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Nicholson DA, Sengupta A, Sung HL, Nesbitt DJ. Amino Acid Stabilization of Nucleic Acid Secondary Structure: Kinetic Insights from Single-Molecule Studies. J Phys Chem B 2018; 122:9869-9876. [PMID: 30289262 DOI: 10.1021/acs.jpcb.8b06872] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Amino acid and nucleic acid interactions are central in biology and may have played a role in the evolutionary development of protein-based life from an early "RNA Universe." To explore the possible role of single amino acids in promoting nucleic acid folding, single-molecule Förster resonance energy transfer experiments have been implemented with a DNA hairpin construct (7 nucleotide double strand with a 40A loop) as a simple model for secondary structure formation. Exposure to positively charged amino acids (arginine and lysine) is found to clearly stabilize the secondary structure. Kinetically, each amino acid promotes folding by generating a large increase in the folding rate with little change in the unfolding rate. From analysis as a function of temperature, arginine and lysine are found to significantly increase the overall exothermicity of folding while imposing only a small entropic penalty on the folding process. Detailed investigations into the kinetics and thermodynamics of this amino acid-induced folding stability reveal arginine and lysine to interact with nucleic acids in a manner reminiscent of monovalent cations. Specifically, these observations are interpreted in the context of an ion atmosphere surrounding the nucleic acid, in which amino acid salts stabilize folding qualitatively like small monovalent cations but also exhibit differences because of the composition of their side chains.
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Affiliation(s)
- David A Nicholson
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
| | - Abhigyan Sengupta
- Department of Bioengineering , University of California at Merced , Merced , California 95340 , United States
| | - Hsuan-Lei Sung
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
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2
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Carr CE, Marky LA. Increased Flexibility between Stems of Intramolecular Three-Way Junctions by the Insertion of Bulges. Biophys J 2018; 114:2764-2774. [PMID: 29925014 PMCID: PMC6026347 DOI: 10.1016/j.bpj.2018.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/25/2018] [Accepted: 05/01/2018] [Indexed: 12/20/2022] Open
Abstract
Intramolecular junctions are a ubiquitous structure within DNA and RNA; three-way junctions in particular have high strain around the junction because of the lack of flexibility, preventing the junctions from adopting conformations that would allow for optimal folding. In this work, we used a combination of calorimetric and spectroscopic techniques to study the unfolding of four intramolecular three-way junctions. The control three-way junction, 3H, has the sequence d(GAAATTGCGCT5GCGCGTGCT5GCACAATTTC), which has three arms of different sequences. We studied three other three-way junctions in which one (2HS1H), two (HS12HS1), and three (HS1HS1HS1) cytosine bulges were placed at the junction to allow the arms to adopt a wider range of conformations that may potentially relieve strain. Through calorimetric studies, it was concluded that bulges produce only minor effects on the enthalpic and thermal stability at physiological salt concentrations for 2HS1H and HS1HS1HS1. HS12HS1 displays the strongest effect, with the GTGC stem lacking a defined transition. In addition to unfolding thermodynamics, the differential binding of counterions, water, and protons was determined. It was found that with each bulge, there was a large increase in the binding of counterions; this correlated with a decrease in the immobilization of structural water molecules. The increase in counterion uptake upon folding likely displaces binding of structural water, which is measured by the osmotic stress method, in favor of electrostricted waters. The cytosine bulges do not affect the binding of protons; this finding indicates that the bulges are not forming base-triplet stacks. These results indicate that bulges in junctions do not affect the unfolding profile or the enthalpy of oligonucleotides but do affect the number and amount of molecules immobilized by the junction.
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Affiliation(s)
- Carolyn E Carr
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska
| | - Luis A Marky
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska.
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3
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Cheung LS, Wei X, Martins D, Song YA. Rapid detection of exosomal microRNA biomarkers by electrokinetic concentration for liquid biopsy on chip. BIOMICROFLUIDICS 2018; 12:014104. [PMID: 30867851 PMCID: PMC6404950 DOI: 10.1063/1.5009719] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/12/2017] [Indexed: 06/09/2023]
Abstract
An ion concentration polarization (ICP)-based electrokinetic concentration device is used for accelerating the surface hybridization reaction between exosomal microRNAs (miRNAs) and morpholinos (MOs) as a synthetic oligo capture probe in the nanomolar concentration range in a microfluidic channel. Compared with standard hybridization at the same concentration, the hybridization time of the miRNA target on MO capture probes could be reduced from ∼24 h to 30 min, with an increase in detection speed by 48 times. This ICP-enhanced hybridization method not only significantly decreases the detection time but also makes workflow simple to use, circumventing use of quantitative reverse transcription polymerase chain reaction or other conventional enzyme-based amplification methods that can cause artifacts.
