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Zheng J, Yang R, Shi M, Wu C, Fang X, Li Y, Li J, Tan W. Rationally designed molecular beacons for bioanalytical and biomedical applications. Chem Soc Rev 2015; 44:3036-55. [PMID: 25777303 PMCID: PMC4431697 DOI: 10.1039/c5cs00020c] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleic acids hold promise as biomolecules for future applications in biomedicine and biotechnology. Their well-defined structures and compositions afford unique chemical properties and biological functions. Moreover, the specificity of hydrogen-bonded Watson-Crick interactions allows the construction of nucleic acid sequences with multiple functions. In particular, the development of nucleic acid probes as essential molecular engineering tools will make a significant contribution to advancements in biosensing, bioimaging and therapy. The molecular beacon (MB), first conceptualized by Tyagi and Kramer in 1996, is an excellent example of a double-stranded nucleic acid (dsDNA) probe. Although inactive in the absence of a target, dsDNA probes can report the presence of a specific target through hybridization or a specific recognition-triggered change in conformation. MB probes are typically fluorescently labeled oligonucleotides that range from 25 to 35 nucleotides (nt) in length, and their structure can be divided into three components: stem, loop and reporter. The intrinsic merit of MBs depends on predictable design, reproducibility of synthesis, simplicity of modification, and built-in signal transduction. Using resonance energy transfer (RET) for signal transduction, MBs are further endowed with increased sensitivity, rapid response and universality, making them ideal for chemical sensing, environmental monitoring and biological imaging, in contrast to other nucleic acid probes. Furthermore, integrating MBs with targeting ligands or molecular drugs can substantially support their in vivo applications in theranositics. In this review, we survey advances in bioanalytical and biomedical applications of rationally designed MBs, as they have evolved through the collaborative efforts of many researchers. We first discuss improvements to the three components of MBs: stem, loop and reporter. The current applications of MBs in biosensing, bioimaging and therapy will then be described. In particular, we emphasize recent progress in constructing MB-based biosensors in homogeneous solution or on solid surfaces. We expect that such rationally designed and functionalized MBs will open up new and exciting avenues for biological and medical research and applications.
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Affiliation(s)
- Jing Zheng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
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Ayele W, Mekonnen Y, Messele T, Mengistu Y, Tsegaye A, Bakker M, Berkhout B, Dorigo-Zetsma W, Wolday D, Goudsmit J, Coutinho R, de Baar M, Paxton WA, Pollakis G. Differences in HIV type 1 RNA plasma load profile of closely related cocirculating Ethiopian subtype C strains: C and C'. AIDS Res Hum Retroviruses 2010; 26:805-13. [PMID: 20624072 DOI: 10.1089/aid.2009.0152] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Two HIV-1 subtype C subclusters have been identified in Ethiopia (C and C') with little knowledge regarding their biological or clinical differences. We longitudinally monitored HIV-1 viral loads and CD4(+) T cell counts for 130 subtype C-infected individuals from Ethiopia over 5 years. The genetic subclusters C and C' were determined and comparisons were made between the groups. None of the study individuals received antiretroviral therapy. Subcluster C' was found to be the more prevalent (72.3%) genotype circulating. Individuals infected with subcluster C' harbored higher viral loads in comparison to subcluster C-infected individuals when the CD4(+) T cell counts were high (500-900 cells/mm(3)), whereas at low CD4(+) T cell counts (0-150 cells/mm(3)) individuals infected with subcluster C viruses showed higher viral loads. We identified a greater number of deaths among individuals infected with subcluster C viruses in comparison to C'. Our results indicate that infection with subcluster C viruses leads to a more rapid onset of disease, despite the initial lower HIV-1 RNA plasma loads. Additionally, the higher viral loads seen for HIV-1 subcluster C' infections at higher CD4(+) T cell counts can help explain the higher prevalence of this subtype in Ethiopia.
