1
|
Liu H, You Y, Zhu Y, Zheng H. Recent advances in the exonuclease III-assisted target signal amplification strategy for nucleic acid detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:5103-5119. [PMID: 34664562 DOI: 10.1039/d1ay01275d] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The detection of nucleic acids has become significantly important in molecular diagnostics, gene therapy, mutation analysis, forensic investigations and biomedical development, and so on. In recent years, exonuclease III (Exo III) as an enzyme in the 3'-5' exonuclease family has evolved as a frequently used technique for signal amplification of low level DNA target detection. Different from the traditional target amplification strategies, the Exo III-assisted amplification strategy has been used for target DNA detection through directly amplifying the amounts of signal reagents. The Exo III-assisted amplification strategy has its unique advantages and characters, because the character of non-specific recognition of Exo III can overcome the limitation of a target-to-probe ratio of 1 : 1 in the traditional nucleic acid hybridization assay and acquire higher sensitivity. In this review, we selectively discuss the recent advances in the Exo III-assisted amplification strategy, including the amplification strategy integrated with nanomaterials, biosensors, hairpin probes and other nucleic acid detection methods. We also discuss the strengths and limitations of each strategy and methods to overcome the limitations.
Collapse
Affiliation(s)
- Hongyu Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
| | - Yuhao You
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
| | - Youzhuo Zhu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
| | - Heng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
| |
Collapse
|
2
|
Peterková K, Durník I, Marek R, Plavec J, Podbevšek P. c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry. Nucleic Acids Res 2021; 49:8947-8960. [PMID: 34365512 PMCID: PMC8421218 DOI: 10.1093/nar/gkab659] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/12/2021] [Accepted: 07/22/2021] [Indexed: 11/23/2022] Open
Abstract
Several sequences forming G-quadruplex are highly conserved in regulatory regions of genomes of different organisms and affect various biological processes like gene expression. Diverse G-quadruplex properties can be modulated via their interaction with small polyaromatic molecules such as pyrene. To investigate how pyrene interacts with G-rich DNAs, we incorporated deoxyuridine nucleotide(s) with a covalently attached pyrene moiety (Upy) into a model system that forms parallel G-quadruplex structures. We individually substituted terminal positions and positions in the pentaloop of the c-kit2 sequence originating from the KIT proto-oncogene with Upy and performed a detailed NMR structural study accompanied with molecular dynamic simulations. Our results showed that incorporation into the pentaloop leads to structural polymorphism and in some cases also thermal destabilization. In contrast, terminal positions were found to cause a substantial thermodynamic stabilization while preserving topology of the parent c-kit2 G-quadruplex. Thermodynamic stabilization results from π–π stacking between the polyaromatic core of the pyrene moiety and guanine nucleotides of outer G-quartets. Thanks to the prevalent overall conformation, our structures mimic the G-quadruplex found in human KIT proto-oncogene and could potentially have antiproliferative effects on cancer cells.
Collapse
Affiliation(s)
- Kateřina Peterková
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Ivo Durník
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia.,CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Radek Marek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia.,CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
| | - Peter Podbevšek
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| |
Collapse
|
3
|
Uhd J, Miotke L, Ji HP, Dunaeva M, Pruijn GJM, Jørgensen CD, Kristoffersen EL, Birkedal V, Yde CW, Nielsen FC, Hansen J, Astakhova K. Ultra-fast detection and quantification of nucleic acids by amplification-free fluorescence assay. Analyst 2021; 145:5836-5844. [PMID: 32648858 DOI: 10.1039/d0an00676a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Two types of clinically important nucleic acid biomarkers, microRNA (miRNA) and circulating tumor DNA (ctDNA) were detected and quantified from human serum using an amplification-free fluorescence hybridization assay. Specifically, miRNAs hsa-miR-223-3p and hsa-miR-486-5p with relevance for rheumatoid arthritis and cancer related mutations BRAF and KRAS of ctDNA were directly measured. The required oligonucleotide probes for the assay were rationally designed and synthesized through a novel "clickable" approach which is time and cost-effective. With no need for isolating nucleic acid components from serum, the fluoresence-based assay took only 1 hour. Detection and absolute quantification of targets was successfully achieved despite their notoriously low abundance, with a precision down to individual nucleotides. Obtained miRNA and ctDNA amounts showed overall a good correlation with current techniques. With appropriate probes, our novel assay and signal boosting approach could become a useful tool for point-of-care measuring other low abundance nucleic acid biomarkers.
