1
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Rudra S, Chauhan K, Singh AR, Kumar S. Force-induced melting of DNA hairpin: Unfolding pathways and phase diagrams. Phys Rev E 2023; 107:054501. [PMID: 37328992 DOI: 10.1103/physreve.107.054501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/27/2023] [Indexed: 06/18/2023]
Abstract
Using the exact enumeration technique, we have studied the force-induced melting of a DNA hairpin on the face centered cubic lattice for two different sequences which differ in terms of loop closing base pairs. The melting profiles obtained from the exact enumeration technique is consistent with the Gaussian network model and Langevin dynamics simulations. Probability distribution analysis based on the exact density of states revealed the microscopic details of the opening of the hairpin. We showed the existence of intermediate states near the melting temperature. We further showed that different ensembles used to model single-molecule force spectroscopy setups may give different force-temperature diagrams. We delineate the possible reasons for the observed discrepancies.
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Affiliation(s)
- Sumitra Rudra
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - Keerti Chauhan
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - Amit Raj Singh
- Department of Physics, Graphic Era Hill University, Dehradun 248002, India
| | - Sanjay Kumar
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
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2
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Li X, Dai X, Pan Y, Sun Y, Yang B, Chen K, Wang Y, Xu JF, Dong Y, Yang YR, Yan LT, Liu D. Studies on the Synergistic Effect of Tandem Semi-Stable Complementary Domains on Sequence-Defined DNA Block Copolymers. J Am Chem Soc 2022; 144:21267-21277. [DOI: 10.1021/jacs.2c08930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Xin Li
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xiaobin Dai
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yufan Pan
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yawei Sun
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (Huadong), Qingdao 258000, China
| | - Bo Yang
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Kun Chen
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - You Wang
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jiang-Fei Xu
- Key Lab of Organic Optoelectronics & Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yuanchen Dong
- CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Yuhe Renee Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Li-Tang Yan
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Dongsheng Liu
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
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3
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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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4
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Chauhan K, Singh AR, Kumar S, Granek R. Can one detect intermediate denaturation states of DNA sequences by following the equilibrium open-close dynamic fluctuations of a single base pair? J Chem Phys 2022; 156:164907. [PMID: 35489993 DOI: 10.1063/5.0088109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Melting of DNA sequences may occur through a few major intermediate states, whose influence on the melting curve has been discussed previously, while their effect on the kinetics has not been explored thoroughly. Here, we chose a simple DNA sequence, forming a hairpin in its native (zipped) state, and study it using molecular dynamic (MD) simulations and a model integrating the Gaussian network model with bond-binding energies-the Gaussian binding energy (GBE) model. We find two major partial denaturation states, a bubble state and a partial unzipping state. We demonstrate the influence of these two states on the closing-opening base pair dynamics, as probed by a tagged bond auto-correlation function (ACF). We argue that the latter is measured by fluorescence correlation spectroscopy experiments, in which one base of the pair is linked to a fluorescent dye, while the complementary base is linked to a quencher, similar to the experiment reported by Altan-Bonnet et al. [Phys. Rev. Lett. 90, 138101 (2003)]. We find that tagging certain base pairs at temperatures around the melting temperature results in a multi-step relaxation of the ACF, while tagging other base pairs leads to an effectively single-step relaxation, albeit non-exponential. Only the latter type of relaxation has been observed experimentally, and we suggest which of the other base pairs should be tagged in order to observe multi-step relaxation. We demonstrate that this behavior can be observed with other sequences and argue that the GBE can reliably predict these dynamics for very long sequences, where MD simulations might be limited.
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Affiliation(s)
- Keerti Chauhan
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - Amit Raj Singh
- Department of Physics, Graphic Era Hill University, Dehradun 248002, India
| | - Sanjay Kumar
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - Rony Granek
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and The Ilse Katz Institute for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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5
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Li F, Luo Y, Xi G, Fu J, Tu J. Single-Molecule Analysis of DNA structures using nanopore sensors. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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6
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Artificial nondirectional site-specific recombination systems. iScience 2022; 25:103716. [PMID: 35072008 PMCID: PMC8762395 DOI: 10.1016/j.isci.2021.103716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/23/2021] [Accepted: 12/29/2021] [Indexed: 11/22/2022] Open
Abstract
Site-specific recombination systems (SRSs) are widely used in studies on synthetic biology and related disciplines. Nondirectional SRSs can randomly trigger excision, integration, reversal, and translocation, which are effective tools to achieve large-scale genome recombination. In this study, we designed 6 new nondirectional SRSs named Vika/voxsym1-4 and Dre/roxsym1-2. All 6 artificial nondirectional SRSs were able to generate random deletion and inversion in Saccharomyces cerevisiae. Moreover, all six SRSs were orthogonal to Cre/loxPsym. The pairwise orthogonal nondirected SRSs can simultaneously initiate large-scale and independent gene recombination in two different regions of the genome, which could not be accomplished using previous orthogonal systems. These SRSs were found to be robust while working in the cells at different growth stages, as well as in the different spatial structure of the chromosome. These artificial pairwise orthogonal nondirected SRSs offer newfound potential for site-specific recombination in synthetic biology. Designed six new artificial nondirectional site-specific recombination systems Pairwise orthogonal nondirected recombination systems in yeast The deletion efficiency of systems is far greater than the inversion efficiency These nondirectional recombination systems were found to be robust
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7
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Ravichandran S, Razzaq M, Parveen N, Ghosh A, Kim KK. The effect of hairpin loop on the structure and gene expression activity of the long-loop G-quadruplex. Nucleic Acids Res 2021; 49:10689-10706. [PMID: 34450640 PMCID: PMC8501965 DOI: 10.1093/nar/gkab739] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/10/2021] [Accepted: 08/24/2021] [Indexed: 12/29/2022] Open
Abstract
G-quadruplex (G4), a four-stranded DNA or RNA structure containing stacks of guanine tetrads, plays regulatory roles in many cellular functions. So far, conventional G4s containing loops of 1–7 nucleotides have been widely studied. Increasing experimental evidence suggests that unconventional G4s, such as G4s containing long loops (long-loop G4s), play a regulatory role in the genome by forming a stable structure. Other secondary structures such as hairpins in the loop might thus contribute to the stability of long-loop G4s. Therefore, investigation of the effect of the hairpin-loops on the structure and function of G4s is required. In this study, we performed a systematic biochemical investigation of model G4s containing long loops with various sizes and structures. We found that the long-loop G4s are less stable than conventional G4s, but their stability increased when the loop forms a hairpin (hairpin-G4). We also verified the biological significance of hairpin-G4s by showing that hairpin-G4s present in the genome also form stable G4s and regulate gene expression as confirmed by in cellulo reporter assays. This study contributes to expanding the scope and diversity of G4s, thus facilitating future studies on the role of G4s in the human genome.
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Affiliation(s)
- Subramaniyam Ravichandran
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Maria Razzaq
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Nazia Parveen
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Ambarnil Ghosh
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
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8
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Bandyopadhyay D, Mishra PP. Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy. Front Mol Biosci 2021; 8:725541. [PMID: 34540899 PMCID: PMC8446445 DOI: 10.3389/fmolb.2021.725541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/30/2021] [Indexed: 12/02/2022] Open
Abstract
In addition to the canonical double helix form, DNA is known to be extrapolated into several other secondary structural patterns involving themselves in inter- and intramolecular type hydrogen bonding. The secondary structures of nucleic acids go through several stages of multiple, complex, and interconvertible heterogeneous conformations. The journey of DNA through these conformers has significant importance and has been monitored thoroughly to establish qualitative and quantitative information about the transition between the unfolded, folded, misfolded, and partially folded states. During this structural interconversion, there always exist specific populations of intermediates, which are short-lived or sometimes even do not accumulate within a heterogeneous population and are challenging to characterize using conventional ensemble techniques. The single-molecule FRET(sm-FRET) microspectroscopic method has the advantages to overcome these limitations and monitors biological phenomena transpiring at a measurable high rate and balanced stochastically over time. Thus, tracing the time trajectory of a particular molecule enables direct measurement of the rate constant of each transition step, including the intermediates that are hidden in the ensemble level due to their low concentrations. This review is focused on the advantages of the employment of single-molecule Forster's resonance energy transfer (sm-FRET), which is worthwhile to access the dynamic architecture and structural transition of various secondary structures that DNA adopts, without letting the donor of one molecule to cross-talk with the acceptor of any other. We have emphasized the studies performed to explore the states of folding and unfolding of several nucleic acid secondary structures, for example, the DNA hairpin, Holliday junction, G-quadruplex, and i-motif.
