1
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Yu H, Han X, Wang W, Zhang Y, Xiang L, Bai D, Zhang L, Weng Z, Lv K, Song L, Luo W, Yin N, Zhang Y, Feng T, Wang L, Xie G. Modified Unit-Mediated Strand Displacement Reactions for Direct Detection of Single Nucleotide Variants in Active Double-Stranded DNA. ACS NANO 2024; 18:12401-12411. [PMID: 38701333 DOI: 10.1021/acsnano.4c01511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Accurate identification of single nucleotide variants (SNVs) in key driver genes holds a significant value for disease diagnosis and treatment. Fluorescent probes exhibit tremendous potential in specific, high-resolution, and rapid detection of SNVs. However, additional steps are required in most post-PCR assays to convert double-stranded DNA (dsDNA) products into single-stranded DNA (ssDNA), enabling them to possess hybridization activity to trigger subsequent reactions. This process not only prolongs the complexity of the experiment but also introduces the risk of losing target information. In this study, we proposed two strategies for enriching active double-stranded DNA, involving PCR based on obstructive groups and cleavable units. Building upon this, we explored the impact of modified units on the strand displacement reaction (SDR) and assessed their discriminatory efficacy for mutations. The results showed that detection of low variant allele frequencies (VAF) as low as 0.1% can be achieved. The proposed strategy allowed orthogonal identification of 45 clinical colorectal cancer tissue samples with 100% specificity, and the results were generally consistent with sequencing results. Compared to existing methods for enriching active targets, our approach offers a more diverse set of enrichment strategies, characterized by the advantage of being simple and fast and preserving original information to the maximum extent. The objective of this study is to offer an effective solution for the swift and facile acquisition of active double-stranded DNA. We anticipate that our work will facilitate the practical applications of SDR based on dsDNA.
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Affiliation(s)
- Hongyan Yu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xiaole Han
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Weitao Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yangli Zhang
- The Center for Clinical Molecular Medical Detection, Biobank Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Linguo Xiang
- The Center for Clinical Molecular Medical Detection, Biobank Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Dan Bai
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Li Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Zhi Weng
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Ke Lv
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Lin Song
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Wang Luo
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Na Yin
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yaoyi Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Tong Feng
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Li Wang
- The Center for Clinical Molecular Medical Detection, Biobank Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
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2
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Amin SM, Islam T, Price NE, Wallace A, Guo X, Gomina A, Heidari M, Johnson KM, Lewis CD, Yang Z, Gates KS. Effects of Local Sequence, Reaction Conditions, and Various Additives on the Formation and Stability of Interstrand Cross-Links Derived from the Reaction of an Abasic Site with an Adenine Residue in Duplex DNA. ACS OMEGA 2022; 7:36888-36901. [PMID: 36278095 PMCID: PMC9583646 DOI: 10.1021/acsomega.2c05736] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
The experiments described here examined the effects of reaction conditions, various additives, and local sequence on the formation and stability interstrand cross-links (ICLs) derived from the reaction of an apurinic/apyrimidinic (AP) site with the exocyclic amino group of an adenine residue on the opposing strand in duplex DNA. Cross-link formation was observed in a range of different buffers, with faster formation rates observed at pH 5. Inclusion of the base excision repair enzyme alkyladenine DNA glycosylase (hAAG) which binds tightly to AP-containing duplexes decreased, but did not completely prevent, formation of the dA-AP ICL. Formation of the dA-AP ICL was not altered by the presence of the biological metal ion Mg2+ or the biological thiol, glutathione. Several organocatalysts of imine formation did not enhance the rate of dA-AP ICL formation. Duplex length did not have a large effect on dA-AP yield, so long as the melting temperature of the duplex was not significantly below the reaction temperature (the duplex must remain hybridized for efficient ICL formation). Formation of the dA-AP ICL was examined in over 40 different sequences that varied the neighboring and opposing bases at the cross-linking site. The results indicate that ICL formation can occur in a wide variety of sequence contexts under physiological conditions. Formation of the dA-AP ICL was strongly inhibited by the aldehyde-trapping agents methoxyamine and hydralazine, by NaBH3CN, by the intercalator ethidium bromide, and by the minor groove-binding agent netropsin. ICL formation was inhibited to some extent in bicarbonate and Tris buffers. The dA-AP ICL showed substantial inherent stability under a variety of conditions and was not a substrate for AP-processing enzymes APE1 or Endo IV. Finally, we characterized cross-link formation in a small (11 bp) stem-loop (hairpin) structure and in DNA-RNA hybrid duplexes.