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Affiliation(s)
- Lucia S Cheung
- Division of Engineering, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | | | - Diogo Martins
- NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
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4
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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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5
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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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6
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Carr CE, Marky LA. Melting Behavior of a DNA Four-Way Junction Using Spectroscopic and Calorimetric Techniques. J Am Chem Soc 2017; 139:14443-14455. [DOI: 10.1021/jacs.7b06429] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Carolyn E. Carr
- 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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Carr CE, Marky LA. Investigation of the Melting Behavior of DNA Three-Way Junctions in the Closed and Open States. Biophys J 2017; 113:529-539. [PMID: 28793208 DOI: 10.1016/j.bpj.2017.06.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/09/2017] [Accepted: 06/14/2017] [Indexed: 10/19/2022] Open
Abstract
Intramolecular three-way junctions are commonly found in both DNA and RNA. These structures are functionally relevant in ribozymes, riboswitches, rRNA, and during replication. In this work, we present a thermodynamic description of the unfolding of DNA intramolecular three-way junctions. We used a combination of spectroscopic and calorimetric techniques to investigate the folding/unfolding thermodynamics of two three-way junctions with a closed (Closed-J) or open (Open-J) junction and their appropriate control stem-loop motifs (GAAATT-Hp, CTATC-Hp, and Dumbbell). The overall results show that both junctions are stable over a wide range of salt concentrations. However, Open-J is more stable due to a higher enthalpy contribution from the formation of a higher number of basepair stacks whereas Closed-J has a defined structure and retains the basepair stacking of all three stems. The comparison of the experimental results of Closed-J and Open-J with those of their component stem-loop motifs allowed us to be more specific about their cooperative unfolding. For instance, Closed-J sacrifices thermal stability of the Dumbbell structure to maintain an overall folded state. At higher salt concentration, the simultaneous unfolding of the above domains is lost, resulting in the unfolding of the three separate stems. In contrast, the junction of Open-J in low salt retains the thermal and enthalpic stability of the Dumbbell structure although sacrificing stability of the CTATC stem. The relative stability of Dumbbell is the primary reason for the higher ΔG°(5), or free energy, value seen for Open-J at low salt. Higher salt not only maintains thermal stability of the Dumbbell structure in Open-J but causes the CTATC stem to fully fold.
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Affiliation(s)
- Carolyn E Carr
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Nebraska Medical Center, Omaha, Nebraska
| | - Luis A Marky
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Nebraska Medical Center, Omaha, Nebraska.
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8
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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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9
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10
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Ogawa A, Tabuchi J, Doi Y, Takamatsu M. Biofunction-assisted DNA detection through RNase H-enhanced 3' processing of a premature tRNA probe in a wheat germ extract. Bioorg Med Chem Lett 2016; 26:3658-61. [PMID: 27289318 DOI: 10.1016/j.bmcl.2016.05.091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/27/2016] [Accepted: 05/31/2016] [Indexed: 12/22/2022]
Abstract
We have developed a novel type of biofunction-assisted, signal-turn-on sensor for simply and homogenously detecting DNA. This sensor system is composed of two types of in vitro-transcribed label-free RNAs (a 3' premature amber suppressor tRNA probe and an amber-mutated mRNA encoding a reporter protein), RNase H, and a wheat germ extract (WGE). A target DNA induces the 3' end maturation of the tRNA probe, which is enhanced by RNase H and leads to the expression of a full-length reporter protein through amber suppression in WGE, while there is almost no expression without the target due to the inactivity of the premature probe. Therefore, the target can be readily detected with the activity of the translated reporter. The catalytic reuse of the target with the help of RNase H in addition to various bioprocesses in WGE enables this sensor system to exhibit relatively high selectivity and sensitivity.
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
| | - Junichiro Tabuchi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Yasunori Doi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Masashi Takamatsu
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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11
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Li W, Zhang F, Yan H, Liu Y. DNA based arithmetic function: a half adder based on DNA strand displacement. NANOSCALE 2016; 8:3775-84. [PMID: 26814628 DOI: 10.1039/c5nr08497k] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Biomolecular programming utilizes the reactions and information stored in biological molecules, such as proteins and nucleic acids, for computational purposes. DNA has proven itself an excellent candidate for building logic operating systems due to its highly predictable molecular behavior. In this work we designed and realized an XOR logic gate and an AND logic gate based on DNA strand displacement reactions. These logic gates utilize ssDNA as input and output signals. The XOR gate and the AND gate were used as building blocks for constructing a half adder logic circuit, which is a primary step in constructing a full adder, a basic arithmetic unit in computing. This work provides the field of DNA molecular programming with a potential universal arithmetic tool.
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Affiliation(s)
- Wei Li
- Center of Molecular Design and Biomimetics at The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA.
| | - Fei Zhang
- Center of Molecular Design and Biomimetics at The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA.
| | - Hao Yan
- Center of Molecular Design and Biomimetics at The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA.
| | - Yan Liu
- Center of Molecular Design and Biomimetics at The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA.
