Genetic cancer definition. Computational and Mathematical Methods in Medicine
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Triple helix forming oligonucleotides, which bind to double-stranded DNA, are of special interest since they are targeted to the gene itself rather than câți viermi de pin trăiesc în mediu its mRNA product as in the antisense strategy. However, the poor stability of some of these structures might genetic cancer definition their use under physiological conditions. Specific ligands can intercalate into DNA triple helices and stabilize them.
This review summarizes recent advances in this field while also highlighting major obstacles that remain to be overcome, before the application of triplex technology to therapeutic gene repair can be achieved. Triple helix formation fig. In intermolecular structures, an oligopyrimidine-oligopurine sequence of DNA duplex is bound by a third-strand oligonucleotide in the major groove [ 3 ].
Figure 1: DNA triple helix Two main types of triple helices have been described, depending on the orientation of the third strand [ 4 ]. The first reported triple-helical complexes involved pyrimidic third strand whose binding rests on Hoogsteen hydrogen bonds between a T-A base pair and thymine, and between a C-G base pair and protonated cytosine [ 56 ].
The T, C -containing oligonucleotide binds parallel to the oligopurine strand in the so-called pyrimidine motif.
A second category of triple helices contains purines in the third strand, which is oriented antiparallel to the oligopurine strand. Oligonucleotides containing T and G can also form triple helices whose orientation depends on the base sequence [ 9 ]. Triple helix formation offers a direct means of selectively manipulating gene expression in cells where DNA triple helices offer new perspectives toward oligonucleotide directed gene regulation fig.
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Synthetic triple helix forming oligonucleotides TFOs bind with high affinity and specificity to the purine strand in the major groove of homopurine- homopyrimidine sequence in double-stranded DNA [ 10 ]. They have been studied in antisense applications, genetic cancer definition they are designed to target mRNAs, antigene applications, where they control gene expression via triple helix formation, and in applications that target proteins, where they are used as aptamers [ 112 - 15 ].
TFOs can also be used in gene therapy where they target DNA sequence of mutated gene to prevent its transcription. Triplex-mediated modulation of transcription has potential application in therapy since it can be used; for example, to reduce levels of proteins thought to be important in disease processes. TFOs can also be used as molecular tools for studying gene expression and they have been proved to be effective in various gene-targeting strategies in living cells.
The specificity of this binding raises the possibility of using triplex formation for directed genome modification, with the ultimate goal of repairing genetic defects in human cells. Several studies have demonstrated that treatment of mammalian cells with TFOs can provoke DNA repair and recombination, in a manner that can be exploited to introduce, desired sequence changes. A number of studies have been reported in which oligonucleotides were utilized as antigene compounds genetic cancer definition the cells [ 2 ].
Formation of triple helix DNA Triple helix formation is a result of oligoinucleotides binding with a high specificity of recognition genetic cancer definition the major groove of double helical DNA by forming Hoogsteen type bonds with purine bases of the Watson-Crick base pairs, the compound rationally designed genetic cancer definition artificial regulation of gene expression [ 16 ].
In the triple helix or antigene strategy, the oligonucleotide binds in the major groove of double-stranded DNA via Hoogsteen hydrogen bonding to form a triple helix [ 56 ]. There are four structural motifs for triplex formation that have been described based on the third-strand composition and its orientation relative to the purine-rich strand of the duplex.
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The antiparallel orientation is favored by a greater number of steps, while a low number of steps favor the parallel orientation [ 18 ]. Once the best motif for binding a particular target sequence is established, problems with natural phosphodiester oligonucleotides limit the success of the antigene approach and the therapeutic applications of oligonucleotides in general.
Oligonucleotides with the natural phosphodiester backbone are susceptible to endo and exonucleases.
The predominant activity that degrades oligonucleotides is 3'-exonuclease activity, but endonuclease activity has also been observed in some settings [ 1920 ]. Thus, for application as therapeutics in vivo TFOs must be able to resist both exonuclease and endonuclease activity in order to reach their target.
A backbone modification that confers nuclease resistance but allows binding to double-stranded DNA with high affinity is required for the in vivo applications of TFOs. Phosphorodiamidate morpholino oligomers are modified backbone genetic cancer definition that have previously been investigated as antisense agents [ 2122 ]. Morpholino oligonucleotides have an uncharged backbone in which the deoxyribose sugar of DNA is replaced by a six-membered ring and the phosphodiester linkage is replaced by a phosphorodiamidate linkage [ 23 ] fig.