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Affiliation(s)
- Debolina Bandyopadhyay
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
- HBNI, Mumbai, India
| | - Padmaja P. Mishra
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
- HBNI, Mumbai, India
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9
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McAdorey A, Bennett HA, Vanloon J, Yan H. Use of anion-exchange HPLC to study DNA conformational polymorphism. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1180:122890. [PMID: 34403914 DOI: 10.1016/j.jchromb.2021.122890] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 10/20/2022]
Abstract
Anion-exchange chromatography carried out under non-denaturing conditions is a versatile tool to differentiate DNA conformations. In this work, the utility of this form of HPLC was demonstrated in four examples. The hairpin and duplex forms of d(CG)9 were readily resolved, which allowed for the studies of the influence of salt on the equilibrium of these two forms of secondary structures. Similarly, the minimum size of Tn in the loop region required for the sequence 5'-d(CCCAA-(T)n-TTGGG)-3' to form hairpin was established to be two nucleotides using anion-exchange HPLC and fluorescence resonance energy transfer. Furthermore, the efficiency of hybridization of partially self-complementary sequences d[(CG)6Nx] was readily monitored by non-denaturing anion-exchange HPLC. Finally, different structures adopted by quadruplex-forming sequences were resolved in the same manner.
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Affiliation(s)
- Alyssa McAdorey
- Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada
| | - Hayley-Ann Bennett
- Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada
| | - Jesse Vanloon
- Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada
| | - Hongbin Yan
- Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada.
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10
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Kumar M, Kaushik M, Kukreti S. Interaction of a photosensitizer methylene blue with various structural forms (cruciform, bulge duplex and hairpin) of designed DNA sequences. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 242:118716. [PMID: 32731146 DOI: 10.1016/j.saa.2020.118716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
Functionally important, local structural transitions in DNA generate various alternative conformations. Cruciform is one of such alternative DNA structures, usually targeted in genomes by various proteins. Symmetry elements in sequence as inverted repeats are the key factor for cruciform formation, facilitated by the presence of the AT-rich regions. Here, we used biophysical and biochemical techniques such as Gel electrophoresis, Circular dichroism (CD), and UV-thermal melting analysis to explore the structural status of the designed DNA sequences, which had potential to form cruciform structures under physiological conditions. The gel electrophoresis analysis revealed that the designed 53-mer DNA oligonucleotide sequence CR forms an intermolecular bulge duplex with flanking ends, while another sequence CRC adopts an intramolecular hairpin structure with flanking ends. Their equimolar complex (CRCRC) bestowed much-retarded migration due to the formation of a quite intriguing cruciform structure. CD studies confirmed that all the alternative structures (cruciform, bulge duplex, and hairpin with flanking ends) exhibit characteristics of B-DNA type conformation. A triphasic UV-thermal melting curve displayed by the complex formed by the equimolar ratio (CRCRC) is also suggestive of the formation of the cruciform structure. The interaction studies of CR, CRC, and their equimolar complex (1:1) with a photosensitizer methylene blue (MB) indicated that MB could not stabilize the discrete structures formed by CR and CRC sequences, however, the cruciform structure showed a quite significant increment in the melting temperature. Such studies facilitate our understanding of various secondary structures possibly present inside the cell and their interactions with drug/dye molecules.
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Affiliation(s)
- Mohan Kumar
- Department of Chemistry, University of Delhi, Delhi, India; Department of Chemistry, Shri Varshney College, Aligarh, Uttar Pradesh, India
| | - Mahima Kaushik
- Nano-bioconjugate Chemistry Lab, Cluster Innovation Centre, University of Delhi, Delhi, India
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11
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Nejad MI, Price NE, Haldar T, Lewis C, Wang Y, Gates KS. Interstrand DNA Cross-Links Derived from Reaction of a 2-Aminopurine Residue with an Abasic Site. ACS Chem Biol 2019; 14:1481-1489. [PMID: 31259519 DOI: 10.1021/acschembio.9b00208] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Efficient methods for the site-specific installation of structurally defined interstrand cross-links in duplex DNA may be useful in a wide variety of fields. The work described here developed a high-yield synthesis of chemically stable interstrand cross-links resulting from a reductive amination reaction between an abasic site and the noncanonical nucleobase 2-aminopurine in duplex DNA. Results from footprinting, liquid chromatography-mass spectrometry, and stability studies support the formation of an N2-alkylamine attachment between the 2-aminopurine residue and the Ap site. The reaction performs best when the 2-aminopurine residue on the opposing strand is offset 1 nt to the 5'-side of the abasic site. The cross-link confers substantial resistance to thermal denaturation (melting). The cross-linking reaction is fast (complete in 4 h), employs only commercially available reagents, and can be used to generate cross-linked duplexes in sufficient quantities for biophysical, structural, and DNA repair studies.
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Affiliation(s)
- Maryam Imani Nejad
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Nathan E. Price
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Tuhin Haldar
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Calvin Lewis
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Kent S. Gates
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
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12
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Liu YM, Fang XY, Fang F, Wu ZY. Investigation of hairpin DNA and chelerythrine interaction by a single bio-nanopore sensing interface. Analyst 2019; 144:4081-4085. [PMID: 31169284 DOI: 10.1039/c9an00113a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Chelerythrine (CHE) is one of the potential drugs for cancer treatments. The interaction between hairpin DNA and CHE has been investigated by spectral and mass spectrometry methods. In this paper, the stability of hairpin DNA with different loop bases and its interaction with CHE were explored with a single α-hemolysin (α-HL) nanopore sensing interface. The results showed that the characteristic current pulses not only relate to the loop composition changes of the hairpin DNA, but also provide interaction information between CHE and the hairpin DNA molecules. The dwell time of current pulses for hairpin DNA was significantly increased (hundreds of ms) due to the addition of CHE, and two characteristic current distributions were recognized for the hairpin with T3 and C3 loops. The two characteristic current groups could be ascribed to the hairpin DNA and the ones with CHE. This study indicates that it is possible to study the interaction between single CHE and single hairpin DNA molecules by the single-nanopore sensing interface as an alternative method to conventional spectrometric methods for therapeutic mechanism and drug screening purposes.
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Affiliation(s)
- Yuan-Min Liu
- Research Center for Analytical Sciences, Chemistry Department, College of Sciences, Northeastern University, Shenyang 110819, China.
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13
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Stellwagen NC, Stellwagen E. DNA Thermal Stability Depends on Solvent Viscosity. J Phys Chem B 2019; 123:3649-3657. [DOI: 10.1021/acs.jpcb.9b01217] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Nancy C. Stellwagen
- Department of Biochemistry, University of Iowa, 51 Newton Road, Iowa City, Iowa 52242, United States
| | - Earle Stellwagen
- Department of Biochemistry, University of Iowa, 51 Newton Road, Iowa City, Iowa 52242, United States
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14
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Zou X, Morganella S, Glodzik D, Davies H, Li Y, Stratton MR, Nik-Zainal S. Short inverted repeats contribute to localized mutability in human somatic cells. Nucleic Acids Res 2017; 45:11213-11221. [PMID: 28977645 PMCID: PMC5737083 DOI: 10.1093/nar/gkx731] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/14/2017] [Accepted: 08/10/2017] [Indexed: 01/09/2023] Open
Abstract
Selected repetitive sequences termed short inverted repeats (SIRs) have the propensity to form secondary DNA structures called hairpins. SIRs comprise palindromic arm sequences separated by short spacer sequences that form the hairpin stem and loop respectively. Here, we show that SIRs confer an increase in localized mutability in breast cancer, which is domain-dependent with the greatest mutability observed within spacer sequences (∼1.35-fold above background). Mutability is influenced by factors that increase the likelihood of formation of hairpins such as loop lengths (of 4-5 bp) and stem lengths (of 7-15 bp). Increased mutability is an intrinsic property of SIRs as evidenced by how almost all mutational processes demonstrate a higher rate of mutagenesis of spacer sequences. We further identified 88 spacer sequences showing enrichment from 1.8- to 90-fold of local mutability distributed across 283 sites in the genome that intriguingly, can be used to inform the biological status of a tumor.