Collapse
Affiliation(s)
- Jesper Uhd
- Department of Chemistry, Technical University of Denmark, 207 Kemitorvet, 2800 Kgs. Lyngby, Denmark.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Carbon Nanotubes-Potent Carriers for Targeted Drug Delivery in Rheumatoid Arthritis. Pharmaceutics 2021; 13:pharmaceutics13040453. [PMID: 33801590 PMCID: PMC8066293 DOI: 10.3390/pharmaceutics13040453] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 01/15/2023] Open
Abstract
Two types of single-walled carbon nanotubes (SWCNTs), HiPco- and carboxyl-SWCNT, are evaluated as drug carriers for the traditional anti-inflammatory drug methotrexate (MTX) and a small interfering RNA (siRNA) targeting NOTCH1 gene. The nanotubes are solubilized by PEGylation and covalently loaded with MTX. The coupling efficiency (CE%) of MTX is 77–79% for HiPco-SWCNT and 71–83% for carboxyl-SWCNT. siRNA is noncovalently attached to the nanotubes with efficiency of 90–97% for HiPco-SWCNT and 87–98% for carboxyl-SWCNT. Through whole body imaging in the second near-infrared window (NIR-II window, 1000–1700 nm), SWCNTs were found to be selectively accumulated in inflamed joints in a serum transfer mouse model. We further investigated the interactions of the siRNA/MTX loaded nanotubes with human blood and mice bone marrow cells. In human blood, both types of unloaded SWCNTs were associated with B cells, monocytes and neutrophils. Interestingly, loading with MTX suppressed SWCNTs targeting specificity to immune cells, especially B cells; in contrast, loading siRNA alone enhanced the targeting specificity. Loading both MTX and siRNA to carboxyl-SWCNT enhanced targeting specificity to neutrophils and monocytes but not B cells. The targeting specificity of SWCNTs can potentially be adjusted by altering the ratio of MTX and siRNA loaded. The combined results show that carbon nanotubes have the potential for delivery of cargo drugs specifically to immune cells involved in rheumatoid arthritis.
Collapse
|
5
|
Novopashina DS, Semikolenova OA, Venyaminova AG. 5'-Monopyrene and 5'-Bispyrene 2'-O-methyl RNA Probes for Detection of RNA Mismatches. Methods Mol Biol 2020; 2063:45-56. [PMID: 31667762 DOI: 10.1007/978-1-0716-0138-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Progress in synthesis of novel fluorescent oligonucleotides has provided effective instruments for nucleic acid detection. Pyrene conjugated oligonucleotides have demonstrated their effectiveness as fluorescent hybridization probes. Here we describe the synthesis, isolation, and analysis of 5'-monopyrene and 5'-bispyrene conjugates of oligo(2'-O-methylribonucleotides) and their application as probes for fluorescent detection of mismatches in RNA targets.
Collapse
Affiliation(s)
- D S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia. .,Novosibirsk State University, Novosibirsk, Russia.
| | | | - A G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| |
Collapse
|
6
|
Khatri S, Psaraftis N, Funaro A, Arinuma Y, Fujieda Y, Mader S, Jørgensen CD, Astakhova K. Serological comparison of systemic lupus erythematosus with neuropsychiatric lupus using synthetic nucleic acid antigens. J Transl Autoimmun 2020; 3:100068. [PMID: 33205038 PMCID: PMC7652778 DOI: 10.1016/j.jtauto.2020.100068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 12/01/2022] Open
Abstract
Neuropsychiatric systemic lupus erythematosus is an autoimmune disorder characterized by an irregular exchange between the central nervous system and the immune system, leading to the outbreak of neurological conditions with possible disabling effects. Although neuropsychiatric systemic lupus erythematosus is the most common expression of lupus condition, it is still poorly understood. In this study, we focus on the development of an advantageous method based on the application of synthetic nucleic acids and protein-based antigen arrays in order to characterize autoreactive antibodies in neuropsychiatric systemic lupus erythematosus. We confirmed the benefits of using synthetic oligonucleotides such as assay reproducibility, elevated affinity and specificity to autoreactive antibodies. We also demonstrated presence of autoantibodies towards three particular synthetic double stranded antigens and verify similarity of antinuclear antibody patterns in ordinary lupus and neuropsychiatric systemic lupus erythematosus.
Collapse
Affiliation(s)
- Sangita Khatri
- Department of Chemistry, Technical University of Denmark, 207 Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Nikos Psaraftis
- Department of Chemistry, Technical University of Denmark, 207 Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Alessia Funaro
- Department of Chemistry, Technical University of Denmark, 207 Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Yoshiyuki Arinuma
- Department of Rheumatology and Infectious Diseases, Kitasato University School of Medicine, 1-15-1, Minamiku, Kitasato, Sagamihara, Kanagawa, 252-0374, Japan
| | - Yuichiro Fujieda
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Simone Mader
- Institute of Clinical Neuroimmunology, Biomedical Center and University Hospital, Ludwig-Maximilians University Munich, Martinsried, Germany
| | | | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, 207 Kemitorvet, 2800, Kgs. Lyngby, Denmark
| |
Collapse
|
7
|
Mariam J, Krishnamoorthy G, Anand R. Use of 6‐Methylisoxanthopterin, a Fluorescent Guanine Analog, to Probe Fob1‐Mediated Dynamics at the Stalling Fork Barrier DNA Sequences. Chem Asian J 2019; 14:4760-4766. [DOI: 10.1002/asia.201901061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/19/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Jessy Mariam
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 Maharashtra India
| | | | - Ruchi Anand
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 Maharashtra India
| |
Collapse
|
8
|
Krasheninina OA, Novopashina DS, Apartsin EK, Venyaminova AG. Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides. Molecules 2017; 22:E2108. [PMID: 29189716 PMCID: PMC6150046 DOI: 10.3390/molecules22122108] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022] Open
Abstract
In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.