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Affiliation(s)
- Saosan
Binth Md. Amin
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Tanhaul Islam
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Nathan E. Price
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Amanda Wallace
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Xu Guo
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Anuoluwapo Gomina
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Marjan Heidari
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Kevin M. Johnson
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Calvin D. Lewis
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Zhiyu Yang
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Kent S. Gates
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
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3
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Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing. Nat Methods 2022; 19:1393-1402. [PMID: 36216958 PMCID: PMC9636025 DOI: 10.1038/s41592-022-01604-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 08/10/2022] [Indexed: 11/21/2022]
Abstract
We present Light-Seq, an approach for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding in fixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially targeted, rapid photocrosslinking of DNA barcodes onto complementary DNAs in situ with a one-step DNA stitching reaction to create pooled, spatially indexed sequencing libraries. This light-directed barcoding enables in situ selection of multiple cell populations in intact fixed tissue samples for full-transcriptome sequencing based on location, morphology or protein stains, without cellular dissociation. Applying Light-Seq to mouse retinal sections, we recovered thousands of differentially enriched transcripts from three cellular layers and discovered biomarkers for a very rare neuronal subtype, dopaminergic amacrine cells, from only four to eight individual cells per section. Light-Seq provides an accessible workflow to combine in situ imaging and protein staining with next generation sequencing of the same cells, leaving the sample intact for further analysis post-sequencing. Light-Seq uses light-directed DNA barcoding in fixed cells and tissues for multiplexed spatial indexing and subsequent next generation sequencing. This approach blends spatial and omics information to enable analysis of rare cell types in complex tissues.
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4
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Zhang L, Wang Y, Guo Y, Chen H, Yu W, Zhang Z, Xie G. A comprehensive system for detecting rare single nucleotide variants based on competitive DNA probe and duplex-specific nuclease. Anal Chim Acta 2021; 1166:338545. [PMID: 34023002 DOI: 10.1016/j.aca.2021.338545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/14/2021] [Accepted: 04/18/2021] [Indexed: 10/21/2022]
Abstract
Single nucleotide variants (SNVs) have emerged as increasingly important biomarkers, particularly in the diagnosis and prognosis of cancers. However, most SNVs are rarely detected in blood samples from cancer patients as they are surrounded by abundant concomitant wild-type nucleic acids. Herein, we design a system that features a combination of competitive DNA probe system (CDPS) and duplex-specific nuclease (DSN) that we referred to as CAD. A theoretical model was established for the CAD system based on reaction networks. Guided by the theoretical model, we found that a minor loss in sensitivity significantly improved the specificity of the system, thus creating a theoretical discrimination factor (DF) > 100 for most conditions. This non-equivalent tradeoff between sensitivity and specificity provides a new concept for the analysis of rare DNA-sequence variants. As a demonstration of practicality, we applied as-proposed CAD system to identify low variant allele frequency (VAF) in a synthetic template (0.1% VAF) and human genomic DNA (1% VAF). This work promises complete guidance for the design of enzyme-based nucleic acid analysis.
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Affiliation(s)
- Li Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yufeng Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yongcan Guo
- Clinical Laboratory of Traditional Chinese Medicine Hospital Affiliated to Southwest Medical University, Luzhou, 646000, PR China
| | - Huajian Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Wen Yu
- Clinical Laboratory of Chongqing University Cancer Hospital, Chongqing, 400016, PR China
| | - Zhang Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
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5
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Elskens J, Madder A. Crosslinker-modified nucleic acid probes for improved target identification and biomarker detection. RSC Chem Biol 2021; 2:410-422. [PMID: 34458792 PMCID: PMC8341421 DOI: 10.1039/d0cb00236d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/11/2021] [Indexed: 01/02/2023] Open
Abstract
Understanding the intricate interaction pattern of nucleic acids with other molecules is essential to gain further insight in biological processes and disease mechanisms. To this end, a multitude of hybridization-based assays have been designed that rely on the non-covalent recognition between complementary nucleic acid sequences. However, the ephemeral nature of these interactions complicates straightforward analysis as low efficiency and specificity are rule rather than exception. By covalently locking nucleic acid interactions by means of a crosslinking agent, the overall efficiency, specificity and selectivity of hybridization-based assays could be increased. In this mini-review we highlight methodologies that exploit the use of crosslinker-modified nucleic acid probes for interstrand nucleic acid crosslinking with the objective to study, detect and identify important targets as well as nucleic acid sequences that can be considered relevant biomarkers. We emphasize on the usefulness and advantages of crosslinking agents and elaborate on the chemistry behind the crosslinking reactions they induce.