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Affiliation(s)
- Xueqing Zou
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - Dominik Glodzik
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Helen Davies
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Yilin Li
- Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
| | | | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 9NB, UK
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15
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Lee HT, Carr CE, Khutsishvili I, Marky LA. Effect of Loop Length and Sequence on the Stability of DNA Pyrimidine Triplexes with TAT Base Triplets. J Phys Chem B 2017; 121:9175-9184. [PMID: 28875701 DOI: 10.1021/acs.jpcb.7b07591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report the thermodynamic contributions of loop length and loop sequence to the overall stability of DNA intramolecular pyrimidine triplexes. Two sets of triplexes were designed: in the first set, the C5 loop closing the triplex stem was replaced with 5'-CTnC loops (n = 1-5), whereas in the second set, both the duplex and triplex loops were replaced with a 5'-GCAA or 5'-AACG tetraloop. For the triplexes with a 5'-CTnC loop, the triplex with five bases in the loop has the highest stability relative to the control. A loop length lower than five compromises the strength of the base-pair stacks without decreasing the thermal stability, leading to a decreased enthalpy, whereas an increase in the loop length leads to a decreased enthalpy and a higher entropic penalty. The incorporation of the GCAA loop yielded more stable triplexes, whereas the incorporation of AACG in the triplex loop yielded a less stable triplex due to an unfavorable enthalpy term. Thus, addition of the GCAA tetraloop can cause an increase in the thermodynamics of the triplex without affecting the sequence or melting behavior and may result in an additional layer of genetic regulation.
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Affiliation(s)
- Hui-Ting Lee
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center , 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Carolyn E Carr
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center , 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Irine Khutsishvili
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center , 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Luis A Marky
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center , 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
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16
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Schöneweiß EC, Saccà B. The collective behavior of spring-like motifs tethered to a DNA origami nanostructure. NANOSCALE 2017; 9:4486-4496. [PMID: 28317958 DOI: 10.1039/c6nr08314e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Dynamic DNA nanotechnology relies on the integration of small switchable motifs at suitable positions of DNA nanostructures, thus enabling the manipulation of matter with nanometer spatial accuracy in a trigger-dependent fashion. Typical examples of such motifs are hairpins, whose elongation into duplexes can be used to perform long-range, translational movements. In this work, we used temperature-dependent FRET spectroscopy to determine the thermal stabilities of distinct sets of hairpins integrated into the central seam of a DNA origami structure. We then developed a hybrid spring model to describe the energy landscape of the tethered hairpins, combining the thermodynamic nearest-neighbor energy of duplex DNA with the entropic free energy of single-stranded DNA estimated using a worm-like chain approximation. We show that the organized scaffolding of multiple hairpins enhances the thermal stability of the device and that the coordinated action of the tethered motors can be used to mechanically unfold a G-quadruplex motif bound to the inner cavity of the origami structure, thus surpassing the operational capabilities of freely diffusing motors. Finally, we increased the complexity of device functionality through the insertion of two sets of parallel hairpins, resulting in four distinct states and in the reversible localization of desired molecules within the reconfigurable regions of the origami architecture.
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Affiliation(s)
- E-C Schöneweiß
- Centre for Medical Biotechnology (ZMB) and Centre for Nano Integration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätstr. 2, 45117 Essen, Germany.
| | - B Saccà
- Centre for Medical Biotechnology (ZMB) and Centre for Nano Integration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätstr. 2, 45117 Essen, Germany.
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17
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Singh AR, Granek R. Sufficient minimal model for DNA denaturation: Integration of harmonic scalar elasticity and bond energies. J Chem Phys 2017; 145:144101. [PMID: 27782499 DOI: 10.1063/1.4964285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We study DNA denaturation by integrating elasticity - as described by the Gaussian network model - with bond binding energies, distinguishing between different base pairs and stacking energies. We use exact calculation, within the model, of the Helmholtz free-energy of any partial denaturation state, which implies that the entropy of all formed "bubbles" ("loops") is accounted for. Considering base pair bond removal single events, the bond designated for opening is chosen by minimizing the free-energy difference for the process, over all remaining base pair bonds. Despite of its great simplicity, for several known DNA sequences our results are in accord with available theoretical and experimental studies. Moreover, we report free-energy profiles along the denaturation pathway, which allow to detect stable or meta-stable partial denaturation states, composed of bubble, as local free-energy minima separated by barriers. Our approach allows to study very long DNA strands with commonly available computational power, as we demonstrate for a few random sequences in the range 200-800 base-pairs. For the latter, we also elucidate the self-averaging property of the system. Implications for the well known breathing dynamics of DNA are elucidated.
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Affiliation(s)
- Amit Raj Singh
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
| | - Rony Granek
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
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18
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Wang J, Dong P, Wu W, Pan X, Liang X. High-throughput thermal stability assessment of DNA hairpins based on high resolution melting. J Biomol Struct Dyn 2016; 36:1-13. [PMID: 28024437 DOI: 10.1080/07391102.2016.1266967] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
On the basis of high-resolution melting, a high-throughput approach to measure melting temperatures (Tms) of short DNA hairpins was developed. With this method, Tms of thousands of triloop, tetraloop, and pentaloop hairpins involving various loop sequences and various closing base pairs (cbp) were obtained in hours. The stability of triloop hairpins decreased with the change of cbp (5'-3') in the order of c-g > g-c > t-a ≥ a-t, showing that the cbp of 5'-Pyr-Pur-3' (Pyr = pyrimidine, Pur = purine) contributed more stability than 5'-Pur-Pyr-3'. For tetraloop hairpins, GNNA, GNAB, and CNNG (N = A, G, C, or T; B = G, C, or T) were found to be highly stable irrespective of the cbp type. TNNA was also stable in both g-c and a-t families, while CGNA only in the c-g family. Pentaloop hairpins of cTGNAGg, cGNYNAg (Y = T or C) and cCGNNAg were exceptionally stable motifs. In most cases, pyrimidine-rich loops were more favorable to stabilize the whole structure than purine-rich ones. The present approach showed a good performance in assessing the thermal stability of large amounts of DNA hairpins comprehensively. These data are useful to understand the sequence dependence of the stability of DNA secondary structures and promising to improve the structure simulation by consummating basic databases.