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12
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Zhang H, Ba S, Co Co S, Lee JY, Guo J, Ye R, Liang Z, Huang D, Li T. An Alternative Method for Evaluating Stabilities of DNA Hairpin Structures. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20150120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Hao Zhang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University
| | - Sai Ba
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University
| | - Sarajane Co Co
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University
| | - Jasmine Yiqin Lee
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University
| | - Juanjuan Guo
- Department of Chemistry, National University of Singapore
| | - Ruijuan Ye
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University
| | - Zhaoxun Liang
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University
| | - Dejian Huang
- Department of Chemistry, National University of Singapore
| | - Tianhu Li
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University
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13
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Sander SA, Van Hall AK, Morrow JR. Zn2+-Selective Switch of Duplex to Hairpin DNA. Inorg Chem 2015; 54:3084-6. [DOI: 10.1021/ic503074p] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Stephanie A. Sander
- Department of Chemistry, University at Buffalo, the State University of New York, Amherst, New York 14260, United States
| | - Alexandra K. Van Hall
- Department of Chemistry, University at Buffalo, the State University of New York, Amherst, New York 14260, United States
| | - Janet R. Morrow
- Department of Chemistry, University at Buffalo, the State University of New York, Amherst, New York 14260, United States
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14
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Reilly SM, Morgan RK, Brooks TA, Wadkins RM. Effect of interior loop length on the thermal stability and pK(a) of i-motif DNA. Biochemistry 2015; 54:1364-70. [PMID: 25619229 DOI: 10.1021/bi5014722] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The four-stranded i-motif (iM) conformation of cytosine-rich DNA is important in a wide variety of biochemical systems ranging from its use in nanomaterials to a potential role in oncogene regulation. An iM is stabilized by acidic pH that allows hemiprotonated cytidines to form a C·C(+) base pair. Fundamental studies that aim to understand how the lengths of loops connecting the protonated C·C(+) pairs affect intramolecular iM physical properties are described here. We characterized both the thermal stability and the pK(a) of intramolecular iMs with differing loop lengths, in both dilute solutions and solutions containing molecular crowding agents. Our results showed that intramolecular iMs with longer central loops form at pHs and temperatures higher than those of iMs with longer outer loops. Our studies also showed that increases in thermal stability of iMs when molecular crowding agents are present are dependent on the loop that is lengthened. However, the increase in pK(a) for iMs when molecular crowding agents are present is insensitive to loop length. Importantly, we also determined the proton activity of solutions containing high concentrations of molecular crowding agents to ascertain whether the increase in pK(a) of an iM is caused by alteration of this activity in buffered solutions. We determined that crowding agents alone increase the apparent pK(a) of a number of small molecules as well as iMs but that increases to iM pK(a) were greater than that expected from a shift in proton activity.
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Affiliation(s)
- Samantha M Reilly
- Department of Chemistry and Biochemistry, University of Mississippi , University, Mississippi 38677, United States
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15
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Ghimire S, Fanwick PE, McMillin DR. DNA-Binding Studies of a Tetraalkyl-Substituted Porphyrin and the Mutually Adaptive Distortion Principle. Inorg Chem 2014; 53:11108-18. [PMID: 25271570 DOI: 10.1021/ic501683t] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Srijana Ghimire
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Phillip E. Fanwick
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - David R. McMillin
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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16
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Gaier AJ, Ghimire S, Fix SE, McMillin DR. Internal Versus External Binding of Cationic Porphyrins to Single-Stranded DNA. Inorg Chem 2014; 53:5467-73. [PMID: 24828700 DOI: 10.1021/ic403105q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Abby J. Gaier
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, Indiana 47907, United States
| | - Srijana Ghimire
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, Indiana 47907, United States
| | - Sarah E. Fix
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, Indiana 47907, United States
| | - David R. McMillin
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, Indiana 47907, United States
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17
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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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18
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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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19
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Srinivasan A, Wang L, Cline CJ, Xie Z, Sobol RW, Xie XQ, Gold B. Identification and characterization of human apurinic/apyrimidinic endonuclease-1 inhibitors. Biochemistry 2012; 51:6246-59. [PMID: 22788932 DOI: 10.1021/bi300490r] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The repair of abasic sites that arise in DNA from hydrolytic depurination/depyrimidination of the nitrogenous bases from the sugar-phosphate backbone and the action of DNA glycosylases on deaminated, oxidized, and alkylated bases are critical to cell survival. Apurinic/apyrimidinic endonuclease-1/redox effector factor-1 (APE-1; aka APE1/ref-1) is responsible for the initial removal of abasic lesions as part of the base excision repair pathway. Deletion of APE-1 activity is embryonic lethal in animals and is lethal in cells. Potential inhibitors of the repair function of APE-1 were identified based upon molecular modeling of the crystal structure of the APE-1 protein. We describe the characterization of several unique nanomolar inhibitors using two complementary biochemical screens. The most active molecules all contain a 2-methyl-4-amino-6,7-dioxolo-quinoline structure that is predicted from the modeling to anchor the compounds in the endonuclease site of the protein. The mechanism of action of the selected compounds was probed by fluorescence and competition studies, which indicate, in a specific case, direct interaction between the inhibitor and the active site of the protein. It is demonstrated that the inhibitors induce time-dependent increases in the accumulation of abasic sites in cells at levels that correlate with their potency to inhibit APE-1 endonuclease excision. The inhibitor molecules also potentiate by 5-fold the toxicity of a DNA methylating agent that creates abasic sites. The molecules represent a new class of APE-1 inhibitors that can be used to probe the biology of this critical enzyme and to sensitize resistant tumor cells to the cytotoxicity of clinically used DNA damaging anticancer drugs.
