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Agrawal K, Kang L, Ji S, Tena J, Jian W. Evaluating the use of locked nucleic acid capture probes in hybrid LC-MS/MS analysis of siRNA analytes. Bioanalysis 2023; 15:1129-1146. [PMID: 37638814 DOI: 10.4155/bio-2023-0079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023] Open
Abstract
Background: Hybrid LC-MS assays for oligonucleotides rely on capture probes to develop assays with high sensitivity and specificity. Locked nucleic acid (LNA) probes are thermodynamically superior to existing capture probes, but are not currently used for hybrid LC-MS assays. Materials & methods: Using two lipid-conjugated double-stranded siRNA compounds as model analytes, hybrid LC-MS/MS assays using LNA probes were developed. Results: The workflows demonstrated the superiority of the LNA probes, optimized sample preparation conditions to maximize analyte recovery, evaluated the need for analyte-specific internal standards, and demonstrated that advanced mass spectrometric technology can increase assay sensitivity by up to 20-fold. Conclusion: The workflow can be used in future bioanalytical studies to develop effective hybrid LC-MS/MS methods for siRNA analytes.
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Affiliation(s)
- Karan Agrawal
- Bioanalysis Discovery & Development Sciences, Janssen Research & Development, Spring House, PA 19477, USA
| | - Lijuan Kang
- Bioanalysis Discovery & Development Sciences, Janssen Research & Development, Spring House, PA 19477, USA
| | - Shaofei Ji
- Translational PK/PD & Investigative Toxicology, Janssen Research & Development, Spring House, PA 19477, USA
| | - Jennyfer Tena
- Therapeutics Discovery, Janssen Research & Development, Brisbane, CA 94005, USA
| | - Wenying Jian
- Bioanalysis Discovery & Development Sciences, Janssen Research & Development, Spring House, PA 19477, USA
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2
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El-Yazbi AF, Elgammal FAH, Moneeb MS, Sabry SM. Sensitive MALDI-TOF MS and 'turn-on' fluorescent genosensor for the determination of DNA damage induced by CNS acting drugs. Int J Biol Macromol 2023; 241:124547. [PMID: 37094646 DOI: 10.1016/j.ijbiomac.2023.124547] [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: 02/14/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 04/26/2023]
Abstract
The genotoxic and carcinogenic adverse effects of various drugs should be considered for assessing drug benefit/risk ratio. On that account, the scope of this study is to examine the kinetics of DNA damage triggered by three CNS acting drugs; carbamazepine, quetiapine and desvenlafaxine. Two precise, simple and green approaches were proposed for probing drug induced DNA impairment; MALDI-TOF MS and terbium (Tb3+) fluorescent genosensor. The results revealed that all the studied drugs induced DNA damage manifested by the MALDI-TOF MS analysis as a significant disappearance of the DNA molecular ion peak with the appearance of other peaks at smaller m/z indicating the formation of DNA strand breaks. Moreover, significant enhancement of Tb3+ fluorescence occurred, proportional to the amount of DNA damage, upon incubation of each drug with dsDNA. Furthermore, the DNA damage mechanism is examined. The proposed Tb3+ fluorescent genosensor showed superior selectivity and sensitivity and is significantly simpler and less expensive than other methods reported for the detection of DNA damage. Moreover, the DNA damaging potency of these drugs was studied using calf thymus DNA in order to clarify the potential safety hazards associated with the studied drugs on natural DNA.
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Affiliation(s)
- Amira F El-Yazbi
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; Faculty of Pharmacy, Department of Pharmaceutical Analytical Chemistry, University of Alexandria, El-Messalah, Alexandria 21521, Egypt.
| | - Feda A H Elgammal
- Faculty of Pharmacy, Department of Pharmaceutical Analytical Chemistry, University of Alexandria, El-Messalah, Alexandria 21521, Egypt
| | - Marwa S Moneeb
- Faculty of Pharmacy, Department of Pharmaceutical Analytical Chemistry, University of Alexandria, El-Messalah, Alexandria 21521, Egypt
| | - Suzy M Sabry
- Faculty of Pharmacy, Department of Pharmaceutical Analytical Chemistry, University of Alexandria, El-Messalah, Alexandria 21521, Egypt
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3
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Swenson C, Argueta-Gonzalez HS, Sterling SA, Robichaux R, Knutson SD, Heemstra JM. Forced Intercalation Peptide Nucleic Acid Probes for the Detection of an Adenosine-to-Inosine Modification. ACS OMEGA 2023; 8:238-248. [PMID: 36643573 PMCID: PMC9835161 DOI: 10.1021/acsomega.2c03568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
The deamination of adenosine to inosine is an important modification in nucleic acids that functionally recodes the identity of the nucleobase to a guanosine. Current methods to analyze and detect this single nucleotide change, such as sequencing and PCR, typically require time-consuming or costly procedures. Alternatively, fluorescent "turn-on" probes that result in signal enhancement in the presence of target are useful tools for real-time detection and monitoring of nucleic acid modification. Here we describe forced-intercalation PNA (FIT-PNA) probes that are designed to bind to inosine-containing nucleic acids and use thiazole orange (TO), 4-dimethylamino-naphthalimide (4DMN), and malachite green (MG) fluorogenic dyes to detect A-to-I editing events. We show that incorporation of the dye as a surrogate base negatively affects the duplex stability but does not abolish binding to targets. We then determined that the identity of the adjacent nucleobase and temperature affect the overall signal and fluorescence enhancement in the presence of inosine, achieving an 11-fold increase, with a limit of detection (LOD) of 30 pM. We determine that TO and 4DMN probes are viable candidates to enable selective inosine detection for biological applications.