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Affiliation(s)
- Jing Wang
- a College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Ping Dong
- a College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Wei Wu
- a College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Xiaoming Pan
- a College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Xingguo Liang
- a College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
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19
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Cao Y, Gao S, Yan Y, Bruist MF, Wang B, Guo X. Assembly of supramolecular DNA complexes containing both G-quadruplexes and i-motifs by enhancing the G-repeat-bearing capacity of i-motifs. Nucleic Acids Res 2016; 45:26-38. [PMID: 27899568 PMCID: PMC5224476 DOI: 10.1093/nar/gkw1049] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/17/2016] [Accepted: 10/20/2016] [Indexed: 12/13/2022] Open
Abstract
The single-step assembly of supramolecular complexes containing both i-motifs and G-quadruplexes (G4s) is demonstrated. This can be achieved because the formation of four-stranded i-motifs appears to be little affected by certain terminal residues: a five-cytosine tetrameric i-motif can bear ten-base flanking residues. However, things become complex when different lengths of guanine-repeats are added at the 3′ or 5′ ends of the cytosine-repeats. Here, a series of oligomers d(XGiXC5X) and d(XC5XGiX) (X = A, T or none; i < 5) are designed to study the impact of G-repeats on the formation of tetrameric i-motifs. Our data demonstrate that tetramolecular i-motif structure can tolerate specific flanking G-repeats. Assemblies of these oligonucleotides are polymorphic, but may be controlled by solution pH and counter ion species. Importantly, we find that the sequences d(TGiAC5) can form the tetrameric i-motif in large quantities. This leads to the design of two oligonucleotides d(TG4AC7) and d(TGBrGGBrGAC7) that self-assemble to form quadruplex supramolecules under certain conditions. d(TG4AC7) forms supramolecules under acidic conditions in the presence of K+ that are mainly V-shaped or ring-like containing parallel G4s and antiparallel i-motifs. d(TGBrGGBrGAC7) forms long linear quadruplex wires under acidic conditions in the presence of Na+ that consist of both antiparallel G4s and i-motifs.
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Affiliation(s)
- Yanwei Cao
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Shang Gao
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Yuting Yan
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Michael F Bruist
- Department of Chemistry & Biochemistry, University of the Sciences, 600 South 43rd Street, Philadelphia, PA 19104, USA
| | - Bing Wang
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Xinhua Guo
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
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20
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Ghimire S, Bork MA, Zhang H, Fanwick PE, Zeller M, Choi JH, McMillin DR. DNA binding of Pd(TC3), a conformable cationic porphyrin with a long-lived triplet state. Dalton Trans 2016; 45:14277-84. [PMID: 27534907 DOI: 10.1039/c6dt01918h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The goal of this work has been to synthesize and investigate Pd(TC3), an intercalating porphyrin that has conformable substituents capable of groove binding to B-form DNA. (TC3 denotes the doubly deprotonated form of 5,10,15,20-tetra[3-(3'-methylimidazolium-1'-yl)prop-1-yl]porphyrin.) Palladium(ii) is an apt choice for the central metal ion because it remains strictly four-coordinate and provides for a luminescent triplet excited state with a long lifetime. The DNA hosts are hairpin-forming sequences programmed to differ in base composition. Luminescence, absorbance, and circular dichroism results are consistent with the idea that congruent structural reorganization takes place at the host and ligand during uptake. Photoexcitation of DNA-bound Pd(TC3) generates a comparatively modest steady state concentration of singlet oxygen, due to a relatively slow reaction with molecular oxygen in solution. The sheer size of the substituent groups disfavors quenching, but groove-binding interactions compound the problem by inhibiting mobility. The results show how ligand design affects adduct structure as well as function.
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Affiliation(s)
- Srijana Ghimire
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA.
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21
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Braunlin W, Völker J, Plum GE, Breslauer KJ. DNA meter: Energy tunable, quantitative hybridization assay. Biopolymers 2016; 99:408-17. [PMID: 23529692 DOI: 10.1002/bip.22213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 01/15/2013] [Indexed: 11/06/2022]
Abstract
We describe a novel hybridization assay that employs a unique class of energy tunable, bulge loop-containing competitor strands (C*) that hybridize to a probe strand (P). Such initial "pre-binding" of a probe strand modulates its effective "availability" for hybridizing to a target site (T). More generally, the assay described here is based on competitive binding equilibria for a common probe strand (P) between such tunable competitor strands (C*) and a target strand (T). We demonstrate that loop variable, energy tunable families of C*P complexes exhibit enhanced discrimination between targets and mismatched targets, thereby reducing false positives/negatives. We refer to a C*P complex between a C* competitor single strand and the probe strand as a "tuning fork," since the C* strand exhibits branch points (forks) at the duplex-bulge interfaces within the complex. By varying the loop to create families of such "tuning forks," one can construct C*P "energy ladders" capable of resolving small differences within the target that may be of biological/functional consequence. The methodology further allows quantification of target strand concentrations, a determination heretofore not readily available by conventional hybridization assays. The dual ability of this tunable assay to discriminate and quantitate targets provides the basis for developing a technology we refer to as a "DNA Meter." Here we present data that establish proof-of-principle for an in solution version of such a DNA Meter. We envision future applications of this tunable assay that incorporate surface bound/spatially resolved DNA arrays to yield enhanced discrimination and sensitivity.
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Affiliation(s)
- William Braunlin
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Rd., Piscataway, NJ, 08854; Rational Affinity Devices, LLC
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22
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Schreck JS, Ouldridge TE, Romano F, Šulc P, Shaw LP, Louis AA, Doye JPK. DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization. Nucleic Acids Res 2015; 43:6181-90. [PMID: 26056172 PMCID: PMC4513862 DOI: 10.1093/nar/gkv582] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/22/2015] [Indexed: 12/29/2022] Open
Abstract
The effect of secondary structure on DNA duplex formation is poorly understood. Using oxDNA, a nucleotide level coarse-grained model of DNA, we study how hairpins influence the rate and reaction pathways of DNA hybridzation. We compare to experimental systems studied by Gao et al. (1) and find that 3-base pair hairpins reduce the hybridization rate by a factor of 2, and 4-base pair hairpins by a factor of 10, compared to DNA with limited secondary structure, which is in good agreement with experiments. By contrast, melting rates are accelerated by factors of ∼100 and ∼2000. This surprisingly large speed-up occurs because hairpins form during the melting process, and significantly lower the free energy barrier for dissociation. These results should assist experimentalists in designing sequences to be used in DNA nanotechnology, by putting limits on the suppression of hybridization reaction rates through the use of hairpins and offering the possibility of deliberately increasing dissociation rates by incorporating hairpins into single strands.
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Affiliation(s)
- John S Schreck
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Thomas E Ouldridge
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, UK Department of Mathematics, Imperial College, 180 Queen's Gate, London, SW7 2AZ, UK
| | - Flavio Romano
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Petr Šulc
- Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Liam P Shaw
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, UK
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, UK
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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23
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Talukder S, Sen S, Chakraborti P, Metzler R, Banik SK, Chaudhury P. Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA. J Chem Phys 2014; 140:125101. [PMID: 24697480 DOI: 10.1063/1.4869112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters is estimated for this purpose for three different DNA sequences. The analysis leads us to a better understanding of the sequence dependent nature of the breathing dynamics of hetero-polymeric DNA. Out of the 14 model parameters for DNA stability in the statistical Poland-Scheraga approach, the hydrogen bond interaction ε(hb)(AT) for an AT base pair and the ring factor ξ turn out to be the most sensitive parameters. In addition, the stacking interaction ε(st)(TA-TA) for an TA-TA nearest neighbor pair of base-pairs is found to be the most sensitive one among all stacking interactions. Moreover, we also establish that the nature of stacking interaction has a deciding effect on the DNA breathing dynamics, not the number of times a particular stacking interaction appears in a sequence. We show that the sensitivity analysis can be used as an effective measure to guide a stochastic optimization technique to find the kinetic rate constants related to the dynamics as opposed to the case where the rate constants are measured using the conventional unbiased way of optimization.
