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Peng HC, Mohan S, Huq MT, Bull JA, Michaud T, Piercy TC, Hilber S, Wettasinghe AP, Slinker JD, Kreutz C, Stelling AL. Isotope-Edited Variable Temperature Infrared Spectroscopy for Measuring Transition Temperatures of Single A-T Watson-Crick Base Pairs in DNA Duplexes. Anal Chem 2024; 96:8868-8874. [PMID: 38775341 DOI: 10.1021/acs.analchem.4c00056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Experimental methods to determine transition temperatures for individual base pair melting events in DNA duplexes are lacking despite intense interest in these thermodynamic parameters. Here, we determine the dimensions of the thymine (T) C2═O stretching vibration when it is within the DNA duplex via isotopic substitutions at other atomic positions in the structure. First, we determined that this stretching state was localized enough to specific atoms in the molecule to make submolecular scale measurements of local structure and stability in high molecular weight complexes. Next, we develop a new isotope-edited variable temperature infrared method to measure melting transitions at various locations in a DNA structure. As an initial test of this "sub-molecular scale thermometer", we applied our T13C2 difference infrared signal to measure location-dependent melting temperatures (TmL) in a DNA duplex via variable temperature attenuated total reflectance Fourier transform infrared (VT-ATR-FTIR) spectroscopy. We report that the TmL of a single Watson-Crick A-T base pair near the end of an A-T rich sequence (poly T) is ∼34.9 ± 0.7°C. This is slightly lower than the TmL of a single base pair near the middle position of the poly T sequence (TmL ∼35.6±0.2°C). In addition, we also report that the TmL of a single Watson-Crick A-T base pair near the end of a 50% G-C sequence (12-mer) is ∼52.5 ± 0.3°C, which is slightly lower than the global melting Tm of the 12-mer sequence (TmL ∼54.0±0.9°C). Our results provide direct physical evidence for end fraying in DNA sequences with our novel spectroscopic methods.
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Affiliation(s)
- Hao-Che Peng
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Shrijaa Mohan
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Muhammad T Huq
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Julie A Bull
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Troy Michaud
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Turner C Piercy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Stefan Hilber
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck 6020, Austria
| | - Ashan P Wettasinghe
- Department of Physics, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jason D Slinker
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck 6020, Austria
| | - Allison L Stelling
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
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Cao B, Ii X, Zhang X, Wang B, Zhang Q, Wei X. Designing Uncorrelated Address Constrain for DNA Storage by DMVO Algorithm. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:866-877. [PMID: 32750895 DOI: 10.1109/tcbb.2020.3011582] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
At present, huge amounts of data are being produced every second, a situation that will gradually overwhelm current storage technology. DNA is a storage medium that features high storage density and long-term stability and is now considered to be a feasible storage solution. Errors are easily made during the sequencing and synthesis of DNA, however. In order to reduce the error rate, novel uncorrelated address constrain are reported, and a Damping Multi-Verse Optimizer (DMVO)algorithm is proposed to construct a set of DNA coding, which is used as the non-payload. The DMVO algorithm exchanges objects through black/white holes in order to achieve a stable state and adds damping factors as disturbances. Compared with previous work, the coding set obtained by the DMVO algorithm is larger in size and of higher quality. The results of this study reveal that the size of the DNA storage coding set obtained by the DMVO algorithm increased by 4-16 percent, and the variance of the melting temperature decreased by 3-18 percent.
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Abstract
Colloidal self-assembly refers to a solution-processed assembly of nanometer-/micrometer-sized, well-dispersed particles into secondary structures, whose collective properties are controlled by not only nanoparticle property but also the superstructure symmetry, orientation, phase, and dimension. This combination of characteristics makes colloidal superstructures highly susceptible to remote stimuli or local environmental changes, representing a prominent platform for developing stimuli-responsive materials and smart devices. Chemists are achieving even more delicate control over their active responses to various practical stimuli, setting the stage ready for fully exploiting the potential of this unique set of materials. This review addresses the assembly of colloids into stimuli-responsive or smart nanostructured materials. We first delineate the colloidal self-assembly driven by forces of different length scales. A set of concepts and equations are outlined for controlling the colloidal crystal growth, appreciating the importance of particle connectivity in creating responsive superstructures. We then present working mechanisms and practical strategies for engineering smart colloidal assemblies. The concepts underpinning separation and connectivity control are systematically introduced, allowing active tuning and precise prediction of the colloidal crystal properties in response to external stimuli. Various exciting applications of these unique materials are summarized with a specific focus on the structure-property correlation in smart materials and functional devices. We conclude this review with a summary of existing challenges in colloidal self-assembly of smart materials and provide a perspective on their further advances to the next generation.