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Affiliation(s)
- Colin
S. Swenson
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | | | - Sierra A. Sterling
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ryan Robichaux
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Steve D. Knutson
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M. Heemstra
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United States
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4
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Deng M, Li J, Xiao B, Ren Z, Li Z, Yu H, Li J, Wang J, Chen Z, Wang X. Ultrasensitive Label-Free DNA Detection Based on Solution-Gated Graphene Transistors Functionalized with Carbon Quantum Dots. Anal Chem 2022; 94:3320-3327. [PMID: 35147418 DOI: 10.1021/acs.analchem.1c05309] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Developing highly sensitive, reliable, cost-effective label-free DNA biosensors is challenging with traditional fluorescence, electrochemical, and other techniques. Most conventional methods require labeling fluorescence, enzymes, or other complex modification. Herein, we fabricate carbon quantum dot (CQD)-functionalized solution-gated graphene transistors for highly sensitive label-free DNA detection. The CQDs are immobilized on the surface of the gate electrode through mercaptoacetic acid with the thiol group. A single-stranded DNA (ssDNA) probe is immobilized on CQDs by strong π-π interactions. The ssDNA probe can hybridize with the ssDNA target and form double-stranded DNA, which led to a shift of Dirac voltage and the channel current response. The limit of detection can reach 1 aM which is 2-5 orders of magnitude lower than those of other methods reported previously. The sensor also exhibits a good linear range from 1 aM to 0.1 nM and has good specificity. It can effectively distinguish one-base mismatched target DNA. The response time is about 326 s for the 1 aM target DNA molecules. This work provides good perspectives on the applications in biosensors.
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Affiliation(s)
- Minghua Deng
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, P. R. China
| | - Jinhua Li
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, P. R. China
| | - Bichen Xiao
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, P. R. China
| | - Zhanpeng Ren
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, P. R. China
| | - Ziqin Li
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, P. R. China
| | - Haiyang Yu
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, P. R. China.,State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, P. R. China
| | - Jiashen Li
- Department of Materials, The University of Manchester, Manchester M13 9PL, U.K
| | - Jianying Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, P. R. China
| | - Zhaowei Chen
- Division of Nephrology, Renmin Hospital of Wuhan University, Wuhan 430060, P. R. China
| | - Xianbao Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, P. R. China
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5
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Sabale P, Ambi UB, Srivatsan SG. Clickable PNA Probes for Imaging Human Telomeres and Poly(A) RNAs. ACS OMEGA 2018; 3:15343-15352. [PMID: 30556003 PMCID: PMC6289544 DOI: 10.1021/acsomega.8b02550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 10/31/2018] [Indexed: 05/10/2023]
Abstract
The ability to bind strongly to complementary nucleic acid sequences, invade complex nucleic acid structures, and resist degradation by cellular enzymes has made peptide nucleic acid (PNA) oligomers as very useful hybridization probes in molecular diagnosis. For such applications, the PNA oligomers have to be labeled with appropriate reporters as they lack intrinsic labels that can be used in biophysical assays. Although solid-phase synthesis is commonly used to attach reporters onto PNA, development of milder and modular labeling methods will provide access to PNA oligomers labeled with a wider range of biophysical tags. Here, we describe the establishment of a postsynthetic modification strategy based on bioorthogonal chemical reactions in functionalizing PNA oligomers in solution with a variety of tags. A toolbox composed of alkyne- and azide-modified monomers were site-specifically incorporated into PNA oligomers and postsynthetically click-functionalized with various tags, ranging from sugar, amino acid, biotin, to fluorophores, by using copper(I)-catalyzed azide-alkyne cycloaddition, strain-promoted azide-alkyne cycloaddition, and Staudinger ligation reactions. As a proof of utility of this method, fluorescent PNA hybridization probes were developed and used in imaging human telomeres in chromosomes and poly(A) RNAs in cells. Taken together, this simple approach of generating a wide range of functional PNA oligomers will expand the use of PNA in molecular diagnosis.
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Abstract
Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years.