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Affiliation(s)
- Srijeeta Talukder
- Department of Chemistry, University of Calcutta, 92 A P C Road, Kolkata 700 009, India
| | - Shrabani Sen
- Department of Chemistry, University of Calcutta, 92 A P C Road, Kolkata 700 009, India
| | - Prantik Chakraborti
- Department of Chemistry, Bose Institute, 93/1 A P C Road, Kolkata 700 009, India
| | - Ralf Metzler
- Institute for Physics and Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany and Physics Department, Tampere University of Technology, FI-33101 Tampere, Finland
| | - Suman K Banik
- Department of Chemistry, Bose Institute, 93/1 A P C Road, Kolkata 700 009, India
| | - Pinaki Chaudhury
- Department of Chemistry, University of Calcutta, 92 A P C Road, Kolkata 700 009, India
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24
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Völker J, Plum GE, Gindikin V, Klump HH, Breslauer KJ. Impact of bulge loop size on DNA triplet repeat domains: Implications for DNA repair and expansion. Biopolymers 2014; 101:1-12. [PMID: 23494673 PMCID: PMC3920904 DOI: 10.1002/bip.22236] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 03/05/2013] [Indexed: 11/12/2022]
Abstract
Repetitive DNA sequences exhibit complex structural and energy landscapes, populated by metastable, noncanonical states, that favor expansion and deletion events correlated with disease phenotypes. To probe the origins of such genotype-phenotype linkages, we report the impact of sequence and repeat number on properties of (CNG) repeat bulge loops. We find the stability of duplexes with a repeat bulge loop is controlled by two opposing effects; a loop junction-dependent destabilization of the underlying double helix, and a self-structure dependent stabilization of the repeat bulge loop. For small bulge loops, destabilization of the underlying double helix overwhelms any favorable contribution from loop self-structure. As bulge loop size increases, the stabilizing loop structure contribution dominates. The role of sequence on repeat loop stability can be understood in terms of its impact on the opposing influences of junction formation and loop structure. The nature of the bulge loop affects the thermodynamics of these two contributions differently, resulting in unique differences in repeat size-dependent minima in the overall enthalpy, entropy, and free energy changes. Our results define factors that control repeat bulge loop formation; knowledge required to understand how this helix imperfection is linked to DNA expansion, deletion, and disease phenotypes.
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Affiliation(s)
- Jens Völker
- Department of Chemistry and Chemical Biology, Rutgers, The
State University of New Jersey, 610 Taylor Rd, Piscataway, NJ 08854
| | - G. Eric Plum
- IBET, Inc., 1507 Chambers Road, Suite 301, Columbus, OH
43212
| | - Vera Gindikin
- Department of Chemistry and Chemical Biology, Rutgers, The
State University of New Jersey, 610 Taylor Rd, Piscataway, NJ 08854
| | - Horst H. Klump
- Department of Molecular and Cell Biology,
University of Cape Town, Private Bag, Rondebosch 7800, South Africa
| | - Kenneth J. Breslauer
- Department of Chemistry and Chemical Biology, Rutgers, The
State University of New Jersey, 610 Taylor Rd, Piscataway, NJ 08854
- The Cancer Institute of New Jersey, New Brunswick,
NJ 08901
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25
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Johnson BN, Mutharasan R. Biosensor-based microRNA detection: techniques, design, performance, and challenges. Analyst 2014; 139:1576-88. [DOI: 10.1039/c3an01677c] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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26
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Takahashi S, Sugimoto N. Effect of pressure on thermal stability of g-quadruplex DNA and double-stranded DNA structures. Molecules 2013; 18:13297-319. [PMID: 24172240 PMCID: PMC6270079 DOI: 10.3390/molecules181113297] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 10/05/2013] [Accepted: 10/24/2013] [Indexed: 11/16/2022] Open
Abstract
Pressure is a thermodynamic parameter that can induce structural changes in biomolecules due to a volumetric decrease. Although most proteins are denatured by pressure over 100 MPa because they have the large cavities inside their structures, the double-stranded structure of DNA is stabilized or destabilized only marginally depending on the sequence and salt conditions. The thermal stability of the G-quadruplex DNA structure, an important non-canonical structure that likely impacts gene expression in cells, remarkably decreases with increasing pressure. Volumetric analysis revealed that human telomeric DNA changed by more than 50 cm3 mol-1 during the transition from a random coil to a quadruplex form. This value is approximately ten times larger than that for duplex DNA under similar conditions. The volumetric analysis also suggested that the formation of G-quadruplex DNA involves significant hydration changes. The presence of a cosolute such as poly(ethylene glycol) largely repressed the pressure effect on the stability of G-quadruplex due to alteration in stabilities of the interactions with hydrating water. This review discusses the importance of local perturbations of pressure on DNA structures involved in regulation of gene expression and highlights the potential for application of high-pressure chemistry in nucleic acid-based nanotechnology.
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Affiliation(s)
- Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan; E-Mail:
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan; E-Mail:
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +81-774-98-2580; Fax: +81-774-98-2585
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27
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Nesterova IV, Elsiddieg SO, Nesterov EE. Design and evaluation of an i-motif-based allosteric control mechanism in DNA-hairpin molecular devices. J Phys Chem B 2013; 117:10115-21. [PMID: 23941235 DOI: 10.1021/jp405230g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Molecular devices designed to assess and manipulate biologically relevant conditions with required accuracy and precision play an essential role in life sciences research. Incorporating allosteric regulation mechanism is an attractive strategy toward more efficient artificial sensing and switching systems. Herein, we report on a new principle of regulating switching parameters of a DNA-based molecular device based on allosteric interaction between spatially separated hairpin stem and a tetraplexed fragment (i.e., i-motif). We characterized thermodynamic and kinetic effects arising from interaction between functional domains of the device and demonstrated the potential of applying the allosteric control principle for rational design of sensors and switches with precisely defined operational characteristics.
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Affiliation(s)
- Irina V Nesterova
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
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28
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Yuann JMP, Tseng WH, Lin HY, Hou MH. The effects of loop size on Sac7d-hairpin DNA interactions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1009-15. [PMID: 22683438 DOI: 10.1016/j.bbapap.2012.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 05/29/2012] [Indexed: 02/07/2023]
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29
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Nakano SI, Yamaguchi D, Tateishi-Karimata H, Miyoshi D, Sugimoto N. Hydration changes upon DNA folding studied by osmotic stress experiments. Biophys J 2012; 102:2808-17. [PMID: 22735531 DOI: 10.1016/j.bpj.2012.05.019] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 05/09/2012] [Accepted: 05/10/2012] [Indexed: 11/26/2022] Open
Abstract
The thermal stability of nucleic acid structures is perturbed under the conditions that mimic the intracellular environment, typically rich in inert components and under osmotic stress. We now describe the thermodynamic stability of DNA oligonucleotide structures in the presence of high background concentrations of neutral cosolutes. Small cosolutes destabilize the basepair structures, and the DNA structures consisting of the same nearest-neighbor composition show similar thermodynamic parameters in the presence of various types of cosolutes. The osmotic stress experiments reveal that water binding to flexible loops, unstable mismatches, and an abasic site upon DNA folding are almost negligible, whereas the binding to stable mismatch pairs is significant. The studies using the basepair-mimic nucleosides and the peptide nucleic acid suggest that the sugar-phosphate backbone and the integrity of the basepair conformation make important contributions to the binding of water molecules to the DNA bases and helical grooves. The study of the DNA hydration provides the basis for understanding and predicting nucleic acid structures in nonaqueous solvent systems.
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Affiliation(s)
- Shu-ichi Nakano
- Faculty of Frontiers of Innovative Research in Science and Technology, Konan University, Kobe, Japan.
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30
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Talukder S, Chaudhury P, Metzler R, Banik SK. Determining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization. J Chem Phys 2012; 135:165103. [PMID: 22047268 DOI: 10.1063/1.3654958] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We suggest that the thermodynamic stability parameters (nearest neighbor stacking and hydrogen bonding free energies) of double-stranded DNA molecules can be inferred reliably from time series of the size fluctuations (breathing) of local denaturation zones (bubbles). On the basis of the reconstructed bubble size distribution, this is achieved through stochastic optimization of the free energies in terms of simulated annealing. In particular, it is shown that even noisy time series allow the identification of the stability parameters at remarkable accuracy. This method will be useful to obtain the DNA stacking and hydrogen bonding free energies from single bubble breathing assays rather than equilibrium data.