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Affiliation(s)
- Workenesh Ayele
- Ethiopian Health and Nutrition Research Institute (EHNRI), Addis Ababa, Ethiopia
| | - Yared Mekonnen
- Ethiopian Health and Nutrition Research Institute (EHNRI), Addis Ababa, Ethiopia
| | - Tsehaynesh Messele
- Ethiopian Health and Nutrition Research Institute (EHNRI), Addis Ababa, Ethiopia
| | - Yohannes Mengistu
- Department of Microbiology, Immunology and Parasitology, Faculty of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Aster Tsegaye
- Ethiopian Health and Nutrition Research Institute (EHNRI), Addis Ababa, Ethiopia
| | - Margreet Bakker
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology–Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology–Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Wendelien Dorigo-Zetsma
- Regional Microbiological and Serological Laboratory, Hospital Hilversum, Hilversum, The Netherlands
| | - Dawit Wolday
- Ethiopian Health and Nutrition Research Institute (EHNRI), Addis Ababa, Ethiopia
| | | | - Roel Coutinho
- Rijksinstituut voor Volksgezondheid en Milieu (RIVM), 3721 MA Bilthoven, The Netherlands
| | | | - William A. Paxton
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology–Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Georgios Pollakis
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology–Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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Novitsky V, Wang R, Lagakos S, Essex M. HIV-1 Subtype C Phylodynamics in the Global Epidemic. Viruses 2010; 2:33-54. [PMID: 21994599 PMCID: PMC3185553 DOI: 10.3390/v2010033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 12/23/2009] [Accepted: 12/27/2009] [Indexed: 11/16/2022] Open
Abstract
The diversity of HIV-1 and its propensity to generate escape mutants present fundamental challenges to control efforts, including HIV vaccine design. Intra-host diversification of HIV is determined by immune responses elicited by an HIV-infected individual over the course of the infection. Complex and dynamic patterns of transmission of HIV lead to an even more complex population viral diversity over time, thus presenting enormous challenges to vaccine development. To address inter-patient viral evolution over time, a set of 653 unique HIV-1 subtype C gag sequences were retrieved from the LANL HIV Database, grouped by sampling year as <2000, 2000, 2001-2002, 2003, and 2004-2006, and analyzed for the site-specific frequency of translated amino acid residues. Phylogenetic analysis revealed that a total of 289 out of 653 (44.3%) analyzed sequences were found within 16 clusters defined by aLRT of more than 0.90. Median (IQR) inter-sample diversity of analyzed gag sequences was 8.7% (7.7%; 9.8%). Despite the heterogeneous origins of analyzed sequences, the gamut and frequency of amino acid residues in wild-type Gag were remarkably stable over the last decade of the HIV-1 subtype C epidemic. The vast majority of amino acid residues demonstrated minor frequency fluctuation over time, consistent with the conservative nature of the HIV-1 Gag protein. Only 4.0% (20 out of 500; HXB2 numbering) amino acid residues across Gag displayed both statistically significant (p<0.05 by both a trend test and heterogeneity test) changes in amino acid frequency over time as well as a range of at least 10% in the frequency of the major amino acid. A total of 59.2% of amino acid residues with changing frequency of 10%+ were found within previously identified CTL epitopes. The time of the most recent common ancestor of the HIV-1 subtype C was dated to around 1950 (95% HPD from 1928 to 1962). This study provides evidence for the overall stability of HIV-1 subtype C Gag among viruses circulating in the epidemic over the last decade. However selected sites across HIV-1C Gag with changing amino acid frequency are likely to be under selection pressure at the population level.
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Affiliation(s)
- Vlad Novitsky
- Department of Immunology and Infectious Diseases, Harvard School of Public Health AIDS Initiative, Harvard School of Public Health, Boston, MA, USA; E-Mail: (M.E.)
- Botswana–Harvard AIDS Institute, Gaborone, Botswana
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-617-432-1225; Fax: +1-617-739-8348
| | - Rui Wang
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; E-Mails: (R.W.); (S.L.)
| | - Stephen Lagakos
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; E-Mails: (R.W.); (S.L.)
| | - Max Essex
- Department of Immunology and Infectious Diseases, Harvard School of Public Health AIDS Initiative, Harvard School of Public Health, Boston, MA, USA; E-Mail: (M.E.)
- Botswana–Harvard AIDS Institute, Gaborone, Botswana
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Abstract
PURPOSE OF REVIEW This review attempts to acquaint the reader with the molecular epidemiology of HIV-1 and to describe some of the more promising approaches to vaccine development in the light of this diversity. RECENT FINDINGS The primary genetic forms of HIV-1 in the world today are subtypes A, B, C, CRF01-AE and CRF02-AG. In sub-Saharan Africa, subtypes A and C and CRF02-AG account for most of the infections. In Asia, there are subtypes B, C and CRF01 AE. Europe, the Americas and the Caribbean are dominated by subtype B, and subtype A is in the former Soviet Union. While the genetic diversity of HIV-1 in the world can seem daunting, the vast majority of infections are actually caused by one of these five genetic forms. Approaches to dealing with this in the development of vaccines include targeting conserved regions of the genome, creating ancestral forms of the virus or putting many different forms together into a cocktail. Each of these approaches shows promise. To optimize the chances of initially showing efficacy in HIV vaccine trials, the genetic form of the vaccine strains will resemble those of the circulating strains in the target population. Once efficacy is demonstrated, however, it will be possible to determine whether genetic subtype is at all predictive of vaccine protection. SUMMARY Although the genetic diversity of HIV-1 is impressive, it is not limitless. Most of the infections worldwide are actually due to a handful of strains. It should be possible for a few vaccine strategies to conquer HIV-1 definitively.