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Affiliation(s)
- Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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7
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El-Yazbi AF, Wong A, Loppnow GR. A luminescent probe of mismatched DNA hybridization: Location and number of mismatches. Anal Chim Acta 2017; 994:92-99. [DOI: 10.1016/j.aca.2017.09.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 01/22/2023]
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8
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Manicardi A, Guidi L, Ghidini A, Corradini R. Pyrene-modified PNAs: Stacking interactions and selective excimer emission in PNA2DNA triplexes. Beilstein J Org Chem 2014; 10:1495-503. [PMID: 25161706 PMCID: PMC4142857 DOI: 10.3762/bjoc.10.154] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/03/2014] [Indexed: 12/17/2022] Open
Abstract
Pyrene derivatives can be incorporated into nucleic acid analogs in order to obtain switchable probes or supramolecular architectures. In this paper, peptide nucleic acids (PNAs) containing 1 to 3 1-pyreneacetic acid units (PNA1–6) with a sequence with prevalence of pyrimidine bases, complementary to cystic fibrosis W1282X point mutation were synthesized. These compounds showed sequence-selective switch-on of pyrene excimer emission in the presence of target DNA, due to PNA2DNA triplex formation, with stability depending on the number and positioning of the pyrene units along the chain. An increase in triplex stability and a very high mismatch-selectivity, derived from combined stacking and base-pairing interactions, were found for PNA2, bearing two distant pyrene units.
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Affiliation(s)
- Alex Manicardi
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy. ; Tel: +39 0521 905410
| | - Lucia Guidi
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy. ; Tel: +39 0521 905410
| | - Alice Ghidini
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy. ; Tel: +39 0521 905410 ; Present Address: Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Hälsovägen 7, 14183, Huddinge, Sweden
| | - Roberto Corradini
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy. ; Tel: +39 0521 905410
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9
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Maneelun N, Vilaivan T. Dual pyrene-labeled pyrrolidinyl peptide nucleic acid as an excimer-to-monomer switching probe for DNA sequence detection. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.10.096] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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10
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Jeong HS, Choi SM, Kim HW, Park JW, Park HN, Park SM, Jang SK, Rhee YM, Kim BH. Fluorescent peptide indicator displacement assay for monitoring interactions between RNA and RNA binding proteins. ACTA ACUST UNITED AC 2013; 9:948-51. [DOI: 10.1039/c2mb25470k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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11
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Zanoli LM, Licciardello M, D'Agata R, Lantano C, Calabretta A, Corradini R, Marchelli R, Spoto G. Peptide nucleic acid molecular beacons for the detection of PCR amplicons in droplet-based microfluidic devices. Anal Bioanal Chem 2013; 405:615-24. [PMID: 22212864 DOI: 10.1007/s00216-011-5638-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 12/05/2011] [Accepted: 12/05/2011] [Indexed: 11/26/2022]
Abstract
The use of droplet-based microfluidics and peptide nucleic acid molecular beacons for the detection of polymerase chain reaction (PCR)-amplified DNA sequences within nanoliter-sized droplets is described in this work. The nanomolar-attomolar detection capabilities of the method were preliminarily tested by targeting two different single-stranded DNA sequences from the genetically modified Roundup Ready soybean and the Olea europaea genomes and detecting the fluorescence generated by peptide nucleic acid molecular beacons with fluorescence microscopy. Furthermore, the detection of 10 nM solutions of PCR amplicon of DNA extracted from leaves of O. europaea L. encapsulated in nanoliter-sized droplets was performed to demonstrate that peptide nucleic acid molecular beacons can discriminate O. europaea L. cultivar species carrying different single-nucleotide polymorphisms.
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Affiliation(s)
- Laura Maria Zanoli
- Scuola Superiore di Catania, c/o Dipartimento di Scienze Chimiche, Università di Catania, Catania, Italy
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12
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Clicked polycyclic aromatic hydrocarbon as a hybridization-responsive fluorescent artificial nucleobase in pyrrolidinyl peptide nucleic acids. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.03.062] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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13
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Boonlua C, Vilaivan C, Wagenknecht HA, Vilaivan T. 5-(Pyren-1-yl)uracil as a base-discriminating fluorescent nucleobase in pyrrolidinyl peptide nucleic acids. Chem Asian J 2011; 6:3251-9. [PMID: 21976408 DOI: 10.1002/asia.201100490] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Indexed: 12/15/2022]
Abstract
A pyrene-labeled uridine (U(Py)) monomer for a pyrrolidinyl peptide nucleic acid with an alternating proline/2-aminocyclopentanecarboxylic acid backbone (acpcPNA) was synthesized and incorporated into the PNA. The U(Py) base in acpcPNA could specifically recognize the base A in its complementary DNA strand as determined by thermal denaturation (T(m)) experiments. The fluorescence of the U(Py)-containing single-stranded acpcPNA was very weak in aqueous buffer. In the presence of a complementary DNA target, the fluorescence was enhanced significantly (2.7-41.9 folds, depending on sequences). The fluorescence enhancement was specific to the pairing between U(Py) and dA, making the U(Py)-modified acpcPNA useful as a hybridization-responsive fluorescence probe for DNA-sequence determination.
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Affiliation(s)
- Chalothorn Boonlua
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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