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Affiliation(s)
- Ajay Srinivasan
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
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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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22
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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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Stellwagen E, Muse JM, Stellwagen NC. Monovalent Cation Size and DNA Conformational Stability. Biochemistry 2011; 50:3084-94. [DOI: 10.1021/bi1015524] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Earle Stellwagen
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Joseph M. Muse
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Nancy C. Stellwagen
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
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Evstigneev MP, Parkinson JA, Lantushenko AO, Kostjukov VV, Pahomov VI. Hexamer oligonucleotide topology and assembly under solution phase NMR and theoretical modeling scrutiny. Biopolymers 2010; 93:1023-38. [PMID: 20623667 DOI: 10.1002/bip.21515] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The entire family of noncomplementary hexamer oligodeoxyribonucleotides d(GCXYGC) (X and Y = A, G, C, or T) were assessed for topological indicators and equilibrium thermodynamics using a priori molecular modeling and solution phase NMR spectroscopy. Feasible modeled hairpin structures formed a basis from which solution structure and equilibria for each oligonucleotide were considered. ¹H and ³¹P variable temperature-dependent (VT) and concentration-dependent NMR data, NMR signal assignments, and diffusion parameters led to d(GCGAGC) and d(GCGGGC) being understood as exceptions within the family in terms of self-association and topological character. A mean diffusion coefficient D(298 K) = (2.0 ± 0.07) × 10⁻¹⁰ m² s⁻¹ was evaluated across all hexamers except for d(GCGAGC) (D(298 K) = 1.7 × 10⁻¹⁰ m² s⁻¹) and d(GCGGGC) (D(298 K) = 1.2 × 10⁻¹⁰ m² s⁻¹). Melting under VT analysis (T(m) = 323 K) combined with supporting NMR evidence confirmed d(GCGAGC) as the shortest tandem sheared GA mismatched duplex. Diffusion measurements were used to conclude that d(GCGGGC) preferentially exists as the shortest stable quadruplex structure. Thermodynamic analysis of all data led to the assertion that, with the exception of XY = GA and GG, the remaining noncomplementary oligonucleotides adopt equilibria between monomer and duplex, contributed largely by monomer random-coil forms. Contrastingly, d(GCGAGC) showed preference for tandem sheared GA mismatch duplex formation with an association constant K = 3.9 × 10⁵M⁻¹. No direct evidence was acquired for hairpin formation in any instance although its potential existence is considered possible for d(GCGAGC) on the basis of molecular modeling studies.
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Affiliation(s)
- Maxim P Evstigneev
- Sevastopol National Technical University, Department of Physics, Sevastopol 99053, Ukraine.
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25
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Reuter JS, Mathews DH. RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics 2010; 11:129. [PMID: 20230624 PMCID: PMC2984261 DOI: 10.1186/1471-2105-11-129] [Citation(s) in RCA: 1271] [Impact Index Per Article: 90.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 03/15/2010] [Indexed: 11/16/2022] Open
Abstract
Background To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence. Results RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained. Conclusion The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure.html.
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Affiliation(s)
- Jessica S Reuter
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY 14642, USA
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Lee HT, Khutsishvili I, Marky LA. DNA Complexes Containing Joined Triplex and Duplex Motifs: Melting Behavior of Intramolecular and Bimolecular Complexes with Similar Sequences. J Phys Chem B 2009; 114:541-8. [DOI: 10.1021/jp9084074] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hui-Ting Lee
- Department of Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, and Eppley Institute for Cancer Research, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025
| | - Irine Khutsishvili
- Department of Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, and Eppley Institute for Cancer Research, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025
| | - Luis A. Marky
- Department of Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, and Eppley Institute for Cancer Research, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025
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27
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Joynt S, Morillo V, Leng F. Binding the mammalian high mobility group protein AT-hook 2 to AT-rich deoxyoligonucleotides: enthalpy-entropy compensation. Biophys J 2009; 96:4144-52. [PMID: 19450485 DOI: 10.1016/j.bpj.2009.02.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Revised: 02/05/2009] [Accepted: 02/09/2009] [Indexed: 10/20/2022] Open
Abstract
HMGA2 is a DNA minor-groove binding protein. We previously demonstrated that HMGA2 binds to AT-rich DNA with very high binding affinity where the binding of HMGA2 to poly(dA-dT)(2) is enthalpy-driven and to poly(dA)poly(dT) is entropy-driven. This is a typical example of enthalpy-entropy compensation. To further study enthalpy-entropy compensation of HMGA2, we used isothermal-titration-calorimetry to examine the interactions of HMGA2 with two AT-rich DNA hairpins: 5'-CCAAAAAAAAAAAAAAAGCCCCCGCTTTTTTTTTTTTTTTGG-3' (FL-AT-1) and 5'-CCATATATATATATATAGCCCCCGCTATATATATATATATGG-3' (FL-AT-2). Surprisingly, we observed an atypical isothermal-titration-calorimetry-binding curve at low-salt aqueous solutions whereby the apparent binding-enthalpy decreased dramatically as the titration approached the end. This unusual behavior can be attributed to the DNA-annealing coupled to the ligand DNA-binding and is eliminated by increasing the salt concentration to approximately 200 mM. At this condition, HMGA2 binding to FL-AT-1 is entropy-driven and to FL-AT-2 is enthalpy-driven. Interestingly, the DNA-binding free energies for HMGA2 binding to both hairpins are almost temperature independent; however, the enthalpy-entropy changes are dependent on temperature, which is another aspect of enthalpy-entropy compensation. The heat capacity change for HMGA2 binding to FL-AT-1 and FL-AT-2 are almost identical, indicating that the solvent displacement and charge-charge interaction in the coupled folding/binding processes for both binding reactions are similar.