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Affiliation(s)
- Joke Elskens
- Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 Building S4 9000 Ghent Belgium +32-9-264-49-98 +32-9-264-44-72
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 Building S4 9000 Ghent Belgium +32-9-264-49-98 +32-9-264-44-72
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6
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Bai S, Xu B, Zhang Y, Zhang Y, Dang H, Yang S, Zuo C, Zhang L, Li J, Xie G. Tuning the specificity of DNA probes using bulge-loops for low-abundance SNV detection. Biosens Bioelectron 2020; 154:112092. [DOI: 10.1016/j.bios.2020.112092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/05/2020] [Accepted: 02/11/2020] [Indexed: 12/15/2022]
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7
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Machyna M, Kiefer L, Simon MD. Enhanced nucleotide chemistry and toehold nanotechnology reveals lncRNA spreading on chromatin. Nat Struct Mol Biol 2020; 27:297-304. [PMID: 32157249 DOI: 10.1038/s41594-020-0390-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/31/2020] [Indexed: 12/12/2022]
Abstract
Understanding the targeting and spreading patterns of long non-coding RNAs (lncRNAs) on chromatin requires a technique that can detect both high-intensity binding sites and reveal genome-wide changes in spreading patterns with high precision and confidence. Here we determine lncRNA localization using biotinylated locked nucleic acid (LNA)-containing oligonucleotides with toehold architecture capable of hybridizing to target RNA through strand-exchange reaction. During hybridization, a protecting strand competitively displaces contaminating species, leading to highly specific RNA capture of individual RNAs. Analysis of Drosophila roX2 lncRNA using this approach revealed that heat shock, unlike the unfolded protein response, leads to reduced spreading of roX2 on the X chromosome, but surprisingly also to relocalization to sites on autosomes. Our results demonstrate that this improved hybridization capture approach can reveal previously uncharacterized changes in the targeting and spreading of lncRNAs on chromatin.
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Affiliation(s)
- Martin Machyna
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA.,Chemical Biology Institute, Yale University, West Haven, CT, USA
| | - Lea Kiefer
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA.,Chemical Biology Institute, Yale University, West Haven, CT, USA
| | - Matthew D Simon
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA. .,Chemical Biology Institute, Yale University, West Haven, CT, USA.
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8
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Askary A, Sanchez-Guardado L, Linton JM, Chadly DM, Budde MW, Cai L, Lois C, Elowitz MB. In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription. Nat Biotechnol 2020; 38:66-75. [PMID: 31740838 PMCID: PMC6954335 DOI: 10.1038/s41587-019-0299-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 09/23/2019] [Accepted: 09/28/2019] [Indexed: 12/12/2022]
Abstract
Molecular barcoding technologies that uniquely identify single cells are hampered by limitations in barcode measurement. Readout by sequencing does not preserve the spatial organization of cells in tissues, whereas imaging methods preserve spatial structure but are less sensitive to barcode sequence. Here we introduce a system for image-based readout of short (20-base-pair) DNA barcodes. In this system, called Zombie, phage RNA polymerases transcribe engineered barcodes in fixed cells. The resulting RNA is subsequently detected by fluorescent in situ hybridization. Using competing match and mismatch probes, Zombie can accurately discriminate single-nucleotide differences in the barcodes. This method allows in situ readout of dense combinatorial barcode libraries and single-base mutations produced by CRISPR base editors without requiring barcode expression in live cells. Zombie functions across diverse contexts, including cell culture, chick embryos and adult mouse brain tissue. The ability to sensitively read out compact and diverse DNA barcodes by imaging will facilitate a broad range of barcoding and genomic recording strategies.
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Affiliation(s)
- Amjad Askary
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Luis Sanchez-Guardado
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - James M Linton
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Duncan M Chadly
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Mark W Budde
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Carlos Lois
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Howard Hughes Medical Institute and Department of Applied Physics, California Institute of Technology, Pasadena, CA, USA.
