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Marcus AH, Matsika S, Heussman D, Sorour MI, Maurer J, Albrecht CS, Enkhbaatar L, Herbert P, Kistler KA, von Hippel PH. Spectroscopic approaches for studies of site-specific DNA base and backbone 'breathing' using exciton-coupled dimer-labeled DNA. ARXIV 2024:arXiv:2403.16251v2. [PMID: 38584614 PMCID: PMC10996769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA 'breathing') play a central role in such processes. Here we review the development and application of novel spectroscopic methods and analyses - both at the ensemble and single-molecule levels - to study structural and dynamic properties of exciton-coupled cyanine and fluorescent nucleobase analogue dimer-labeled DNA constructs at key positions involved in protein-DNA complex assembly and function. The exciton-coupled dimer probes act as 'sensors' of the local conformations adopted by the sugar-phosphate backbones and bases immediately surrounding the dimer probes. These methods can be used to study the mechanisms of protein binding and function at these sites.
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Affiliation(s)
- Andrew H. Marcus
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Dylan Heussman
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Mohammed I. Sorour
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Jack Maurer
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Claire S. Albrecht
- Center for Optical, Molecular and Quantum Science, Department of Physics, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Physics, and University of Oregon, Eugene, Oregon 97403
| | - Lulu Enkhbaatar
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Patrick Herbert
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
| | - Kurt A. Kistler
- Department of Chemistry, Brandywine Campus, The Pennsylvania State University, Media, Pennsylvania 19063
| | - Peter H. von Hippel
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, and University of Oregon, Eugene, Oregon 97403
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Albrecht CS, Scatena LF, von Hippel PH, Marcus AH. Two-photon excitation two-dimensional fluorescence spectroscopy (2PE-2DFS) of the fluorescent nucleobase 6-MI. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2024; 12863:1286305. [PMID: 39149416 PMCID: PMC11326479 DOI: 10.1117/12.3001802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Base stacking is fundamentally important to the stability of double-stranded DNA. However, few experiments can directly probe the local conformations and conformational fluctuations of the DNA bases. Here we report a new spectroscopic approach to study the local conformations of DNA bases using the UV-absorbing fluorescent guanine analogue, 6-methyl isoxanthopterin (6-MI), which can be used as a site-specific probe to label DNA. In these experiments, we apply a two-photon excitation (2PE) approach to two-dimensional fluorescence spectroscopy (2DFS), which is a fluorescence-detected nonlinear Fourier transform spectroscopy. In 2DFS, a repeating sequence of four collinear laser pulses (with center wavelength ~ 675 nm and relative phases swept at radio frequencies) is used to excite the lowest energy electronic-vibrational (vibronic) transitions of 6-MI (with center wavelength ~ 340 nm). The ensuing low flux fluorescence is phase-synchronously detected at the level of individual photons and as a function of inter-pulse delay. The 2PE transition pathways that give rise to electronically excited state populations include optical coherences between electronic ground and excited states and non-resonant (one-photon-excited) virtual states. Our results indicate that 2PE-2DFS experiments can provide information about the electronic-vibrational spectrum of the 6-MI monomer, in addition to the conformation-dependent exciton coupling between adjacent 6-MI monomers within a (6-MI)2 dimer. In principle, this approach can be used to determine the local base-stacking conformations of (6-MI)2 dimer-substituted DNA constructs.