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Affiliation(s)
- Suzanne Joynt
- Department of Chemistry & Biochemistry, Florida International University, Miami, Florida 33199, USA
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28
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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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29
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Unfolding Thermodynamics of DNA Intramolecular Complexes Involving Joined Triple- and Double-Helical Motifs. Methods Enzymol 2009; 466:477-502. [DOI: 10.1016/s0076-6879(09)66020-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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30
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Olsen CM, Lee HT, Marky LA. Unfolding Thermodynamics of Intramolecular G-Quadruplexes: Base Sequence Contributions of the Loops. J Phys Chem B 2008; 113:2587-95. [DOI: 10.1021/jp806853n] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chris M. Olsen
- Department of Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, and Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025
| | - Hui-Ting Lee
- Department of Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, and Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025
| | - Luis A. Marky
- Department of Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, and Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025
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31
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Karimata H, Nakano SI, Sugimoto N. Effects of Polyethylene Glycol on DNA Duplex Stability at Different NaCl Concentrations. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.1987] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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32
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Kostjukov V, Pahomov V, Andrejuk D, Davies D, Evstigneev M. Investigation of the complexation of the anti-cancer drug novantrone with the hairpin structure of the deoxyheptanucleotide 5′-d(GpCpGpApApGpC). J Mol Struct 2007. [DOI: 10.1016/j.molstruc.2006.12.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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33
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Stampfl S, Lempradl A, Koehler G, Schroeder R. Monovalent ion dependence of neomycin B binding to an RNA aptamer characterized by spectroscopic methods. Chembiochem 2007; 8:1137-45. [PMID: 17539031 DOI: 10.1002/cbic.200700030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Understanding the interactions of small molecules like antibiotics with RNA is a prerequisite for the development of novel drugs. In this study we address structural and thermodynamic features of such interactions by using a simple model system: the binding of the highly charged antibiotic neomycin B to a short hairpin RNA molecule. Nucleotide A16, which acts as a flap over the neomycin B binding pocket, was substituted by the fluorescent adenine analogue 2-aminopurine (2-AP). Steady-state and time-resolved fluorescence measurements were complemented by UV-melting and circular dichroism studies. The binding of neomycin B at three sites was found to have a strong inverse correlation with Na(+) concentration. For the highest-affinity site, both fluorescence and UV absorption experiments were consistent with a model assuming at least three neomycin NH(3) (+) groups participating in addition to hydrogen bonds in electrostatic interactions with the RNA. The variation of fluorescence intensity and lifetime upon neomycin B binding indicated unstacking of 2-AP16 from neighbouring bases as it flipped over the binding pocket. RNA conformational changes upon binding of the antibiotic were confirmed by circular dichroism. The two weaker binding sites were characterized as unspecific binding to the aptamer, while the high-affinity binding event was shown to be highly specific even at high ionic concentration. In addition, 2-AP was confirmed to be a noninvasive fluorescent probe; it serves as a sensitive spectroscopic tool to investigate details of the interactions between small molecules and RNA.
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Affiliation(s)
- Sabine Stampfl
- Department of Biochemistry, Max F. Perutz Laboratories, Campus Vienna Biocenter 5/1, 1030 Vienna, Austria
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34
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Kostyukov VV, Rogova OV, Pakhomov VI, Evstigneev MP. Structural and thermodynamic analysis of the conformational states of self-complementary hexanucleotides 5′-d(GCATGC) and 5′-d(GCTAGC) in Aqueous Solution. Biophysics (Nagoya-shi) 2007. [DOI: 10.1134/s0006350907040033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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35
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Olsen CM, Gmeiner WH, Marky LA. Unfolding of G-quadruplexes: energetic, and ion and water contributions of G-quartet stacking. J Phys Chem B 2007; 110:6962-9. [PMID: 16571009 DOI: 10.1021/jp0574697] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It has been shown that DNA oligonucleotides composed, in part, of G repeat sequences can adopt G-quadruplex structures in the presence of specific metal ions. In this work, we use a combination of spectroscopic and calorimetric techniques to determine the spectral and thermodynamic characteristics of two DNA aptamers, d(G2T2G2TGTG2T2G2), G2, and d(G3T2G3TGTG3T2G3), G3; a sequence in the promoter region of the c-MYC oncogene, d(TG4AG3TG4AG3TG4A2G2), NHE-III; and the human telomere sequence d(AG3T2AG3T2AG3T2AG3), 22GG. The circular dichroism spectra of these oligonucleotides in the presence of K+ indicate that all form G-quadruplexes with G-quartets in an antiparallel arrangement (G2), in a parallel arrangement (NHE-III and 22GG), or in a mixed parallel and antiparallel G-quartet arrangement (G3). Melting profiles show transition temperatures, TM, above 45 degrees C that are independent of strand concentration, consistent with the formation of very stable intramolecular G-quadruplexes. We used differential scanning calorimetry to obtain complete thermodynamic profiles for the unfolding of each quadruplex. Subtracting the thermodynamic folding profiles of G2 from those of G3 yielded the following thermodynamic profile for the formation of a G-quartet stack: DeltaG degrees 20 = -2.2 kcal/mol, DeltaHcal = -14.6 kcal/mol, TDeltaScal = -12.4 kcal/mol, DeltanK+ = -0.3 mol of K+/mol, and DeltanW = 13 mol of H2O/mol. Furthermore, we used this profile to estimate the thermodynamic contributions of the loops and/or extra base sequences of each oligonucleotide in the G-quadruplex state. The average free energy contributions of the latter indicate that the incorporation of loops and base overhangs stabilizes quadruplex structures. This stabilization is enthalpy-driven and is due to base-stacking contributions.
