1
|
Mu ZC, Tan YL, Zhang BG, Liu J, Shi YZ. Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions. PLoS Comput Biol 2022; 18:e1010501. [PMID: 36260618 PMCID: PMC9621594 DOI: 10.1371/journal.pcbi.1010501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/31/2022] [Accepted: 09/27/2022] [Indexed: 11/07/2022] Open
Abstract
The three-dimensional (3D) structure and stability of DNA are essential to understand/control their biological functions and aid the development of novel materials. In this work, we present a coarse-grained (CG) model for DNA based on the RNA CG model proposed by us, to predict 3D structures and stability for both dsDNA and ssDNA from the sequence. Combined with a Monte Carlo simulated annealing algorithm and CG force fields involving the sequence-dependent base-pairing/stacking interactions and an implicit electrostatic potential, the present model successfully folds 20 dsDNAs (≤52nt) and 20 ssDNAs (≤74nt) into the corresponding native-like structures just from their sequences, with an overall mean RMSD of 3.4Å from the experimental structures. For DNAs with various lengths and sequences, the present model can make reliable predictions on stability, e.g., for 27 dsDNAs with/without bulge/internal loops and 24 ssDNAs including pseudoknot, the mean deviation of predicted melting temperatures from the corresponding experimental data is only ~2.0°C. Furthermore, the model also quantificationally predicts the effects of monovalent or divalent ions on the structure stability of ssDNAs/dsDNAs. To determine 3D structures and quantify stability of single- (ss) and double-stranded (ds) DNAs is essential to unveil the mechanisms of their functions and to further guide the production and development of novel materials. Although many DNA models have been proposed to reproduce the basic structural, mechanical, or thermodynamic properties of dsDNAs based on the secondary structure information or preset constraints, there are very few models can be used to investigate the ssDNA folding or dsDNA assembly from the sequence. Furthermore, due to the polyanionic nature of DNAs, metal ions (e.g., Na+ and Mg2+) in solutions can play an essential role in DNA folding and dynamics. Nevertheless, ab initio predictions for DNA folding in ion solutions are still an unresolved problem. In this work, we developed a novel coarse-grained model to predict 3D structures and thermodynamic stabilities for both ssDNAs and dsDNAs in monovalent/divalent ion solutions from their sequences. As compared with the extensive experimental data and available existing models, we showed that the present model can successfully fold simple DNAs into their native-like structures, and can also accurately reproduce the effects of sequence and monovalent/divalent ions on structure stability for ssDNAs including pseudoknot and dsDNAs with/without bulge/internal loops.
Collapse
Affiliation(s)
- Zi-Chun Mu
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
- School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan, China
| | - Ya-Lan Tan
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
| | - Ben-Gong Zhang
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
| | - Jie Liu
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
- * E-mail:
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Carr CE, Marky LA. Effect of GCAA stabilizing loops on three- and four-way intramolecular junctions. Phys Chem Chem Phys 2018; 20:5046-5056. [PMID: 29388988 DOI: 10.1039/c7cp08329g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Tetraloops are a common way of changing the melting behavior of a DNA or RNA structure without changing the sequence of the stem. Because of the ubiquitous nature of tetraloops, our goal is to understand the effect a GCAA tetraloop, which belongs to the GNRA family of tetraloops, has on the unfolding thermodynamics of intramolecular junctions. Specifically, we have described the melting behavior of intramolecular three-way and four-way junctions where a T5 loop has been replaced with a GCAA tetraloops in different positions. Their thermodynamic profiles, including ΔnNa+ and ΔnW, were analyzed based on the position of the tetraloop. We obtained between -16.7 and -27.5 kcal mol-1 for all junctions studied. The experimental data indicates the influence of the GCAA tetraloop is primarily dictated by the native unfolding of the junction; if the tetraloop is placed on a stem that unfolds as a single domain when the tetraloop is not present, it will unfold as a single domain when the tetraloop is present but with a higher thermal stability. Conversely, if the tetraloop is placed on a stem which unfolds cooperatively with other stems when the tetraloop is not present, the tetraloop will increase the thermal stability of all the stems in the melting domain. The oligonucleotide structure and not the tetraloop itself affects ion uptake; three-way junctions do not gain an increase in ion uptake, but four-way junctions do. This is not the case for water immobilization, where the position of the tetraloop dictates the amount of water immobilized.