Collapse
Affiliation(s)
- Olga A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Evgeny K Apartsin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| |
Collapse
|
9
|
Krasheninina OA, Lomzov AA, Fishman VS, Novopashina DS, Venyaminova AG. Rational design and studies of excimer forming novel dual probes to target RNA. Bioorg Med Chem 2017; 25:2244-2250. [PMID: 28279557 DOI: 10.1016/j.bmc.2017.02.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 01/31/2017] [Accepted: 02/22/2017] [Indexed: 11/18/2022]
Abstract
In this paper, we report structure-based rational design and physico-chemical and biological studies of novel pyrene excimer forming dual probes for visualization of intracellular RNAs. Herein, the probes based on 2'-O-methyl RNA with linkers of different structure and length between pyrene moiety and ribose are studied with respect to their hybridization and spectral properties. We found optimal linkers that provide more intense excimer emission (at ∼480nm) of RNA-bound probes; particularly, the length of the linker arm of the 3'-component of dual probes plays a key role in formation of pyrene excimer. Calculated molecular dynamics trajectories and probability distributions of pyrene-pyrene dimer formation upon hybridization of the dual probes with RNA target are in agreement with the obtained fluorescence spectroscopy data for the corresponding duplexes. Our study demonstrates the excellent binding properties of new dual probes to structured RNA and their feasibility for the visualization of intracellular RNA targets.
Collapse
Affiliation(s)
- O A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogov str., Novosibirsk 630090, Russia.
| | - A A Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogov str., Novosibirsk 630090, Russia
| | - V S Fishman
- Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - D S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogov str., Novosibirsk 630090, Russia
| | - A G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia
| |
Collapse
|
10
|
Junager NPL, Kongsted J, Astakhova K. Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes. SENSORS 2016; 16:s16081173. [PMID: 27472344 PMCID: PMC5017339 DOI: 10.3390/s16081173] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 01/08/2023]
Abstract
Nucleic acid mutations are of tremendous importance in modern clinical work, biotechnology and in fundamental studies of nucleic acids. Therefore, rapid, cost-effective and reliable detection of mutations is an object of extensive research. Today, Förster resonance energy transfer (FRET) probes are among the most often used tools for the detection of nucleic acids and in particular, for the detection of mutations. However, multiple parameters must be taken into account in order to create efficient FRET probes that are sensitive to nucleic acid mutations. In this review; we focus on the design principles for such probes and available computational methods that allow for their rational design. Applications of advanced, rationally designed FRET probes range from new insights into cellular heterogeneity to gaining new knowledge of nucleic acid structures directly in living cells.
Collapse
Affiliation(s)
- Nina P L Junager
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Kira Astakhova
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| |
Collapse
|
11
|
Clutter DS, Rojas Sánchez P, Rhee SY, Shafer RW. Genetic Variability of HIV-1 for Drug Resistance Assay Development. Viruses 2016; 8:v8020048. [PMID: 26875985 PMCID: PMC4776203 DOI: 10.3390/v8020048] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 12/17/2022] Open
Abstract
A hybridization-based point-of-care (POC) assay for HIV-1 drug resistance would be useful in low- and middle-income countries (LMICs) where resistance testing is not routinely available. The major obstacle in developing such an assay is the extreme genetic variability of HIV-1. We analyzed 27,203 reverse transcriptase (RT) sequences from the Stanford HIV Drug Resistance Database originating from six LMIC regions. We characterized the variability in a 27-nucleotide window surrounding six clinically important drug resistance mutations (DRMs) at positions 65, 103, 106, 181, 184, and 190. The number of distinct codons at each DRM position ranged from four at position 184 to 11 at position 190. Depending on the mutation, between 11 and 15 of the 24 flanking nucleotide positions were variable. Nonetheless, most flanking sequences differed from a core set of 10 flanking sequences by just one or two nucleotides. Flanking sequence variability was also lower in each LMIC region compared with overall variability in all regions. We also describe an online program that we developed to perform similar analyses for mutations at any position in RT, protease, or integrase.