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Affiliation(s)
- Chris M Olsen
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025, USA
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36
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Rangel DP, Brewood GP, Fujimoto BS, Schurr JM. Effects of ethylene glycol on the torsion elastic constant and hydrodynamic radius of p30δ DNA. Biopolymers 2007; 85:222-32. [PMID: 17111396 DOI: 10.1002/bip.20634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Upon increasing the concentration of ethylene glycol (EG) at 37 degrees C, the twist energy parameter, E(T), which governs the supercoiling free energy, was recently found to undergo a decreasing (or reverse) sigmoidal transition with a midpoint near 20 w/v % EG. In this study, the effects of adding 20 w/v % EG on the torsion elastic constant (alpha) of linear p30delta DNA and on the hydrodynamic radius (R(H)) of a synthetic 24 bp duplex DNA were examined at both 40 and 20 degrees C. The time-resolved fluorescence intensity and fluorescence polarization anisotropy (FPA) of intercalated ethidium were measured in order to assess the effects of 20 w/v % EG on: (1) alpha; (2) R(H); (3) the lifetimes of intercalated and non-intercalated dye; (4) the amplitude of dye wobble in its binding site; and (5) the binding constant for intercalation. The effects of 20 w/v % EG on the circular dichroism (CD) spectrum of the DNA and on the emission spectrum of the free dye were also measured. At 40 degrees C, addition of 20 w/v % EG caused a substantial (1.27- to 1.35-fold) increase in alpha, a significant change in the CD spectrum, and a very small, marginally significant increase in R(H), but little or no change in the amplitude of dye wobble in its binding site or the lifetime of intercalated dye. Together with previously reported measurements of E(T), these results imply that the bending elastic constant of DNA is significantly decreased by 20 w/v % EG at 40 degrees C. At 20 degrees C, addition of 20 w/v % EG caused a marginally significant decrease in alpha and very little change in any other measured properties. Also at 20 degrees C, addition of 30 w/v % betaine caused a marginally significant increase in alpha and significant but modest change in the CD spectrum, but very little change in any other properties.
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Affiliation(s)
- David P Rangel
- Department of Chemistry, Box 351700, University of Washington, Seattle, WA 98195-1700, USA
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37
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Kim J, Doose S, Neuweiler H, Sauer M. The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy. Nucleic Acids Res 2006; 34:2516-27. [PMID: 16687657 PMCID: PMC1459409 DOI: 10.1093/nar/gkl221] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Conformational fluctuations of single-stranded DNA (ssDNA) oligonucleotides were studied in aqueous solution by monitoring contact-induced fluorescence quenching of the oxazine fluorophore MR121 by intrinsic guanosine residues (dG). We applied fluorescence correlation spectroscopy as well as steady-state and time-resolved fluorescence spectroscopy to analyze kinetics of DNA hairpin folding. We first characterized the reporter system by investigating bimolecular quenching interactions between MR121 and guanosine monophosphate in aqueous solution estimating rate constants, efficiency and stability for formation of quenched complexes. We then studied the kinetics of complex formation between MR121 and dG residues site-specifically incorporated in DNA hairpins. To uncover the initial steps of DNA hairpin folding we investigated complex formation in ssDNA carrying one or two complementary base pairs (dC–dG pairs) that could hybridize to form a short stem. Our data show that incorporation of a single dC–dG pair leads to non-exponential decays for opening and closing kinetics and reduces rate constants by one to two orders of magnitude. We found positive activation enthalpies independent of the number of dC–dG pairs. These results imply that the rate limiting step of DNA hairpin folding is not determined by loop dynamics, or by mismatches in the stem, but rather by interactions between stem and loop nucleotides.
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Affiliation(s)
| | - Sören Doose
- To whom correspondence should be addressed. Tel: +49 521 106 5440; Fax: +49 521 106 2958;
| | | | - Markus Sauer
- Correspondence may also be addressed to Markus Sauer. Tel: +49 521 106 5450; Fax: +49 521 106 2958;
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Abstract
A novel method, based upon primer extension, has been developed for measuring the reopening temperature of a single type of DNA hairpin structure. Two DNA oligonucleotides have been utilized and designated as primers 1 and 2. Primer 1, with its 5- and 3'-termini fully complementary to the hairpin flanking sequences, was used to evaluate primer extension conditions, and primer 2, with its 3'-end competing with the DNA hairpin stem, was used to detect the DNA hairpin reopening temperature. A single DNA hairpin structure was formed on the DNA template by thermal denaturation and renaturation, and this hairpin structure was predicted to prevent the annealing of the 3'-end of primer 2 with the template DNA, which leads to no primer extension. By incubating at different temperatures, the DNA hairpin structure can be reopened at a particular temperature where the primer extension can be carried out. This resulted in the appearance of double-stranded DNA that was detected on an agarose gel. This temperature is defined here as the hairpin reopening temperature.