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Affiliation(s)
- Claire S Albrecht
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
- Department of Physics, University of Oregon, Eugene, Oregon 97403
| | - Lawrence F Scatena
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
| | - Peter H von Hippel
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
| | - Andrew H Marcus
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
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Russel NS, Kodali G, Stanley RJ, Narayanan M. Screening for Novel Fluorescent Nucleobase Analogues Using Computational and Experimental Methods: 2-Amino-6-chloro-8-vinylpurine (2A6Cl8VP) as a Case Study. J Phys Chem B 2023; 127:7858-7871. [PMID: 37698525 DOI: 10.1021/acs.jpcb.3c03618] [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: 09/13/2023]
Abstract
Novel fluorescent nucleic acid base analogues (FBAs) with improved optical properties are needed in a variety of biological applications. 2-Amino-6-chloro-8-vinylpurine (2A6Cl8VP) is structural analogue of two existing highly fluorescent FBAs, 2-aminopurine (2AP) and 8-vinyladenine (8VA), and can therefore be expected to have similar base pairing as well as better optical properties compared to its counterparts. In order to determine the absorption and fluorescence properties of 2A6Cl8VP, as a first step, we used TD-DFT calculations and the polarizable continuum model for simulating the solvents and computationally predicted absorption and fluorescence maxima. To test the computational predictions, we also synthesized 2A6Cl8VP and measured its UV/vis absorbance, fluorescence emission, and fluorescence lifetime. The computationally predicted absorbance and fluorescence maxima of 2A6Cl8VP are in reasonable agreement to the experimental values and are significantly redshifted compared to 2AP and 8VA, allowing for its specific excitation. The fluorescence quantum yield of 2A6Cl8VP, however, is significantly lower than those of 2AP and 8VA. Overall, 2A6Cl8VP is a novel fluorescent nucleobase analogue, which can be useful in studying structural, biophysical, and biochemical applications.
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Affiliation(s)
- Nadim Shahriar Russel
- Department of Chemistry, Temple University, 1901 N. Broad Street, Philadelphia, Pennsylvania 19122, United States
| | - Goutham Kodali
- GlowDNA LLC., Malvern, Pennsylvania 19355, United States
| | - Robert J Stanley
- Department of Chemistry, Temple University, 1901 N. Broad Street, Philadelphia, Pennsylvania 19122, United States
| | - Madhavan Narayanan
- Department of Physical Sciences, Benedictine University, 5700 College Rd, Lisle, Illinois 60532, United States
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Determination of two-photon absorption in nucleobase analogues: a QR-DFT perspective. Photochem Photobiol Sci 2022; 21:529-543. [PMID: 35179700 DOI: 10.1007/s43630-022-00182-7] [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: 08/13/2021] [Accepted: 01/27/2022] [Indexed: 10/19/2022]
Abstract
With the prevalence of fluorescence spectroscopy in biological systems, and the benefits of two-photon absorption techniques, presented here is an assessment of the two-photon accessibility of modern fluorescent nucleobase analogues utilising quadratic response DFT. Due to the complex environment experienced by these nucleobases, the two-photon spectra of each analogue has been assessed in the presence of both [Formula: see text]-stacked and hydrogen-bonding interactions involving the canonical nucleobases. Findings suggest that the [Formula: see text]-stacking environment provides a more significant effect on the spectra of the analogues studies than a hydrogen-bonding environment; analogue structures presenting high two-photon cross-section values for one or more states coincide with polycyclic extensions to preserved canonical base structure, as observed in the qA family of analogues, while analogue structures more closely resembling the structure of the base in question present a much more muted spectra in comparison. Results from this investigation have also allowed for the derivation of a number of design rules for the development of potential, two-photon specific, analogues for future use in both imaging and potential photochemical activation.
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Ji H, Johnson NP, von Hippel PH, Marcus AH. Local DNA Base Conformations and Ligand Intercalation in DNA Constructs Containing Optical Probes. Biophys J 2019; 117:1101-1115. [PMID: 31474304 PMCID: PMC6818173 DOI: 10.1016/j.bpj.2019.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/31/2019] [Accepted: 08/05/2019] [Indexed: 01/18/2023] Open
Abstract
Understanding local conformations of DNA at the level of individual nucleic acid bases and base pairs is important for elucidating molecular processes that depend on DNA sequence. Here, we apply linear absorption and circular dichroism measurements to the study of local DNA conformations, using the guanine base analog 6-methyl isoxanthopterin (6-MI) as a structural probe. We show that the spectroscopic properties of this probe can provide detailed information about the average local base and basepair conformations as a function of the surrounding DNA sequence. Based on these results we apply a simple theoretical model to calculate the circular dichroism spectra of 6-MI-substituted DNA constructs and show that our model can be used to extract information about how the local conformations of the 6-MI probe are influenced by the local base or basepair environment. We also use this probe to examine the pathway for the insertion (intercalation) of a tethered acridine ligand (9-amino-6-chloro methoxyacridine) into duplex DNA. We show that this model intercalator interacts with duplex DNA by a "displacement insertion intercalation" mechanism, whereby the acridine moiety is inserted into the DNA structure and displaces the base located opposite its attachment site. These findings suggest that site-specifically positioned base analog probes can be used to characterize the molecular and structural details of binding ligand effects on local base stacking and unstacking reactions in single- and double-stranded DNA and thus may help to define the molecular mechanisms of DNA-protein interactions that involve the site-specific intercalation of aromatic amino acid side chains into genomic DNA.