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Affiliation(s)
- Srijeeta Talukder
- Department of Chemistry, University of Calcutta, 92 A P C Road, Kolkata 700 009, India
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31
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Yadav D, D. Sheardy R. A single base permutation in any loop of a folded intramolecular quadruplex influences its structure and stability. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/jbpc.2012.34042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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32
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Guo H, Tse LV, Nieh AW, Czornyj E, Williams S, Oukil S, Liu VB, Miller JF. Target site recognition by a diversity-generating retroelement. PLoS Genet 2011; 7:e1002414. [PMID: 22194701 PMCID: PMC3240598 DOI: 10.1371/journal.pgen.1002414] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 10/27/2011] [Indexed: 11/29/2022] Open
Abstract
Diversity-generating retroelements (DGRs) are in vivo sequence diversification machines that are widely distributed in bacterial, phage, and plasmid genomes. They function to introduce vast amounts of targeted diversity into protein-encoding DNA sequences via mutagenic homing. Adenine residues are converted to random nucleotides in a retrotransposition process from a donor template repeat (TR) to a recipient variable repeat (VR). Using the Bordetella bacteriophage BPP-1 element as a prototype, we have characterized requirements for DGR target site function. Although sequences upstream of VR are dispensable, a 24 bp sequence immediately downstream of VR, which contains short inverted repeats, is required for efficient retrohoming. The inverted repeats form a hairpin or cruciform structure and mutational analysis demonstrated that, while the structure of the stem is important, its sequence can vary. In contrast, the loop has a sequence-dependent function. Structure-specific nuclease digestion confirmed the existence of a DNA hairpin/cruciform, and marker coconversion assays demonstrated that it influences the efficiency, but not the site of cDNA integration. Comparisons with other phage DGRs suggested that similar structures are a conserved feature of target sequences. Using a kanamycin resistance determinant as a reporter, we found that transplantation of the IMH and hairpin/cruciform-forming region was sufficient to target the DGR diversification machinery to a heterologous gene. In addition to furthering our understanding of DGR retrohoming, our results suggest that DGRs may provide unique tools for directed protein evolution via in vivo DNA diversification. Diversity-generating retroelements function through a unique, reverse transcriptase–mediated “copy and replace” mechanism that enables repeated rounds of protein diversification, selection, and optimization. The ability of DGRs to introduce targeted diversity into protein-coding DNA sequences has the potential to dramatically accelerate the evolution of adaptive traits. The utility of these elements in nature is underscored by their widespread distribution throughout the bacterial domain. Here we define DNA sequences and structures that are necessary and sufficient to direct the diversification machinery to specified target sequences. In addition to providing mechanistic insights into conserved features of DGR activity, our results provide a blueprint for the use of DGRs for a broad range of protein engineering applications.
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Affiliation(s)
- Huatao Guo
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Longping V. Tse
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Angela W. Nieh
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Elizabeth Czornyj
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Steven Williams
- AvidBiotics Corporation, South San Francisco, California, United States of America
| | - Sabrina Oukil
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Vincent B. Liu
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jeff F. Miller
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- The Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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33
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Chang CYJ, Stellwagen NC. Tandem GA residues on opposite sides of the loop in molecular beacon-like DNA hairpins compact the loop and increase hairpin stability. Biochemistry 2011; 50:9148-57. [PMID: 21942650 DOI: 10.1021/bi201263n] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The free solution electrophoretic mobilities and thermal stabilities of hairpins formed by two complementary 26-nucleotide oligomers have been measured by capillary electrophoresis. The oligomers are predicted to form molecular beacon-like hairpins with 5 bp stems and 16 nucleotides in the loop. One hairpin, called hairpin2 (hp2), migrates with a relatively fast free solution mobility and exhibits melting temperatures that are reasonably well predicted by the popular structure-prediction program Mfold. Its complement, called hairpin1 (hp1), migrates with a slower free solution mobility and forms a stable hairpin only in solutions containing ≥200 mM Na(+). The melting temperatures observed for hp1 are ~18 °C lower than those observed for hp2 and ~20 °C lower than those predicted by Mfold. The greater thermal stability of hp2 is due to the presence of tandem GA residues on opposite sides of the loop. If the corresponding TC residues in the hp1 loop are replaced by tandem GA residues, the melting temperatures of the modified hairpin are close to those observed for hp2. Eliminating the tandem GA residues in the hp2 loop significantly decreases the thermal stability of hp2. If the loops are replaced by a loop of 16 thymine residues, the free solution mobilities and thermal stabilities of the T-loop hairpin are equal to those observed for hp1. Hence, the loop of hp1 appears to be relatively unstructured, with few base-base stacking interactions. Interactions between tandem GA residues on opposite sides of the hp2 loop appear to compact the loop and increase hairpin stability.
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Affiliation(s)
- Chun Yaw Joel Chang
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
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34
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Lah J, Seručnik M, Vesnaver G. Influence of a hairpin loop on the thermodynamic stability of a DNA oligomer. J Nucleic Acids 2011; 2011:513910. [PMID: 21904665 PMCID: PMC3166569 DOI: 10.4061/2011/513910] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 05/16/2011] [Indexed: 11/23/2022] Open
Abstract
DSC was used to evaluate the mechanism of the thermally induced unfolding of the single-stranded hairpin HP = 5′-CGGAATTCCGTCTCCGGAATTCCG-3′ and its core duplex D (5′-CGGAATTCCG-3′)2. The DSC melting experiments performed at several salt concentrations were successfully described for HP and D in terms of a three-state transition model HP↔I (intermediate state) ↔ S (unfolded single-stranded state) and two state transition model D↔2S, respectively. Comparison of the model-based thermodynamic parameters obtained for each HP and D transition shows that in unfolding of HP only the HP↔I transition is affected by the TCTC loop. This observation suggests that in the intermediate state its TCTC loop part exhibits significantly more flexible structure than in the folded state while its duplex part remains pretty much unchanged.
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Affiliation(s)
- Jurij Lah
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, 1000 Ljubljana, Slovenia
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35
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Amiri AR, Macgregor RB. The effect of hydrostatic pressure on the thermal stability of DNA hairpins. Biophys Chem 2011; 156:88-95. [DOI: 10.1016/j.bpc.2011.02.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Revised: 02/02/2011] [Accepted: 02/08/2011] [Indexed: 11/29/2022]
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36
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Abstract
Repetition of trinucleotide sequences is the molecular basis of ~30 hereditary neurological and neurodegenerative diseases, and alternate structures adopted by these sequences are implicated in the etiology of such diseases. Elucidating these structures is important for advancing mechanistic understanding and ultimately treatment. Studies of (CAG) repeats are motivated by their involvement in a number of these diseases, and the structures favored by (CAG)₈ are discussed in this contribution. Utilizing the strong effect of base stacking on fluorescence quantum yield, 2-aminopurine is used in place of adenine to determine the secondary structures adopted by such repeated sequences. Alone, (CAG)₈ folds into a hairpin comprised of a duplex stem and a single-stranded loop. Energetic studies indicate that the hairpin is anchored by the interactions in the stem and has a strained loop environment. As a model for intermediates that form during repeat expansion, (CAG)₈ was also incorporated into a duplex to form a three-way junction. In contrast to the isolated (CAG)₈, this integrated repeat adopts an open, unfolded loop. Enthalpy and entropy changes associated with denaturation indicate that the stability of the three-way junction is dominated by interactions in the duplex arms and that the repeated sequence tracks global unfolding. Because 2-aminopurine provides both structural and energetic information via fluorescence and also is an innocuous substitution for adenine, significant progress in elucidating the secondary structures of (CAG) repeats will be achieved.
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37
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Degtyareva NN, Reddish MJ, Sengupta B, Petty JT. Structural studies of a trinucleotide repeat sequence using 2-aminopurine. Biochemistry 2010; 48:2340-6. [PMID: 19170594 DOI: 10.1021/bi802225y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The secondary structure of repeated trinucleotide sequences results in the development of several neurodegenerative diseases, and these studies consider the (CAG)(8) sequence that forms a stem-loop hairpin. The structural and thermodynamic properties of this hairpin are assessed using 2-aminopurine substitutions for adenine at six positions in this repeated sequence. Circular dichroism spectra and thermal denaturation experiments show that the secondary structure is not disturbed by the modifications. The local structure of the hairpin was monitored using the fluorescence intensities of 2-aminopurines, the changes in the intensity relative to the denatured state, and the sensitivity of the fluorescence to quenching by acrylamide. To establish the stem and loop characteristics in (CAG)(8), known reference points for stem, loop, and exposed base motifs were used. In the vicinity of the loop, the bases become more solvent exposed, which suggests that the instability associated with this repeated hairpin influences the global secondary structure. These results provide the basis to interpret the structures adopted by other repeated (CAG) structures.