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Affiliation(s)
- Xuefeng Pan
- Institute of Microbiology, The Chinese Academy of Sciences, Beijing, China. ,
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39
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Chien FC, Liu JS, Su HJ, Kao LA, Chiou CF, Chen WY, Chen SJ. An investigation into the influence of secondary structures on DNA hybridization using surface plasmon resonance biosensing. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Raukas E, Kooli K. Protonation of deoxycytidine residues in dC4 tetraloops: UV spectrophotometric study of dC10 and d(A14C4T14). Biophys Chem 2003; 104:429-47. [PMID: 12878311 DOI: 10.1016/s0301-4622(03)00032-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
It is shown that component analysis could be applied to study the UV difference spectra of cytidine oligomers and hairpin oligonucleotides with cytidines in the loop region in order to account for the melting and titration results in terms of cytidine stacking and protonation. Upon acid titration, the dC(10) oligomer undergoes cooperative conformational transition at pH 6.3 accompanied by protonation and formation of the i-structure with half of the residues protonated. The stability of the hemiprotonated structure increases with decreasing pH, the i-structure persisting still in the region of pH<pK of cytidine. An UV difference spectrum that reflects the stacking/unstacking of hemiprotonated cytidine residues was acquired from the melting and titration experiments of the dC(10) oligomer and used to describe the behavior of the dC(4) loop of the hairpin oligonucleotide d(A(14)C(4)T(14)). It is shown that upon titration, the 50% level of protonation of the deoxycytidine tetraloop is attained at pH 5.0. Simultaneously, the stacking interactions of cytidine residues reach the maximum at this pH with two residues stacked, and thereafter decline again. Only marginal stabilization of the oligomer hairpin (DeltaT(m)=1.5 degrees C) is found to accompany the formation of this single hemiprotonated dC.dC(+) base pair. We propose that at pH 5 the cytidines of the dC(4) loop form a hemiprotonated dC.dC(+) pair stacked with the last dA.dT base pair of the hairpin stem.
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Affiliation(s)
- E Raukas
- Institute of Experimental Biology, Estonian Agricultural University, 76902, Harku, Estonia.
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41
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Rudolph JG, White S, Sokolsky C, Bozak D, Mazzanti C, Lipsky RH, Goldman D. Determination of melting temperature for variant detection using dHPLC: a comparison between an empirical approach and DNA melting prediction software. GENETIC TESTING 2003; 6:169-76. [PMID: 12490056 DOI: 10.1089/109065702761403324] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Detection of DNA sequence variants by the use of denaturing high-performance liquid chromatography (dHPLC) is a relatively new method (Underhill et al., 1997) and has distinct advantages over other methods such as single-strand conformation polymorphism (SSCP), direct sequencing, and DNA chip hybridization. The dHPLC-based single-nucleotide polymorphism (SNP) screening relies on different DNA thermodynamic properties between perfectly matched base pairs in homoduplex molecules and single base-pair mismatches in heteroduplex DNAs. Separation of the two forms of duplex DNAs by dHPLC is based on ionic forces between the negatively charged DNA and the hydrophobic stationary phase, which consists of C(18) chains on PSDVB (polystyrene-divinylbenzene) beads coated with a positively charged ion-pairing agent (TEAA, triethylammonium acetate). Removal of the DNA from the TEAA-coated beads is dependent upon a mobile organic phase, in the form of a linear acetonitrile gradient. The major factor that influences the success of dHPLC to detect sequence variation is the thermal stability of the duplex DNA, which is determined by the melting temperature (TM(50)), where 50% of the DNA strand is single stranded and 50% is double stranded. The TM(50) predicts the best probability of detecting a single base-pair change based on the altered thermodynamics it imparts to the DNA duplex. Generally, there are two ways to determine this melting temperature, either empirically or with the aid of predictive DNA melting analysis software. Such programs include the DNAMelt program located on the Stanford University DNA Sequencing and Technology Center website, MeltCalc (Schutz and von Ahsen 1999), and WAVEMAKER, the proprietary melting analysis software provided with the Transgenomic WAVE dHPLC system. The goal of the current study was to determine whether currently available predictive DNA melting programs could be used to increase efficiency and throughput of SNP detection. A wide range of amplicons, differing in both size and GC composition, were selected for analysis to simulate the broad spectrum of PCR products that may be encountered during a large-scale dHPLC screening project.
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Abstract
Single-stranded DNA and RNA molecules in solution can be driven through a nanoscopic pore by an applied electric field. As each molecule occupies the pore, a characteristic blockade of ionic current is produced. Information about length, composition, structure, and dynamic motion of the molecule can be deduced from modulations of the current blockade.
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Affiliation(s)
- David W Deamer
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA.
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Rentzeperis D, Shikiya R, Maiti S, Ho J, Marky LA. Folding of Intramolecular DNA Hairpin Loops: Enthalpy−Entropy Compensations and Hydration Contributions. J Phys Chem B 2002. [DOI: 10.1021/jp0260853] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Dionisios Rentzeperis
- Departments of Pharmaceutical Sciences and Biochemistry and Molecular Biology and Eppley Institute for Cancer Research and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025
| | - Ronald Shikiya
- Departments of Pharmaceutical Sciences and Biochemistry and Molecular Biology and Eppley Institute for Cancer Research and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025
| | - Souvik Maiti
- Departments of Pharmaceutical Sciences and Biochemistry and Molecular Biology and Eppley Institute for Cancer Research and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025
| | - James Ho
- Departments of Pharmaceutical Sciences and Biochemistry and Molecular Biology and Eppley Institute for Cancer Research and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025
| | - Luis A. Marky
- Departments of Pharmaceutical Sciences and Biochemistry and Molecular Biology and Eppley Institute for Cancer Research and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025
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Affiliation(s)
- Yiqing Shen
- Department of Physics (M/C 273) and Department of Bioengineering (M/C 063), University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607
| | - Serguei V. Kuznetsov
- Department of Physics (M/C 273) and Department of Bioengineering (M/C 063), University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607
| | - Anjum Ansari
- Department of Physics (M/C 273) and Department of Bioengineering (M/C 063), University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607
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45
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Kushon SA, Jordan JP, Seifert JL, Nielsen H, Nielsen PE, Armitage BA. Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins. J Am Chem Soc 2001; 123:10805-13. [PMID: 11686681 DOI: 10.1021/ja016310e] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The binding of a series of PNA and DNA probes to a group of unusually stable DNA hairpins of the tetraloop motif has been observed using absorbance hypochromicity (ABS), circular dichroism (CD), and a colorimetric assay for PNA/DNA duplex detection. These results indicate that both stable PNA-DNA and DNA-DNA duplexes can be formed with these target hairpins, even when the melting temperatures for the resulting duplexes are up to 50 degrees C lower than that of the hairpin target. Both hairpin/single-stranded and hairpin/hairpin interactions are considered in the scope of these studies. Secondary structures in both target and probe molecules are shown to depress the melting temperatures and free energies of the probe-target duplexes. Kinetic analysis of hybridization yields reaction rates that are up to 160-fold slower than hybridization between two unstructured strands. The thermodynamic and kinetic obstacles to hybridization imposed by both target and probe secondary structure are significant concerns for the continued development of antisense agents and especially diagnostic probes.