Collapse
Affiliation(s)
- Dana S Clutter
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, 300 Pasteur Drive, L-134, Stanford, CA 94035, USA.
| | - Patricia Rojas Sánchez
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Ramón y Cajal-IRYCIS and CIBER-ESP, Madrid 28034, Spain.
| | - Soo-Yon Rhee
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, 300 Pasteur Drive, L-134, Stanford, CA 94035, USA.
| | - Robert W Shafer
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, 300 Pasteur Drive, L-134, Stanford, CA 94035, USA.
| |
Collapse
|
12
|
Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA. Sci Rep 2015; 5:8721. [PMID: 25735213 PMCID: PMC4348642 DOI: 10.1038/srep08721] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 01/23/2015] [Indexed: 12/18/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are a prime source of genetic diversity. Discriminating between different SNPs provides an enormous leap towards the better understanding of the uniqueness of biological systems. Here we report on a new approach for SNP discrimination using toehold-mediated DNA strand displacement. The distinctiveness of the approach is based on the combination of both 3- and 4-way branch migration mechanisms, which allows for reliable discrimination of SNPs within double-stranded DNA generated from real-life human mitochondrial DNA samples. Aside from the potential diagnostic value, the current study represents an additional way to control the strand displacement reaction rate without altering other reaction parameters and provides new insights into the influence of single nucleotide substitutions on 3- and 4-way branch migration efficiency and kinetics.
Collapse
|
13
|
Toward Non-Enzymatic Ultrasensitive Identification of Single Nucleotide Polymorphisms by Optical Methods. CHEMOSENSORS 2014. [DOI: 10.3390/chemosensors2030193] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
14
|
Astakhova IK, Wengel J. Scaffolding along nucleic acid duplexes using 2'-amino-locked nucleic acids. Acc Chem Res 2014; 47:1768-77. [PMID: 24749544 DOI: 10.1021/ar500014g] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
CONSPECTUS: Incorporation of chemically modified nucleotide scaffolds into nucleic acids to form assemblies rich in function is an innovative area with great promise for nanotechnology and biomedical and material science applications. The intrinsic biorecognition potential of nucleic acids combined with advanced properties of the locked nucleic acids (LNAs) provide opportunities to develop new nanomaterials and devices like sensors, aptamers, and machines. In this Account, we describe recent research on preparation and investigation of the properties of LNA/DNA hybrids containing functionalized 2'-amino-LNA nucleotides. By application of different chemical reactions, modification of 2'-amino-LNA scaffolds can be efficiently performed in high yields and with various tags, postsynthetically or during the automated oligonucleotide synthesis. The choice of a synthetic method for scaffolding along 2'-amino-LNA mainly depends on the chemical nature of the modification, its price, its availability, and applications of the product. One of the most useful applications of the product LNA/DNA scaffolds containing 2'-amino-LNA is to detect complementary DNA and RNA targets. Examples of these applications include sensing of clinically important single-nucleotide polymorphisms (SNPs) and imaging of nucleic acids in vitro, in cell culture, and in vivo. According to our studies, 2'-amino-LNA scaffolds are efficient within diagnostic probes for DNA and RNA targets and as therapeutics, whereas both 2'-amino- and isomeric 2'-α-l-amino-LNA scaffolds have promising properties for stabilization and detection of DNA nanostructures. Attachment of fluorescent groups to the 2'-amino group results in very high fluorescent quantum yields of the duplexes and remarkable sensitivity of the fluorescence signal to target binding. Notably, fluorescent LNA/DNA probes bind nucleic acid targets with advantages of high affinity and specificity. Thus, molecular motion of nanodevices and programmable self-assembly of chemically modified LNA/DNA nanomaterials can be followed by bright fluorescence signaling from the functionalized LNA units. Another appealing aspect of the amino-LNA scaffolds is specific targeting of nucleic acids and proteins for therapeutic applications. 2'-Amino-LNA/DNA conjugates containing peptide and polyaromatic hydrocarbon (PAH) groups are promising in this context as well as for advanced imaging and diagnostic purposes in vivo. For imaging applications, photostability of fluorescence dyes is of crucial importance. Chemically stable and photostable fluorescent PAH molecules attached to 2'-amino functionality of the 2'-amino-LNA are potent for in vitro and in vivo imaging of DNA and RNA targets. We believe that rational evolution of the biopolymers of Nature may solve the major challenges of the future material science and biomedicine. However, this requires strong scientific progress and efficient interdisciplinary research. Examples of this Account demonstrate that among other synthetic biopolymers, synthetic nucleic acids containing functionalized 2'-amino-LNA scaffolds offer great opportunities for material science, diagnostics, and medicine of the future.
Collapse
Affiliation(s)
- I. Kira Astakhova
- Nucleic Acid Center,
Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Jesper Wengel
- Nucleic Acid Center,
Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| |
Collapse
|