleotides immediately upstream of the DIS hairpin significantly reduced in vitro ED formation. In this study, we tested such mutants in vivo for the importance of the ED in HIV-1 biology. Mutants with a stabilized DIS hairpin replicated less efficiently than WT HIV-1. This defect was most severe when the upstream sequence motif was altered. Virus evolution experiments with the defective mutants yielded fast replicating HIV-1 variants with second site mutations that (partially) restored the WT hairpin stability. Characterization of the mutant and revertant RNA molecules and the corresponding viruses confirmed the correlation between in vitro ED RNA dimer formation and efficient virus replication, thus indicating that the ED structure is important for HIV-1 replication.
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Affiliation(s)
- Nikki van Bel
- From the Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Centre Amsterdam, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands and
| | - Atze T Das
- From the Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Centre Amsterdam, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands and
| | - Marion Cornelissen
- From the Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Centre Amsterdam, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands and
| | - Truus E M Abbink
- From the Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Centre Amsterdam, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands and the Department of Medicine, Addenbrooke's Hospital, Cambridge CB2 0SP, United Kingdom
| | - Ben Berkhout
- From the Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Centre Amsterdam, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands and
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16
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New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e183. [PMID: 25093707 PMCID: PMC4221594 DOI: 10.1038/mtna.2014.34] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 06/10/2014] [Indexed: 12/24/2022]
Abstract
Single-stranded oligonucleotide aptamers have attracted great attention in the past decade because of their diagnostic and therapeutic potential. These versatile, high affinity and specificity reagents are selected by an iterative in vitro process called SELEX, Systematic Evolution of Ligands by Exponential Enrichment. Numerous SELEX methods have been developed for aptamer selections; some that are simple and straightforward, and some that are specialized and complicated. The method of SELEX is crucial for selection of an aptamer with desired properties; however, success also depends on the starting aptamer library, the target molecule, aptamer enrichment monitoring assays, and finally, the analysis and characterization of selected aptamers. Here, we summarize key recent developments in aptamer selection methods, as well as other aspects of aptamer selection that have significant impact on the outcome. We discuss potential pitfalls and limitations in the selection process with an eye to aid researchers in the choice of a proper SELEX strategy, and we highlight areas where further developments and improvements are desired. We believe carefully designed multiplexed selection methods, when complemented with high-throughput downstream analysis and characterization assays, will yield numerous high-affinity aptamers to protein and small molecule targets, and thereby generate a vast array of reagents for probing basic biological mechanisms and implementing new diagnostic and therapeutic applications in the near future.
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17
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van Hemert F, van der Kuyl AC, Berkhout B. On the nucleotide composition and structure of retroviral RNA genomes. Virus Res 2014; 193:16-23. [PMID: 24675274 DOI: 10.1016/j.virusres.2014.03.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/13/2014] [Accepted: 03/13/2014] [Indexed: 01/01/2023]
Abstract
Retroviral RNA genomes display a rich variety in their nucleotide composition. For instance, the single-stranded RNA genome of human T cell leukemia virus (HTLV-1) is C-rich and G-poor and that of the human immunodeficiency virus (HIV-1) is A-rich and C-poor. Animal retroviruses add further variation to this unexplained, but many times remarkable virus-specific property. We previously described that the nucleotide bias is even more extreme in the unpaired regions of the structured HIV-1 RNA genome, which has been probed by SHAPE technology. We now document that the same trend is apparent for the MFold-predicted RNA structure of HIV-1 RNA and subsequently investigated the predicted structures of the RNA genomes of other retroviruses. We conclude that all virus-specific signatures are enhanced for the unpaired nucleotides in the RNA genome. Consequently, the differences in nucleotide count between the diverse human and animal retroviruses are further exposed in the single stranded genome regions. We used a skew analysis to visualize these striking differences in nucleotide usage. Evolutionary events responsible for these nucleotide signatures will be discussed.
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Affiliation(s)
- Formijn van Hemert
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands.
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