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Affiliation(s)
- Natalya N Degtyareva
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA
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38
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Dupouy C, Millard P, Boissonnet A, Escudier JM. α,β-D-CNA preorganization of unpaired loop moiety stabilizes DNA hairpin. Chem Commun (Camb) 2010; 46:5142-4. [DOI: 10.1039/c0cc00244e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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39
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Peng Y, Song Y, Feng L, Ren J, Qu X. 7-Amino actinomycin D bound to single-stranded hairpin DNA enhanced by loop sequence-dependent luminescent Eu3+ and Tb3+ binding. J Inorg Biochem 2009; 103:1675-9. [DOI: 10.1016/j.jinorgbio.2009.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Revised: 09/15/2009] [Accepted: 09/16/2009] [Indexed: 01/10/2023]
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40
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Keene FR, Smith JA, Collins JG. Metal complexes as structure-selective binding agents for nucleic acids. Coord Chem Rev 2009. [DOI: 10.1016/j.ccr.2009.01.004] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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41
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Ma Q, Akiyama Y, Xu Z, Konishi K, Hecht SM. Identification and Cleavage Site Analysis of DNA Sequences Bound Strongly by Bleomycin. J Am Chem Soc 2009; 131:2013-22. [DOI: 10.1021/ja808629s] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Qian Ma
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904
| | - Yoshitsugu Akiyama
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904
| | - Zhidong Xu
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904
| | - Kazuhide Konishi
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904
| | - Sidney M. Hecht
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904
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42
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Abstract
The thermodynamics of the stacking to unstacking transitions of 24 single-stranded DNA sequences (ssDNA), 10-12 bases in length, in sodium phosphate buffer were determined from 10 to 95 degrees C, using differential scanning calorimetry (DSC). An additional 22 ssDNA sequences did not exhibit an S<=>U transition in this temperature range. The transition properties of the ssDNA sequences with <or=60% self-complementarily in the reverse direction were independent of concentration with transition temperatures ranging from 15 to 70 degrees C, van't Hoff transition enthalpies from 92 to 201 kJ mol(-1) and transition enthalpies from 5 to 75% of the corresponding van't Hoff transition enthalpies. Since all the 16 doublets and 60 of the 64 triplets are present in both the transition and the non-transition ssDNA sequences, it is unlikely that the nucleation subset initiating stacking of the sequence is a specific doublet or triplet subset. Of the 141 quadruplet subsets of the 46 sequences, each transition ssDNA sequence contained at least one or more quadruplets not found in the non-transition ssDNA sequences. It could be concluded that the thermal stability of the stacked conformation was dependent on the presence of a possible nucleation quadruplet and the length of the ssDNA sequence and not on the G or C content of the ssDNA sequence, nor on the number of purine bases in the sequence.
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Affiliation(s)
- Jayanthi Ramprakash
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
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43
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Bai LP, Cai Z, Zhao ZZ, Nakatani K, Jiang ZH. Site-specific binding of chelerythrine and sanguinarine to single pyrimidine bulges in hairpin DNA. Anal Bioanal Chem 2008; 392:709-16. [DOI: 10.1007/s00216-008-2302-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2008] [Revised: 06/02/2008] [Accepted: 07/17/2008] [Indexed: 11/30/2022]
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44
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Aihara H, Huang WM, Ellenberger T. An interlocked dimer of the protelomerase TelK distorts DNA structure for the formation of hairpin telomeres. Mol Cell 2007; 27:901-13. [PMID: 17889664 PMCID: PMC2041798 DOI: 10.1016/j.molcel.2007.07.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Revised: 06/11/2007] [Accepted: 07/25/2007] [Indexed: 12/27/2022]
Abstract
The termini of linear chromosomes are protected by specialized DNA structures known as telomeres that also facilitate the complete replication of DNA ends. The simplest type of telomere is a covalently closed DNA hairpin structure found in linear chromosomes of prokaryotes and viruses. Bidirectional replication of a chromosome with hairpin telomeres produces a catenated circular dimer that is subsequently resolved into unit-length chromosomes by a dedicated DNA cleavage-rejoining enzyme known as a hairpin telomere resolvase (protelomerase). Here we report a crystal structure of the protelomerase TelK from Klebsiella oxytoca phage varphiKO2, in complex with the palindromic target DNA. The structure shows the TelK dimer destabilizes base pairing interactions to promote the refolding of cleaved DNA ends into two hairpin ends. We propose that the hairpinning reaction is made effectively irreversible by a unique protein-induced distortion of the DNA substrate that prevents religation of the cleaved DNA substrate.
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Affiliation(s)
- Hideki Aihara
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., Campus Box 8231, St. Louis, MO 63110
| | - Wai Mun Huang
- Department of Pathology, EEJ Medical Research Building, Room 5200B 15 N. Medical Dr. East, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - Tom Ellenberger
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., Campus Box 8231, St. Louis, MO 63110
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45
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Völker J, Klump HH, Breslauer KJ. The energetics of i-DNA tetraplex structures formed intermolecularly by d(TC5) and intramolecularly by d[(C5T3)3C5]. Biopolymers 2007; 86:136-47. [PMID: 17330895 DOI: 10.1002/bip.20712] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cytosine-rich DNA at low pH adopts an antiparallel tetraplex structure via the intercalation of two partially protonated, parallel stranded duplexes. This intriguing structural motif has been named i-DNA. We have used a combination of spectroscopic and calorimetric techniques to characterize the properties of an intermolecular i-DNA formed by d(TC(5)) and an intramolecular i-DNA formed by d[(C(5)T(3))(3)C(5)]. Our measurements reveal that both i-DNA complexes are enthalpically stabilized by 6.5-7.0 kcal/mol(base) and entropically destabilized by 20 cal/mol(base)/K. These values are about 50% larger than the corresponding enthalpy and entropy values per base for Watson and Crick duplexes and for Hoogsteen triplexes, while being similar to per base enthalpy and entropy values reported for G-quadruplexes. Our data also reveal a positive heat capacity change between 20 and 30 cal/mol(base)/K, values similar to that reported for polymeric Watson & Crick DNA duplexes. Solution-dependent studies reveal the overall thermal and thermodynamic stability of i-DNA complexes to be dictated by an interplay between pH and ionic strength. Based on the thermodynamic data measured, we discuss the feasibility of i-DNA formation in the context of conventional DNA sequences, while commenting on potential roles for this structural motif in biological regulatory mechanisms.
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Affiliation(s)
- Jens Völker
- Department of Chemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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46
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Stellwagen E, Renze A, Stellwagen NC. Capillary electrophoresis is a sensitive monitor of the hairpin-random coil transition in DNA oligomers. Anal Biochem 2007; 365:103-10. [PMID: 17416339 PMCID: PMC1995437 DOI: 10.1016/j.ab.2007.03.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Accepted: 03/08/2007] [Indexed: 10/23/2022]
Abstract
Capillary electrophoresis (CE) has been used to characterize the hairpin-random coil transition of four octamers in the GCxxxxGC minihairpin family, where xxxx is GAAA, TTTC, TTTT, or AAAA. The transition can be monitored by CE because differences in the frictional coefficients of the hairpin and coil forms of each octamer lead to a difference of approximately 9% in the free solution mobilities of the two conformations. The GAAA octamer is unusually stable, with a melting temperature of 65 degrees C. The TTTT octamer forms a minihairpin with a melting temperature of 29 degrees C, the TTTC octamer has a melting temperature of 16 degrees C, and the AAAA octamer has a melting temperature below 0 degrees C. The thermal transitions of the TTTT, TTTC, and AAAA octamers are well fitted by a structure prediction algorithm; however, the GAAA minihairpin is considerably more stable than predicted. The melting temperature of the GAAA minihairpin is reduced to 47 degrees C in aqueous buffers containing 7.2M urea and to 33 degrees C in buffers containing 7.2M urea plus 40% (v/v) formamide. The combined results indicate that CE is a sensitive technique for monitoring conformational transitions in small DNA molecules.