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Affiliation(s)
- Huiying Ji
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon
| | - Neil P Johnson
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon
| | - Peter H von Hippel
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon
| | - Andrew H Marcus
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon; Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon.
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Johnson NP, Ji H, Steinberg TH, von Hippel PH, Marcus AH. Sequence-Dependent Conformational Heterogeneity and Proton-Transfer Reactivity of the Fluorescent Guanine Analogue 6-Methyl Isoxanthopterin (6-MI) in DNA. J Phys Chem B 2015; 119:12798-807. [PMID: 26368400 DOI: 10.1021/acs.jpcb.5b06361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The local conformations of individual nucleic acid bases in DNA are important components in processes fundamental to gene regulation. Fluorescent nucleic acid base analogues, which can be substituted for natural bases in DNA, can serve as useful spectroscopic probes of average local base conformation and conformational heterogeneity. Here we report excitation-emission peak shift (EES) measurements of the fluorescent guanine (G) analogue 6-methyl isoxanthoptherin (6-MI), both as a ribonucleotide monophosphate (NMP) in solution and as a site-specific substituent for G in various DNA constructs. Changes in the peak positions of the fluorescence spectra as a function of excitation energy indicate that distinct subpopulations of conformational states exist in these samples on time scales longer than the fluorescence lifetime. Our pH-dependent measurements of the 6-MI NMP in solution show that these states can be identified as protonated and deprotonated forms of the 6-MI fluorescent probe. We implement a simple two-state model, which includes four vibrationally coupled electronic levels to estimate the free energy change, the free energy of activation, and the equilibrium constant for the proton transfer reaction. These parameters vary in single-stranded and duplex DNA constructs, and also depend on the sequence context of flanking bases. Our results suggest that proton transfer in 6-MI-substituted DNA constructs is coupled to conformational heterogeneity of the probe base, and can be interpreted to suggest that Watson-Crick base pairing between 6-MI and its complementary cytosine in duplex DNA involves a "low-barrier-hydrogen-bond". These findings may be important in using the 6-MI probe to understand local base conformational fluctuations, which likely play a central role in protein-DNA and ligand-DNA interactions.
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Affiliation(s)
- Neil P Johnson
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States.,Oregon Center for Optics and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States
| | - Huiying Ji
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States.,Oregon Center for Optics and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States
| | - Thomas H Steinberg
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States
| | - Peter H von Hippel
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States
| | - Andrew H Marcus
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States.,Oregon Center for Optics and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States
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Saif M, Widom JR, Xu S, Abbey ER, Liu SY, Marcus AH. Electric Dipole Transition Moments and Solvent-Dependent Interactions of Fluorescent Boron-Nitrogen Substituted Indole Derivatives. J Phys Chem B 2015; 119:7985-93. [PMID: 26000556 DOI: 10.1021/acs.jpcb.5b03485] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescent analogues of the indole side chain of tryptophan can be useful spectroscopic probes of protein-protein and protein-DNA interactions. Here we present linear dichroism and solvent-dependent spectroscopic studies of two fluorescent analogues of indole, in which the organic C═C unit is substituted with the isosteric inorganic B-N unit. We studied the so-called "external" BN indole, which has C2v symmetry, and the "fused" BN indole with Cs symmetry. We performed a combination of absorption and fluorescence spectroscopy, ultraviolet linear dichroism (UV-LD) in stretched poly(ethylene) (PE) films, and quantum chemical calculations on both BN indole compounds. Our measurements allowed us to characterize the degree of alignment for both molecules in stretched PE films. We thus determined the orientations and magnitudes of the two lowest energy electric dipole transition moments (EDTMs) for external BN indole, and the two lowest energy EDTMs for fused BN indole within the 30 000-45 000 cm(-1) spectral range. We compared our experimental results to those of quantum chemical calculations using standard density functional theory (DFT). Our theoretical predictions for the low-energy EDTMs are in good agreement with our experimental data. The absorption and fluorescence spectra of the external and the fused BN indoles are sensitive to solvent polarity. Our results indicate that the fused BN indole experiences much greater solvation interactions with polar solvents than does the external BN indole.