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9
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Abstract
Recent advances in localisation-based super-resolution microscopy have enabled researchers to visualise single molecular features down to individual molecular components (~5 nm), but do not yet allow manipulation of single-molecule targets in a user-prescribed, context-dependent manner. Here we report an “Action-PAINT” strategy for super-resolution labelling upon visualisation on single molecules. This approach monitors and localises DNA binding events in real-time with DNA-PAINT, and upon visualisation of binding to a desired location, photo-crosslinks the DNA to affix the molecular label. We showed the efficiency of 3-cyanovinylcarbazole nucleoside (CNVK) photo-inducible crosslinking on single molecular targets and developed a software package for real-time super-resolution imaging and crosslinking control. We then benchmarked our super-resolution labelling method on synthetic DNA nanostructures and demonstrated targeted multi-point labelling on various complex patterns with 30 nm selectivity. Finally, we performed targeted in situ labelling on fixed microtubule samples with 40 nm target size and custom-controlled, sub-diffraction spacing.
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10
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Nejad MI, Guo X, Housh K, Nel C, Yang Z, Price NE, Wang Y, Gates KS. Preparation and Purification of Oligodeoxynucleotide Duplexes Containing a Site-Specific, Reduced, Chemically Stable Covalent Interstrand Cross-Link Between a Guanine Residue and an Abasic Site. Methods Mol Biol 2019; 1973:163-175. [PMID: 31016701 DOI: 10.1007/978-1-4939-9216-4_10] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Methods for the preparation of DNA duplexes containing interstrand covalent cross-links may facilitate research in the fields of biochemistry, molecular biology, nanotechnology, and materials science. Here we report methods for the synthesis and isolation of DNA duplexes containing a site-specific, chemically stable, reduced covalent interstrand cross-link between a guanine residue and an abasic site. The method uses experimental techniques and equipment that are common in most biochemical laboratories and inexpensive, commercially available oligonucleotides and reagents.
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Affiliation(s)
| | - Xu Guo
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Kurt Housh
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Christopher Nel
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Zhiyu Yang
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Nathan E Price
- Department of Chemistry, University of California Riverside, Riverside, CA, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside, Riverside, CA, USA
| | - Kent S Gates
- Department of Chemistry, University of Missouri, Columbia, MO, USA. .,Department of Biochemistry, University of Missouri, Columbia, MO, USA.
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11
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Wan YH, Zhou YJ, Xiao KJ, Nie CP, Zhang J, Liu C, Chen TT, Chu X. Target-assisted self-cleavage DNAzyme probes for multicolor simultaneous imaging of tumor-related microRNAs with signal amplification. Chem Commun (Camb) 2019; 55:3278-3281. [DOI: 10.1039/c9cc00451c] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel and highly selective signal amplification strategy was developed based on target-assisted self-cleavage DNAzyme probes for imaging of miRNA-222 and miRNA-223.
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Affiliation(s)
- Yuan-Hui Wan
- Institute of Chemical Biology and Nanomedicine
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
| | - Yu-Jie Zhou
- Institute of Chemical Biology and Nanomedicine
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
| | - Ke-Jing Xiao
- Institute of Chemical Biology and Nanomedicine
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
| | - Cun-Peng Nie
- Institute of Chemical Biology and Nanomedicine
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
| | - Juan Zhang
- Institute of Chemical Biology and Nanomedicine
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
| | - Chang Liu
- Institute of Chemical Biology and Nanomedicine
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
| | - Ting-Ting Chen
- Institute of Chemical Biology and Nanomedicine
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
| | - Xia Chu
- Institute of Chemical Biology and Nanomedicine
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
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12
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Guo X, Nejad MI, Gu LQ, Gates KS. Selective covalent capture of a DNA sequence corresponding to a cancer-driving C>G mutation in theKRASgene by a chemically reactive probe: optimizing a cross-linking reaction with non-canonical duplex structures. RSC Adv 2019; 9:32804-32810. [PMID: 35529740 PMCID: PMC9073178 DOI: 10.1039/c9ra08009k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/07/2019] [Indexed: 11/21/2022] Open
Abstract
A covalent cross-linking reaction used for selective capture of a disease-relevant DNA sequence.