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Affiliation(s)
- S A Kushon
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA
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Kuznetsov SV, Shen Y, Benight AS, Ansari A. A semiflexible polymer model applied to loop formation in DNA hairpins. Biophys J 2001; 81:2864-75. [PMID: 11606297 PMCID: PMC1301751 DOI: 10.1016/s0006-3495(01)75927-9] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
A statistical mechanical "zipper" model is applied to describe the equilibrium melting of short DNA hairpins with poly(dT) loops ranging from 4 to 12 bases in the loop. The free energy of loop formation is expressed in terms of the persistence length of the chain. This method provides a new measurement of the persistence length of single-stranded DNA, which is found to be approximately 1.4 nm for poly(dT) strands in 100 mM NaCl. The free energy of the hairpin relative to the random coil state is found to scale with the loop size with an apparent exponent of > or = 7, much larger than the exponent of approximately 1.5-1.8 expected from considerations of loop entropy alone. This result indicates a strong dependence of the excess stability of the hairpins, from stacking interactions of the bases within the loop, on the size of the loop. We interpret this excess stability as arising from favorable hydrophobic interactions among the bases in tight loops and which diminish as the loops get larger. Free energy profiles along a generalized reaction coordinate are calculated from the equilibrium zipper model. The transition state for hairpin formation is identified as an ensemble of looped conformations with one basepair closing the loop, and with a lower enthalpy than the random coil state. The equilibrium model predicts apparent activation energy of approximately -11 kcal/mol for the hairpin closing step, in remarkable agreement with the value obtained from kinetics measurements.
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Affiliation(s)
- S V Kuznetsov
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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Gmeiner WH, Hudalla CJ, Soto AM, Marky L. Binding of ethidium to DNA measured using a 2D diffusion-modulated gradient COSY NMR experiment. FEBS Lett 2000; 465:148-52. [PMID: 10631323 DOI: 10.1016/s0014-5793(99)01741-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The binding of ethidium bromide to a DNA hairpin (dU(5)-hairpin) was investigated using a novel 2D diffusion-modulated gradient correlation spectroscopy (DMG-COSY) experiment to evaluate the applicability of this technique for studying the binding of drugs to DNA. The DMG-COSY experiment includes a preparation period during which coherent magnetization is attenuated due to molecular self-diffusion. Magnetization then evolves due to scalar coupling during an evolution delay, and is detected using gradient pulses for coherence selection. The time-domain data are processed in an analogous manner as for gradient-selected COSY experiments. The diffusion coefficient for uridine in DMSO solution was determined from the H5-H6 crosspeak intensities for a series of 2D DMG-COSY experiments that differed in the magnitude of the gradient pulses applied during the preparation period of the DMG-COSY experiment. The diffusion coefficient for uridine calculated from the DMG-COSY experiments was identical (within experimental error) to that determined from 1D diffusion experiments (5.24x10(-6) cm(2)/s at 26 degrees C). The diffusion coefficients for ethidium bromide and for the dU(5)-hairpin were first measured separately using the DMG-COSY experiment, and then measured in the putative complex. The diffusion coefficient for free ethidium bromide (4.15x10(-6) cm(2)/s at 26 degrees C) was considerably larger than for the dU(5)-hairpin (1. 60x10(-6) cm(2)/s at 26 degrees C), as expected for the smaller molecule. The diffusion coefficient for ethidium was markedly decreased upon addition of the dU(5)-hairpin, consistent with complex formation (1.22x10(-6) cm(2)/s at 26 degrees C). Complex formation of 1:1 stoichiometry between ethidium and the stem of the dU(5)-hairpin was verified independently by fluorescence spectroscopy. These results demonstrate the utility of the DMG-COSY experiment for investigating the binding of drugs to DNA in aqueous solution.
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Affiliation(s)
- W H Gmeiner
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Medical Center, Omaha, NE 68198-6805, USA
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Eggleston MK, Crites DK, McMillin DR. Studies of the Base-Dependent Binding of Cu(T4) to DNA Hairpins (H2T4 = meso-Tetrakis(4-(N-methylpyridiumyl))porphyrin). J Phys Chem A 1998. [DOI: 10.1021/jp980059g] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
| | - Denise K. Crites
- Department of Chemistry, Purdue University, W. Lafayette, Indiana 47907-1393
| | - David R. McMillin
- Department of Chemistry, Purdue University, W. Lafayette, Indiana 47907-1393
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