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Affiliation(s)
- Earle Stellwagen
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
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47
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Ormond TK, Spear D, Stoll J, Mackey MA, St John PM. Increase in hybridization rates with oligodeoxyribonucleotides containing locked nucleic acids. J Biomol Struct Dyn 2006; 24:171-82. [PMID: 16928140 DOI: 10.1080/07391102.2006.10507110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Locked nucleic acids (LNAs) incorporated into either stable single stranded oligonucleotides containing tetraloops or their complements have been found to increase second order hybridization rate constants by an order of magnitude compared to the all-DNA hybridization rate constants. Model sequences composed of 20 bases in length that can form hairpins due to a stable GAAA tetraloop were used where LNAs were substituted for the nucleotides in the loop, stem, or end regions of the strand and in the complementary strand. Substitution of the LNAs to the loop predictably raised the melting temperatures of the duplex however, the hybridization rates between the tetraloop and the complementary sequence also increased. In contrast, when LNAs were substituted in the stem, the hybridization rate decreased implying the formation of a more stable hairpin. Substitution of LNAs into the end region of the sequence had little effect on the hybridization rate constants although melting temperatures still showed a predictable increase. Rates also increased when LNAs were substituted into complementary strands of DNA tetraloops. The increase in hybridization rate constant is being attributed to changes in the structure of the stable single strands.
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Affiliation(s)
- Thomas K Ormond
- Chemistry Department, SUNY New Paltz, New Paltz, NY 12561, USA
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48
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DeGuzman VS, Lee CC, Deamer DW, Vercoutere WA. Sequence-dependent gating of an ion channel by DNA hairpin molecules. Nucleic Acids Res 2006; 34:6425-37. [PMID: 17130164 PMCID: PMC1702491 DOI: 10.1093/nar/gkl754] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DNA hairpins produce ionic current signatures when captured by the alpha-hemolysin nano-scale pore under conditions of single molecule electrophoresis. Gating patterns produced by individual DNA hairpins when captured can be used to distinguish differences of a single base pair or even a single nucleotide [Vercoutere,W.A. et al. (2003) Nucleic Acids Res., 31, 1311–1318]. Here we investigate the mechanism(s) that may account for the ionic current gating signatures. The ionic current resistance profile of conductance states produced by DNA hairpin molecules with 3–12 bp stems showed a plateau in resistance between 10 and 12 bp, suggesting that hairpins with 10–12 bp stems span the pore vestibule. DNA hairpins with 9–12 bp stems produced gating signatures with the same relative conductance states. Systematic comparison of the conductance state dwell times and apparent activation energies for a series of 9–10 bp DNA hairpins suggest that the 3′ and 5′ ends interact at or near the limiting aperture within the vestibule of the alpha-hemolysin pore. The model presented may be useful in predicting and interpreting DNA detection using nanopore detectors. In addition, this well-defined molecular system may prove useful for investigating models of ligand-gated channels in biological membranes.
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Affiliation(s)
- Veronica S. DeGuzman
- Ames Associate, Life Sciences Division, NASA Ames Research CenterMoffett Field, CA, USA
- MAP PharmaceuticalsPalo Alto, CA, USA
| | | | - David W. Deamer
- Center for Biomolecular Science and Engineering, University of CaliforniaSanta Cruz, CA 95064
| | - Wenonah A. Vercoutere
- Life Sciences Division, NASA Ames Research CenterMoffett Field, CA, USA
- To whom correspondence should be addresssed at NASA Ames Research Center, Mail Stop 236-7 Moffett Field, CA, USA. Tel: +1 650 604 6014; Fax: +1 650 604 3159;
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49
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Winters-Hilt S, Landry M, Akeson M, Tanase M, Amin I, Coombs A, Morales E, Millet J, Baribault C, Sendamangalam S. Cheminformatics methods for novel nanopore analysis of HIV DNA termini. BMC Bioinformatics 2006; 7 Suppl 2:S22. [PMID: 17118144 PMCID: PMC1683570 DOI: 10.1186/1471-2105-7-s2-s22] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Channel current feature extraction methods, using Hidden Markov Models (HMMs) have been designed for tracking individual-molecule conformational changes. This information is derived from observation of changes in ionic channel current blockade "signal" upon that molecule's interaction with (and occlusion of) a single nanometer-scale channel in a "nanopore detector". In effect, a nanopore detector transduces single molecule events into channel current blockades. HMM analysis tools described are used to help systematically explore DNA dinucleotide flexibility, with particular focus on HIV's highly conserved (and highly flexible/reactive) viral DNA termini. One of the most critical stages in HIV's attack is the binding between viral DNA and the retroviral integrase, which is influenced by the dynamic-coupling induced high flexibility of a CA/TG dinucleotide positioned precisely two base-pairs from the blunt terminus of the duplex viral DNA. This suggests the study of a family of such CA/TG dinucleotide molecules via nanopore measurement and cheminformatics analysis. RESULTS HMMs are used for level identification on the current blockades, HMM/EM with boosted variance emissions are used for level projection pre-processing, and time-domain FSAs are used to parse the level-projected waveform for kinetic information. The observed state kinetics of the DNA hairpins containing the CA/TG dinucleotide provides clear evidence for HIV's selection of a peculiarly flexible/interactive DNA terminus.
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Affiliation(s)
- Stephen Winters-Hilt
- Department of Computer Science, University of New Orleans, New Orleans, LA, 70148, USA
- The Research Institute for Children, 200 Henry Clay Ave., New Orleans, LA 70118, USA
| | - Matthew Landry
- Department of Computer Science, University of New Orleans, New Orleans, LA, 70148, USA
| | - Mark Akeson
- Department of Chemistry, University of California – Santa Cruz, Santa Cruz, CA 90560, USA
| | - Maria Tanase
- The Research Institute for Children, 200 Henry Clay Ave., New Orleans, LA 70118, USA
| | - Iftekhar Amin
- The Research Institute for Children, 200 Henry Clay Ave., New Orleans, LA 70118, USA
| | - Amy Coombs
- Department of Chemistry, University of California – Santa Cruz, Santa Cruz, CA 90560, USA
| | - Eric Morales
- The Research Institute for Children, 200 Henry Clay Ave., New Orleans, LA 70118, USA
| | - John Millet
- Department of Computer Science, University of New Orleans, New Orleans, LA, 70148, USA
| | - Carl Baribault
- Department of Computer Science, University of New Orleans, New Orleans, LA, 70148, USA
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50
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Kincaid K, Kuchta RD. A mass spectrometry-based approach for identifying novel DNA polymerase substrates from a pool of dNTP analogues. Nucleic Acids Res 2006; 34:e109. [PMID: 16945949 PMCID: PMC1636374 DOI: 10.1093/nar/gkl632] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
There has been a long-standing interest in the discovery of unnatural nucleotides that can be incorporated into DNA by polymerases. However, it is difficult to predict which nucleotide analogs will prove to have biological relevance. Therefore, we have developed a new screening method to identify novel substrates for DNA polymerases. This technique uses the polymerase itself to select a dNTP from a pool of potential substrates via incorporation onto a short oligonucleotide. The unnatural nucleotide(s) is then identified by high-resolution mass spectrometry. By using a DNA polymerase as a selection tool, only the biologically relevant members of a small nucleotide library can be quickly determined. We have demonstrated that this method can be used to discover unnatural base pairs in DNA with a detection threshold of ≤10% incorporation.
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Affiliation(s)
| | - Robert D. Kuchta
- To whom correspondence should be addressed. Tel: +1 303 492 7027; Fax: +1 303 492 5894;
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