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Affiliation(s)
- Xu Guo
- Department of Chemistry
- University of Missouri
- Columbia
- USA
| | | | - Li-Qun Gu
- Department of Bioengineering
- Dalton Cardiovascular Research Center
- University of Missouri
- Columbia
- USA
| | - Kent S. Gates
- Department of Chemistry
- University of Missouri
- Columbia
- USA
- Department of Biochemistry
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13
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Shi R, Nejad MI, Zhang X, Gu LQ, Gates KS. Generation and Single-Molecule Characterization of a Sequence-Selective Covalent Cross-Link Mediated by Mechlorethamine at a C–C Mismatch in Duplex DNA for Discrimination of a Disease-Relevant Single Nucleotide Polymorphism. Bioconjug Chem 2018; 29:3810-3816. [DOI: 10.1021/acs.bioconjchem.8b00663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Ruicheng Shi
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | | | - Xinyue Zhang
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Li-Qun Gu
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
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14
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Xiao X, Wu T, Xu L, Chen W, Zhao M. A branch-migration based fluorescent probe for straightforward, sensitive and specific discrimination of DNA mutations. Nucleic Acids Res 2017; 45:e90. [PMID: 28201758 PMCID: PMC5449635 DOI: 10.1093/nar/gkx117] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 02/08/2017] [Indexed: 12/29/2022] Open
Abstract
Genetic mutations are important biomarkers for cancer diagnostics and surveillance. Preferably, the methods for mutation detection should be straightforward, highly specific and sensitive to low-level mutations within various sequence contexts, fast and applicable at room-temperature. Though some of the currently available methods have shown very encouraging results, their discrimination efficiency is still very low. Herein, we demonstrate a branch-migration based fluorescent probe (BM probe) which is able to identify the presence of known or unknown single-base variations at abundances down to 0.3%-1% within 5 min, even in highly GC-rich sequence regions. The discrimination factors between the perfect-match target and single-base mismatched target are determined to be 89-311 by measurement of their respective branch-migration products via polymerase elongation reactions. The BM probe not only enabled sensitive detection of two types of EGFR-associated point mutations located in GC-rich regions, but also successfully identified the BRAF V600E mutation in the serum from a thyroid cancer patient which could not be detected by the conventional sequencing method. The new method would be an ideal choice for high-throughput in vitro diagnostics and precise clinical treatment.
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Affiliation(s)
- Xianjin Xiao
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tongbo Wu
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lei Xu
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wei Chen
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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15
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Nejad MI, Shi R, Zhang X, Gu LQ, Gates KS. Sequence-Specific Covalent Capture Coupled with High-Contrast Nanopore Detection of a Disease-Derived Nucleic Acid Sequence. Chembiochem 2017; 18:1383-1386. [PMID: 28422400 PMCID: PMC6139021 DOI: 10.1002/cbic.201700204] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 01/12/2023]
Abstract
Hybridization-based methods for the detection of nucleic acid sequences are important in research and medicine. Short probes provide sequence specificity, but do not always provide a durable signal. Sequence-specific covalent crosslink formation can anchor probes to target DNA and might also provide an additional layer of target selectivity. Here, we developed a new crosslinking reaction for the covalent capture of specific nucleic acid sequences. This process involved reaction of an abasic (Ap) site in a probe strand with an adenine residue in the target strand and was used for the detection of a disease-relevant T→A mutation at position 1799 of the human BRAF kinase gene sequence. Ap-containing probes were easily prepared and displayed excellent specificity for the mutant sequence under isothermal assay conditions. It was further shown that nanopore technology provides a high contrast-in essence, digital-signal that enables sensitive, single-molecule sensing of the cross-linked duplexes.