Collapse
Affiliation(s)
- Carolyn E Carr
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA.
| | | |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Minetti CASA, Remeta DP, Iden CR, Johnson F, Grollman AP, Breslauer KJ. Impact of thymine glycol damage on DNA duplex energetics: Correlations with lesion-induced biochemical and structural consequences. Biopolymers 2016; 103:491-508. [PMID: 25991500 DOI: 10.1002/bip.22680] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 05/08/2015] [Accepted: 05/12/2015] [Indexed: 11/08/2022]
Abstract
The magnitude and nature of lesion-induced energetic perturbations empirically correlate with mutagenicity/cytotoxicity profiles and can be predictive of lesion outcomes during polymerase-mediated replication in vitro. In this study, we assess the sequence and counterbase-dependent energetic impact of the Thymine glycol (Tg) lesion on a family of deoxyoligonucleotide duplexes. Tg damage arises from thymine and methyl-cytosine exposure to oxidizing agents or radiation-generated free-radicals. The Tg lesion blocks polymerase-mediated DNA replication in vitro and the unrepaired site elicits cytotoxic lethal consequences in vivo. Our combined calorimetric and spectroscopic characterization correlates Tg -induced energetic perturbations with biological and structural properties. Specifically, we incorporate a 5R-Tg isomer centered within the tridecanucleotide sequence 5'-GCGTACXCATGCG-3' (X = Tg or T) which is hybridized with the corresponding complementary sequence 5'-CGCATGNGTACGC-3' (N = A, G, T, C) to generate families of Tg -damaged (Tg ·N) and lesion-free (T·N) duplexes. We demonstrate that the magnitude and nature of the Tg destabilizing impact is dependent on counterbase identity (i.e., A ∼ G < T < C). The observation that a Tg lesion is less destabilizing when positioned opposite purines suggests that favorable counterbase stacking interactions may partially compensate lesion-induced perturbations. Moreover, the destabilizing energies of Tg ·N duplexes parallel their respective lesion-free T·N mismatch counterparts (i.e., G < T < C). Elucidation of Tg-induced destabilization relative to the corresponding undamaged mismatch energetics allows resolution of lesion-specific and sequence-dependent impacts. The Tg-induced energetic perturbations are consistent with its replication blocking properties and may serve as differential recognition elements for discrimination by the cellular repair machinery.
Collapse
Affiliation(s)
- Conceição A S A Minetti
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, NJ, 08854
| | - David P Remeta
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, NJ, 08854
| | - Charles R Iden
- Department of Pharmacological Sciences, School of Medicine, Stony Brook University, Stony Brook, NY, 11794
| | - Francis Johnson
- Department of Pharmacological Sciences, School of Medicine, Stony Brook University, Stony Brook, NY, 11794
| | - Arthur P Grollman
- Department of Pharmacological Sciences, School of Medicine, Stony Brook University, Stony Brook, NY, 11794
| | - Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, NJ, 08854.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08901
| |
Collapse
|
8
|
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
| |
Collapse
|
9
|
Reiling C, Khutsishvili I, Huang K, Marky LA. Loop Contributions to the Folding Thermodynamics of DNA Straight Hairpin Loops and Pseudoknots. J Phys Chem B 2015; 119:1939-46. [DOI: 10.1021/jp5116417] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Calliste Reiling
- 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
| | - Kai Huang
- 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
| |
Collapse
|
10
|
Prislan I, Lee HT, Lee C, Marky LA. The size of the internal loop in DNA hairpins influences their targeting with partially complementary strands. J Phys Chem B 2014; 119:96-104. [PMID: 25486129 PMCID: PMC4291056 DOI: 10.1021/jp510131c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Targeting of noncanonical DNA structures,
such as hairpin loops,
may have significant diagnostic and therapeutic potential. Oligonucleotides
can be used for binding to mRNA, forming a DNA/RNA hybrid duplex that
inhibits translation. This kind of modulation of gene expression is
called the antisense approach. In order to determine the best strategy
to target a common structural motif in mRNA, we have designed a set
of stem-loop DNA molecules with sequence: d(GCGCTnGTAAT5GTTACTnGCGC),
where n = 1, 3, or 5, “T5” is an end loop of five thymines. We used a combination
of calorimetric and spectroscopy techniques to determine the thermodynamics
for the reaction of a set of hairpins containing internal loops with
their respective partially complementary strands. Our aim was to determine
if internal- and end-loops are promising regions for targeting with
their corresponding complementary strands. Indeed, all targeting reactions
were accompanied by negative changes in free energy, indicating that
reactions proceed spontaneously. Further investigation showed that
these negative free energy terms result from a net balance of unfavorable
entropy and favorable enthalpy contributions. In particular, unfolding
of hairpins and duplexes is accompanied by positive changes in heat
capacity, which may be a result of exposure of hydrophobic groups
to the solvent. This study provides a new method for the targeting
of mRNA in order to control gene expression.
Collapse
Affiliation(s)
- Iztok Prislan
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center , 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
| | | | | | | |
Collapse
|
11
|
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.