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Affiliation(s)
- Zhiwei Li
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Qingsong Fan
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yadong Yin
- Department of Chemistry, University of California, Riverside, California 92521, United States
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Kotb OM, Brozhik DS, Verbenko VN, Gulevich EP, Ezhov VF, Karlin DL, Pak FA, Paston SV, Polyanichko AM, Khalikov AI, Chikhirzhina EV. Investigation of DNA Damage Induced by Proton and Gamma Radiation. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921020123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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Akulenkova EV, Demidov VN, Martynova AO, Paston SV. The Interaction of DNA with Phenanthroline and New Phenanthrocyanine Complexes of Zn(II). Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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6
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Development of a rapid field-applicable molecular diagnostic for knockdown resistance (kdr) markers in An. gambiae. Parasit Vectors 2018; 11:307. [PMID: 29776379 PMCID: PMC5960117 DOI: 10.1186/s13071-018-2893-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 05/09/2018] [Indexed: 01/02/2023] Open
Abstract
Background The spread of insecticide resistance (IR) is a major threat to vector control programmes for mosquito-borne diseases. Early detection of IR using diagnostic markers could help inform these programmes, especially in remote locations where gathering reliable bioassay data is challenging. Most current molecular tests for genetic IR markers are only suitable for use in well-equipped laboratory settings. There is an unmet need for field-applicable diagnostics. Methods A single-cartridge test was designed to detect key IR mutations in the major African vector of malaria, Anopheles gambiae. Developed on the portable, rapid, point-of-care compatible PCR platform - Genedrive® (genedrive® plc), the test comprises two assays which target single nucleotide polymorphisms (SNPs) in the voltage gated sodium channel (VGSC) gene that exert interactive effects on knockdown resistance (kdr): L1014F, L1014S and N1575Y. Results Distinct melt peaks were observed for each allele at each locus. Preliminary validation of these assays using a test panel of 70 An. gambiae samples showed complete agreement of our assays with the widely-used TaqMan assays, achieving a sensitivity and specificity of 100%. Conclusion Here we show the development of an insecticide resistance detection assay for use on the Genedrive® platform that has the potential to be the first field-applicable diagnostic for kdr.
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Chang CL, Fridman AS, Wartell RM, Hu CK, Lando DY. Relationship between calorimetric profiles and differential melting curves for natural DNAs. Int J Biol Macromol 2017; 102:591-598. [DOI: 10.1016/j.ijbiomac.2017.04.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 10/19/2022]
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Singh A, Singh N. DNA melting in the presence of molecular crowders. Phys Chem Chem Phys 2017; 19:19452-19460. [DOI: 10.1039/c7cp03624h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We study the opening of double stranded DNA (dsDNA) in the presence of molecular crowders using the Peyrard–Bishop–Dauxois (PBD) model.
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Affiliation(s)
- Amar Singh
- Department of Physics
- BITS Pilani
- Pilani Campus
- India
| | - Navin Singh
- Department of Physics
- BITS Pilani
- Pilani Campus
- India
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Chang CL, Fridman AS, Grigoryan IE, Galyuk EN, Murashko ON, Hu CK, Lando DY. Estimation of the diversity between DNA calorimetric profiles, differential melting curves and corresponding melting temperatures. Biopolymers 2016; 105:832-9. [PMID: 27422497 DOI: 10.1002/bip.22918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 06/28/2016] [Accepted: 07/13/2016] [Indexed: 11/08/2022]
Abstract
The Poland-Fixman-Freire formalism was adapted for modeling of calorimetric DNA melting profiles, and applied to plasmid pBR 322 and long random sequences. We studied the influence of the difference (HGC -HAT ) between the helix-coil transition enthalpies of AT and GC base pairs on the calorimetric melting profile and on normalized calorimetric melting profile. A strong alteration of DNA calorimetrical profile with HGC -HAT was demonstrated. In contrast, there is a relatively slight change in the normalized profiles and in corresponding ordinary (optical) normalized differential melting curves (DMCs). For fixed HGC -HAT , the average relative deviation (S) between DMC and normalized calorimetric profile, and the difference between their melting temperatures (Tcal -Tm ) are weakly dependent on peculiarities of the multipeak fine structure of DMCs. At the same time, both the deviation S and difference (Tcal -Tm ) enlarge with the temperature melting range of the helix-coil transition. It is shown that the local deviation between DMC and normalized calorimetric profile increases in regions of narrow peaks distant from the melting temperature.
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Affiliation(s)
- Chun-Ling Chang
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Alexander S Fridman
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, 220141, Belarus
| | | | - Elena N Galyuk
- Department of Bioorganic Chemistry, Belarusian State Medical University, Minsk, 220116, Belarus
| | - Oleg N Murashko
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Chin-Kun Hu
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan.,National Center for Theoretical Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan.,Business School, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Dmitri Y Lando
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan.,Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, 220141, Belarus
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