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Affiliation(s)
- Maryam Imani Nejad
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Ruicheng Shi
- Department of Bioengineering and, Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - Xinyue Zhang
- Department of Bioengineering and, Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - Li-Qun Gu
- Department of Bioengineering and, Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - Kent S Gates
- Departments of Chemistry and Biochemistry, University of Missouri, Columbia, MO, 65211, USA
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16
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Wolfe BR, Porubsky NJ, Zadeh JN, Dirks RM, Pierce NA. Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering. J Am Chem Soc 2017; 139:3134-3144. [DOI: 10.1021/jacs.6b12693] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Brian R. Wolfe
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Nicholas J. Porubsky
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Joseph N. Zadeh
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Robert M. Dirks
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Niles A. Pierce
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
- Division of Engineering & Applied Science, California Institute of Technology, Pasadena, California 91125, United States
- Weatherall
Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
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17
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Rezzoug F, Thomas SD, Rouchka EC, Miller DM. Discovery of a Family of Genomic Sequences Which Interact Specifically with the c-MYC Promoter to Regulate c-MYC Expression. PLoS One 2016; 11:e0161588. [PMID: 27551915 PMCID: PMC4995011 DOI: 10.1371/journal.pone.0161588] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/08/2016] [Indexed: 12/14/2022] Open
Abstract
G-quadruplex forming sequences are particularly enriched in the promoter regions of eukaryotic genes, especially of oncogenes. One of the most well studied G-quadruplex forming sequences is located in the nuclease hypersensitive element (NHE) III1 of the c-MYC promoter region. The oncoprotein c-MYC regulates a large array of genes which play important roles in growth regulation and metabolism. It is dysregulated in >70% of human cancers. The silencer NHEIII1 located upstream of the P1 promoter regulates up-to 80% of c-MYC transcription and includes a G-quadruplex structure (Pu27) that is required for promoter inhibition. We have identified, for the first time, a family of seventeen G-quadruplex-forming motifs with >90% identity with Pu27, located on different chromosomes throughout the human genome, some found near or within genes involved in stem cell maintenance or neural cell development. Notably, all members of the Pu27 family interact specifically with NHEIII1 sequence, in vitro. Crosslinking studies demonstrate that Pu27 oligonucleotide binds specifically to the C-rich strand of the NHEIII1 resulting in the G-quadruplex structure stabilization. Pu27 homologous sequences (Pu27-HS) significantly inhibit leukemic cell lines proliferation in culture. Exposure of U937 cells to the Pu27-HS induces cell growth inhibition associated with cell cycle arrest that is most likely due to downregulation of c-MYC expression at the RNA and/or protein levels. Expression of SOX2, another gene containing a Pu27-HS, was affected by Pu27-HS treatment as well. Our data suggest that the oligonucleotides encoding the Pu27 family target complementary DNA sequences in the genome, including those of the c-MYC and SOX2 promoters. This effect is most likely cell type and cell growth condition dependent. The presence of genomic G-quadruplex-forming sequences homologous to Pu27 of c-MYC silencer and the fact that they interact specifically with the parent sequence suggest a common regulatory mechanism for genes whose promoters contain these sequences.
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Affiliation(s)
- Francine Rezzoug
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville Kentucky, United States of America
- * E-mail: (FR); (DMM)
| | - Shelia D. Thomas
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville Kentucky, United States of America
| | - Eric C. Rouchka
- Department of Computer Engineering and Computer Science, Speed School of Engineering, University of Louisville, Kentucky, United States of America
| | - Donald M. Miller
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville Kentucky, United States of America
- * E-mail: (FR); (DMM)
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18
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Chandrasekaran AR, Wady H, Subramanian HKK. Nucleic Acid Nanostructures for Chemical and Biological Sensing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:2689-2700. [PMID: 27040036 DOI: 10.1002/smll.201503854] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 01/23/2016] [Indexed: 06/05/2023]
Abstract
The nanoscale features of DNA have made it a useful molecule for bottom-up construction of nanomaterials, for example, two- and three-dimensional lattices, nanomachines, and nanodevices. One of the emerging applications of such DNA-based nanostructures is in chemical and biological sensing, where they have proven to be cost-effective, sensitive and have shown promise as point-of-care diagnostic tools. DNA is an ideal molecule for sensing not only because of its specificity but also because it is robust and can function under a broad range of biologically relevant temperatures and conditions. DNA nanostructure-based sensors provide biocompatibility and highly specific detection based on the molecular recognition properties of DNA. They can be used for the detection of single nucleotide polymorphism and to sense pH both in solution and in cells. They have also been used to detect clinically relevant tumor biomarkers. In this review, recent advances in DNA-based biosensors for pH, nucleic acids, tumor biomarkers and cancer cell detection are introduced. Some challenges that lie ahead for such biosensors to effectively compete with established technologies are also discussed.