Collapse
Affiliation(s)
- Irina V Nesterova
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
| | | | | |
Collapse
|
12
|
Melting behavior and ligand binding of DNA intramolecular secondary structures. Biophys Chem 2011; 159:162-71. [DOI: 10.1016/j.bpc.2011.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Revised: 06/08/2011] [Accepted: 06/10/2011] [Indexed: 11/23/2022]
|
13
|
Smiatek J, Chen C, Liu D, Heuer A. Stable conformations of a single stranded deprotonated DNA i-motif. J Phys Chem B 2011; 115:13788-95. [PMID: 21995652 DOI: 10.1021/jp208640a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present molecular dynamics simulations of a single stranded deprotonated DNA i-motif in explicit solvent. Our results indicate that hairpin structures are stable equilibrium conformations at 300 K. The entropic preference of these configurations is explained by strong water ordering effects due to the present number of hydrogen bonds. We observe a full unfolding at higher temperatures in good agreement with experimental results.
Collapse
Affiliation(s)
- Jens Smiatek
- Institut für Physikalische Chemie, Universität Münster, D-48149 Münster, Germany.
| | | | | | | |
Collapse
|
14
|
|
15
|
del Mundo IMA, Fountain MA, Morrow JR. Recognition of thymine in DNA bulges by a Zn(II) macrocyclic complex. Chem Commun (Camb) 2011; 47:8566-8. [PMID: 21706105 DOI: 10.1039/c1cc12074c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A Zn(II) macrocyclic complex with appended quinoline is a bifunctional recognition agent that uses both the Zn(II) center and the pendent aromatic group to bind to thymine in bulges with good selectivity over DNA containing G, C or A bulges. Spectroscopic studies show that the stem containing the bulge stays largely intact in a DNA hairpin with the Zn(II) complex bound to the thymine bulge.
Collapse
Affiliation(s)
- Imee Marie A del Mundo
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY, USA
| | | | | |
Collapse
|
16
|
Shikiya R, Marky LA. Calorimetric unfolding of intramolecular triplexes: length dependence and incorporation of single AT --> TA substitutions in the duplex domain. J Phys Chem B 2007; 109:18177-83. [PMID: 16853334 DOI: 10.1021/jp052327y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA triplexes have been the subject of great interest due to their ability to interfere with gene expression. The inhibition of gene expression involves the design of stable triplexes under physiological conditions; therefore, it is important to have a clear understanding of the energetic contributions controlling their stability. We have used a combination of UV spectroscopy and differential scanning calorimetric (DSC) techniques to investigate the unfolding of intramolecular triplexes, d(A(n)C5T(n)C5T(n)), where n is 5-7, 9, and 11, and related triplexes with a single AT --> TA substitution in their duplex stem. Specifically, we obtain standard thermodynamic profiles for the unfolding of each triplex in buffer solutions containing 0.1 M or 1 M NaCl. The triplexes unfold in monophasic or biphasic transitions (triplex --> duplex --> coil) depending on the concentration of salt used and position of the substitution, and their transition temperatures are independent of strand concentration. The DSC curves of the unsubstituted triplexes yielded an unfolding heat of 13.9 kcal/mol for a TAT/TAT base-triplet stack and a heat capacity of 505 cal/ degrees C.mol. The incorporation of a single substitution destabilizes triplex formation (association of the third strand) to a larger extent in 0.1 M NaCl, and the magnitude of the effects also depends on the position of the substitution. The combined results show that a single AT --> TA substitution in a homopurine/homopyrimidine duplex does not allow triplex formation of the neighboring five TAT base triplets, indicating that the in vivo formation of triplexes, such as H-DNA, is exclusive to homopurine/homopyrimidine sequences.
Collapse
Affiliation(s)
- Ronald Shikiya
- Department of Pharmaceutical Sciences and Biochemistry and Molecular Biology, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | | |
Collapse
|
17
|
Strohsahl CM, Krauss TD, Miller BL. Identification of high-stringency DNA hairpin probes by partial gene folding. Biosens Bioelectron 2007; 23:233-40. [PMID: 17512187 DOI: 10.1016/j.bios.2007.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Revised: 03/13/2007] [Accepted: 04/05/2007] [Indexed: 10/23/2022]
Abstract
Hairpin DNA sequences are widely used as probes for oligonucleotides in a broad range of assays, often as "molecular beacons". A potential disadvantage of the standard methodology for molecular beacon design is the need to add several self-complementary bases to each end of the probe, since these do not correspond to the target sequence. We describe a conceptually new method of hairpin DNA probe identification, in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within an expressed gene having the requisite hairpin structure. Intuitively, such probes should have significantly improved performance over "traditional" hairpin probes, because they are fully complementary with the target. We present experimental evidence verifying this hypothesis for a series of hairpin probes targeting the pag gene of Bacillus anthracis.
Collapse
Affiliation(s)
- Christopher M Strohsahl
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, USA
| | | | | |
Collapse
|