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Ayele W, Assefa T, Lulseged S, Tegbaru B, Berhanu H, Tamene W, Ahmedin Z, Tensai BW, Tafesse M, Goudsmit J, Berkhout B, Paxton WA, deBaar MP, Messele T, Pollakis G. RNA Detection and Subtype C Assessment of HIV-1 in Infants with Diarrhea in Ethiopia. Open AIDS J 2009; 3:19-23. [PMID: 19554214 PMCID: PMC2701272 DOI: 10.2174/1874613600903010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Revised: 02/18/2009] [Accepted: 02/20/2009] [Indexed: 11/22/2022] Open
Abstract
In the absence of chemoprophylaxis, HIV-1 transmission occurs in 13-42% of infants born to HIV-1 positive mothers. All exposed infants acquire maternal HIV-1 antibodies that persist for up to 15 months, thereby hampering diagnosis. In resource limited settings, clinical symptoms are the indices of established infection against validated laboratorybased markers. Here we enrolled 1200 children hospitalized for diarrheal and other illnesses. 20-25% of those tested, aged 15 months or younger, were found to be HIV-1-seropositive. Where sufficient plasma was available, HIV-1 RNA detection was performed using a subtype-insensitive assay, with 71.1% of seropositive infants presenting with diarrhea showing positive. From sub-typing analysis, we identified that viruses of the C’ sub-cluster were predominated amongst infants. Although this study may overestimate the HIV-1 frequency through testing symptomatic infants, diarrhea can be seen as a useful marker indicating HIV-1 infection in infants less than 15 months old.
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Wang K, Tang Z, Yang C, Kim Y, Fang X, Li W, Wu Y, Medley C, Cao Z, Li J, Colon P, Lin H, Tan W. Molekulartechnische DNA-Modifizierung: Molecular Beacons. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200800370] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Wang K, Tang Z, Yang CJ, Kim Y, Fang X, Li W, Wu Y, Medley CD, Cao Z, Li J, Colon P, Lin H, Tan W. Molecular engineering of DNA: molecular beacons. Angew Chem Int Ed Engl 2009; 48:856-70. [PMID: 19065690 PMCID: PMC2772660 DOI: 10.1002/anie.200800370] [Citation(s) in RCA: 492] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Molecular beacons (MBs) are specifically designed DNA hairpin structures that are widely used as fluorescent probes. Applications of MBs range from genetic screening, biosensor development, biochip construction, and the detection of single-nucleotide polymorphisms to mRNA monitoring in living cells. The inherent signal-transduction mechanism of MBs enables the analysis of target oligonucleotides without the separation of unbound probes. The MB stem-loop structure holds the fluorescence-donor and fluorescence-acceptor moieties in close proximity to one another, which results in resonant energy transfer. A spontaneous conformation change occurs upon hybridization to separate the two moieties and restore the fluorescence of the donor. Recent research has focused on the improvement of probe composition, intracellular gene quantitation, protein-DNA interaction studies, and protein recognition.
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Affiliation(s)
- Kemin Wang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Zhiwen Tang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Chaoyong James Yang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (P.R. China)
| | - Youngmi Kim
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Xiaohong Fang
- Institute of Chemistry, Chinese Academy of Sciences 2 Zhongguancun Beiyijie, Beijing 100190 (P.R. China)
| | - Wei Li
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Yanrong Wu
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Colin D. Medley
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Zehui Cao
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Jun Li
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Patrick Colon
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Hui Lin
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Weihong Tan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
- Biomedical Engineering Center, 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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Abstract
Infection with HIV and subsequent development of AIDS is a pandemic. The Joint United Nations Program on HIV/AIDS together with the WHO and many relevant funding bodies demand that those infected should be reliably identified so that people who need, or will need, therapy may be provided for over time. This means that there is a renewed interest in testing for HIV and in laboratories' performances and quality. Whatever the conditions under which testing is performed, and whatever the levels of training, the tests and their outcomes must exhibit equivalent, high standards of performance and reliable results. This is regardless of whether testing is conducted in the most sophisticated laboratories (either diagnostic or transfusion screening) to voluntary testing and counseling centers where those conducting testing may not be technically trained. This is not currently the case, especially in some places where HIV is most prevalent. To achieve uniformly high performance standards, quality assurance programs are imperative, but currently not sufficiently valued to be well supported with adequate funding or human resources. Accurate HIV testing is a cornerstone of blood safety, diagnosis of infection, patient management and surveillance.
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Affiliation(s)
- Denison Chang
- World Health Organization Collaborating Centre on HIV/AIDS, Fitzroy, Victoria, Australia.
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