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Affiliation(s)
| | - Heitham Wady
- Upstate Medical University, State University of New York, Syracuse, NY, 13210, USA
| | - Hari K K Subramanian
- Department of Mechanical Engineering, University of California, Riverside, CA, 92521, USA
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19
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Li X, Ye S, Luo X. Sensitive SERS detection of miRNA via enzyme-free DNA machine signal amplification. Chem Commun (Camb) 2016; 52:10269-72. [DOI: 10.1039/c6cc04391g] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Coupling SERS technology with a DNA fueled molecular machine, an enzyme-free signal amplified detection platform is described for miRNA detection.
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Affiliation(s)
- Xiaoxiao Li
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Sujuan Ye
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Xiliang Luo
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
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20
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Wolfe BR, Pierce NA. Sequence Design for a Test Tube of Interacting Nucleic Acid Strands. ACS Synth Biol 2015; 4:1086-100. [PMID: 25329866 DOI: 10.1021/sb5002196] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We describe an algorithm for designing the equilibrium base-pairing properties of a test tube of interacting nucleic acid strands. A target test tube is specified as a set of desired "on-target" complexes, each with a target secondary structure and target concentration, and a set of undesired "off-target" complexes, each with vanishing target concentration. Sequence design is performed by optimizing the test tube ensemble defect, corresponding to the concentration of incorrectly paired nucleotides at equilibrium evaluated over the ensemble of the test tube. To reduce the computational cost of accepting or rejecting mutations to a random initial sequence, the structural ensemble of each on-target complex is hierarchically decomposed into a tree of conditional subensembles, yielding a forest of decomposition trees. Candidate sequences are evaluated efficiently at the leaf level of the decomposition forest by estimating the test tube ensemble defect from conditional physical properties calculated over the leaf subensembles. As optimized subsequences are merged toward the root level of the forest, any emergent defects are eliminated via ensemble redecomposition and sequence reoptimization. After successfully merging subsequences to the root level, the exact test tube ensemble defect is calculated for the first time, explicitly checking for the effect of the previously neglected off-target complexes. Any off-target complexes that form at appreciable concentration are hierarchically decomposed, added to the decomposition forest, and actively destabilized during subsequent forest reoptimization. For target test tubes representative of design challenges in the molecular programming and synthetic biology communities, our test tube design algorithm typically succeeds in achieving a normalized test tube ensemble defect ≤1% at a design cost within an order of magnitude of the cost of test tube analysis.
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Affiliation(s)
- Brian R. Wolfe
- Division of Biology and Biological
Engineering and ‡Division of Engineering and Applied
Science, California Institute of Technology, Pasadena, California 91125, United States
| | - Niles A. Pierce
- Division of Biology and Biological
Engineering and ‡Division of Engineering and Applied
Science, California Institute of Technology, Pasadena, California 91125, United States
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21
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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.
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22
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Causa F, Aliberti A, Cusano AM, Battista E, Netti PA. Supramolecular Spectrally Encoded Microgels with Double Strand Probes for Absolute and Direct miRNA Fluorescence Detection at High Sensitivity. J Am Chem Soc 2015; 137:1758-61. [DOI: 10.1021/ja511644b] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Filippo Causa
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
- Interdisciplinary
Research Centre on Biomaterials (CRIB), University “‘Federico II”’, Piazzale Tecchio 80, 80125 Naples, Italy
- Dipartimento
di Ingegneria Chimica, dei Materiali e della Produzione Industriale
(DICMAPI), University “‘Federico II”’, Piazzale
Tecchio 80, 80125 Naples, Italy
| | - Anna Aliberti
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Angela M. Cusano
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Edmondo Battista
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Paolo A. Netti
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
- Interdisciplinary
Research Centre on Biomaterials (CRIB), University “‘Federico II”’, Piazzale Tecchio 80, 80125 Naples, Italy
- Dipartimento
di Ingegneria Chimica, dei Materiali e della Produzione Industriale
(DICMAPI), University “‘Federico II”’, Piazzale
Tecchio 80, 80125 Naples, Italy
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23
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Zhang H, Liu Y, Gao J, Zhen J. A sensitive SERS detection of miRNA using a label-free multifunctional probe. Chem Commun (Camb) 2015; 51:16836-9. [DOI: 10.1039/c5cc06225j] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A novel surface enhanced Raman scattering (SERS) detection method is fabricated for miRNA based on a smart multifunctional probe for dual cyclical nucleic acid strand-displacement polymerization (CNDP).