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Affiliation(s)
- Mari Saif
- †Department of Chemistry and Biochemistry, Oregon Center for Optics, and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Julia R Widom
- ‡Department of Chemistry, University of Michigan at Ann Arbor, Ann Arbor, Michigan 48109, United States
| | - Senmiao Xu
- §Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Suzhou, Jiangsu 215000, China
| | - Eric R Abbey
- ∥Chemistry Department, Eastern Washington University, Cheney, Washington 99004, United States
| | - Shih-Yuan Liu
- ⊥Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Andrew H Marcus
- †Department of Chemistry and Biochemistry, Oregon Center for Optics, and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
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Raymer MG, Marcus AH, Widom JR, Vitullo DLP. Entangled Photon-Pair Two-Dimensional Fluorescence Spectroscopy (EPP-2DFS). J Phys Chem B 2013; 117:15559-75. [DOI: 10.1021/jp405829n] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. G. Raymer
- Oregon
Center for Optics and Department of Physics, University of Oregon, Eugene, Oregon 97403, United States
| | - Andrew H. Marcus
- Oregon
Center for Optics, Institute of Molecular Biology and Department of
Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Julia R. Widom
- Oregon
Center for Optics, Institute of Molecular Biology and Department of
Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Dashiell L. P. Vitullo
- Oregon
Center for Optics and Department of Physics, University of Oregon, Eugene, Oregon 97403, United States
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Single-molecule FRET and linear dichroism studies of DNA breathing and helicase binding at replication fork junctions. Proc Natl Acad Sci U S A 2013; 110:17320-5. [PMID: 24062430 DOI: 10.1073/pnas.1314862110] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA "breathing" is a thermally driven process in which base-paired DNA sequences transiently adopt local conformations that depart from their most stable structures. Polymerases and other proteins of genome expression require access to single-stranded DNA coding templates located in the double-stranded DNA "interior," and it is likely that fluctuations of the sugar-phosphate backbones of dsDNA that result in mechanistically useful local base pair opening reactions can be exploited by such DNA regulatory proteins. Such motions are difficult to observe in bulk measurements, both because they are infrequent and because they often occur on microsecond time scales that are not easy to access experimentally. We report single-molecule fluorescence experiments with polarized light, in which tens-of-microseconds rotational motions of internally labeled iCy3/iCy5 donor-acceptor Förster resonance energy transfer fluorophore pairs that have been rigidly inserted into the backbones of replication fork constructs are simultaneously detected using single-molecule Förster resonance energy transfer and single-molecule fluorescence-detected linear dichroism signals. Our results reveal significant local motions in the ∼100-μs range, a reasonable time scale for DNA breathing fluctuations of potential relevance for DNA-protein interactions. Moreover, we show that both the magnitudes and the relaxation times of these backbone breathing fluctuations are significantly perturbed by interactions of the fork construct with a nonprocessive, weakly binding bacteriophage T4-coded helicase hexamer initiation complex, suggesting that these motions may play a fundamental role in the initial binding, assembly, and function of the processive helicase-primase (primosome) component of the bacteriophage T4-coded DNA replication complex.
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