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Affiliation(s)
- Hao Zhang
- Department of Chemistry
- Qilu University of Technology
- Jinan 250353
- China
| | - Yu Liu
- Department of Chemistry
- Qilu University of Technology
- Jinan 250353
- China
| | - Jian Gao
- Department of Chemistry
- Qilu University of Technology
- Jinan 250353
- China
| | - Junhui Zhen
- School of Medicine
- Shandong University
- Jinan 250012
- China
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24
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Zhang D, Huang T, Lukeman PS, Paukstelis PJ. Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad. Nucleic Acids Res 2014; 42:13422-9. [PMID: 25389267 PMCID: PMC4245957 DOI: 10.1093/nar/gku1122] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We have determined the 1.50 Å crystal structure of the DNA decamer, d(CCA(CNV)KGCGTGG) ((CNV)K, 3-cyanovinylcarbazole), which forms a G-quadruplex structure in the presence of Ba(2+). The structure contains several unique features including a bulged nucleotide and the first crystal structure observation of a C-tetrad. The structure reveals that water molecules mediate contacts between the divalent cations and the C-tetrad, allowing Ba(2+) ions to occupy adjacent steps in the central ion channel. One ordered Mg(2+) facilitates 3'-3' stacking of two quadruplexes in the asymmetric unit, while the bulged nucleotide mediates crystal contacts. Despite the high diffraction limit, the first four nucleotides including the (CNV)K nucleoside are disordered though they are still involved in crystal packing. This work suggests that the bulky hydrophobic groups may locally influence the formation of non-Watson-Crick structures from otherwise complementary sequences. These observations lead to the intriguing possibility that certain types of DNA damage may act as modulators of G-quadruplex formation.
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Affiliation(s)
- Diana Zhang
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure and Organization, Maryland NanoCenter, University of Maryland, College Park, MD 20742, USA
| | - Terry Huang
- Chemistry and Biochemistry Department, California State Polytechnic University, 3801 West Temple Avenue, Pomona, CA 91768, USA
| | - Philip S. Lukeman
- Chemistry Department, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Paul J. Paukstelis
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure and Organization, Maryland NanoCenter, University of Maryland, College Park, MD 20742, USA,To whom correspondence should be addressed. Tel: 301.405.9933; Fax: 301.314.0386;
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25
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Nowak-Karnowska J, Chebib Z, Milecki J, Franzen S, Skalski B. Highly efficient fluorescent interstrand photo-crosslinking of DNA duplexes labeled with 5-fluoro-4-thio-2'-o-methyluridine. Chembiochem 2014; 15:2045-9. [PMID: 25111776 DOI: 10.1002/cbic.201402182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Indexed: 02/03/2023]
Abstract
The formation of a fluorescent photoadduct between 5-fluoro-4-thiouridine ((FS) U), in the sequence context 5'-A(FS) UA-3' and incorporated into a synthetic oligonucleotide either at its 3'- or 5'-end, and one of the thymines of the TAT motif in a complementary target DNA strand led to photo-crosslinking of the two strands for several oligonucleotide constructs. Enzymatic digestion, MS, UV, and fluorescence spectral analyses of the interstrand crosslinked oligonucleotides revealed the identity of the thymidine that participates in the photo-crosslinking reaction as well as the diastereomeric structures of the crosslinks. The proposed pathways of interstrand photo-crosslinking are supported by experiments with isotopically labeled oligonucleotide constructs and visualized by means of molecular dynamics simulations.
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Affiliation(s)
- Joanna Nowak-Karnowska
- Centre of Advanced Technology, Adam Mickiewicz University, Grunwaldzka 6, 60-780 Poznań (Poland)
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26
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Larkey NE, Almlie CK, Tran V, Egan M, Burrows SM. Detection of miRNA Using a Double-Strand Displacement Biosensor with a Self-Complementary Fluorescent Reporter. Anal Chem 2014; 86:1853-63. [DOI: 10.1021/ac403866g] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Nicholas E. Larkey
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - C. Kyle Almlie
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Victoria Tran
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Marianne Egan
- School of Design and Human Environment, Oregon State University, 230 Milam Hall, Corvallis, Oregon 97331, United States
| | - Sean M. Burrows
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
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