Morpholino oligonucleotides are genetic cancer definition to enzymatic degradation [ 24 ] and appear to function as antisense agents by arresting translation or interfering with pre-mRNA conjunctiva squamous papilloma rather than by activating RNase H [ 2526 ]. They have been successfully delivered to tissue culture cells by methods that physically disrupt the cell membrane, and one study comparing several of these methods found that scrape-loading was the most efficient method of delivery; however, because the morpholino backbone is uncharged, cationic lipids are not effective mediators of morpholino oligonucleotide uptake in cells [ 27 ].
A recent report demonstrated triplex formation by a morpholino oligonucleotide and, because of the non-ionic backbone, these studies showed that the morpholino oligonucleotide was capable of triplex formation in the absence of magnesium [ 28 ]. Figure 3: Structural presentation of phosphodiester DNA and morpholino Cations have been shown to play an important role in triple helix formation. When phosphodiester oligonucleotides are used as TFOs, magnesium is generally required for genetic cancer definition formation with purine and mixed motif TFOs; it also speeds the reaction and stabilizes the triplex formed with pyrimidine motif TFOs [ 29 - 31 ].
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Other divalent cations have been shown to function in the same capacity as magnesium with regard to triplex formation [ 32 ]. Magnesium occurs at a concentration of ~0. Potassium occurs in the cell at a concentration of ~ mM, and at 4 mM in the blood.
High concentrations of potassium can inhibit triplex formation with guanine-rich oligonucleotides designed as TFOs by favoring other secondary DNA structures, such as dimers and quadruplexes [ 1834 - 38 ]. It will be necessary to overcome the limited ability of phosphodiester TFOs to form a triplex in low magnesium and high potassium genetic cancer definition them to be effective under physiological conditions.
In a recent study of morpholino TFOs, triplex formation was demonstrated in the absence of magnesium and in the presence of potassium. These properties make morpholino TFOs good genetic cancer definition for further study as antigene therapeutics. Molecular modeling DNA triplex structure can be constructed by molecular modeling techniques by using coordinates that correctly take into account the sugar conformation of T,C -motif triple helices [ 39 ].
This structure is closer to genetic cancer definition B-form DNA as reported by NMR studies [ 4041 ] as compared to the structure proposed [ 42 ], based on fiber X-ray diffraction. Using molecular modeling, one can demonstrate the possibility of forming a parallel triple helix in which the single strand interacts with the intact duplex in the minor groove, via novel base interactions [ 44 ].
JUMNA uses a mixture of helical and internal coordinates valence and dihedral angles to describe nucleic acid flexibility. The helical parameters position each 3'monophosphate nucleotide with respect to a fixed-axis system. Junctions between successive nucleotides are maintained with quadratic restraints on the O5'-C5' distances.
In addition to a reduced number of variables with respect to Cartesian coordinate programs, papilloma intraductal adalah choice of physically meaningful variables allows large, concerted conformational moves during minimization, together with an efficient control of the structure and easy introduction of constraints or restraints.
Available tools include both adiabatic mapping and combinatorial searches with respect to chosen structural parameters. The slope S, the plateau genetic cancer definition at long distance D, and the initial value D0 of the function are adjustable, with default values of 0.
First, the base triplets are restrained to be coplanar to avoid any possible interbase triplet interactions. Such interactions easily form during the construction of stretched helices but cannot play a role in recognition or strand exchange, since these processes are independent of the overall sequence. It has been checked out that the optimized structure of the minor-groove triplex is independent of these restraints.
For this reason preliminary studies have been limited to sequences with trinucleotide repeat. Specific restraints or constraints are needed for genetic cancer definition cancer definition construction and manipulation. The trinucleotide symmetry constraint implies the equivalence of the variables describing each successive group of three nucleotides. Stretching dsDNA, so that the twist decreases and the minor groove opens have been previously achieved by restraining the distance between the terminal O3' atoms of the trinucleotide symmetry unit.
This restraint has been slightly modified because the O3'-O3' distance can be altered by a lateral displacement of the backbones during strand exchange. In a recent work, only the component of the O3'-O3' vector parallel to the helix axis genetic cancer definition restrained.
Genetic cancer definition restraints on the groove width, calibrated with the help of numerical Poisson-Boltzmann electrostatic calculations, were used to avoid groove narrowing due to the lack of explicit solvent molecules [ 47 ].
Base pair switching is studied by base rotation, using the approach defined genetic cancer definition Bernet et al [ 48 ].
This involves a restraint applied to the angle θ between the glycosidic bond purine: C1'-N9 or pyrimidine: C1'-N1 and the vector joining the two C1' atoms of a base pair, projected on the plane perpendicular to a local helical axis.
Obstacles and limitations encountered in triple helix formation Biological applications of TFOs are compromised by fundamental biophysical considerations, as well as limitations imposed by physiological conditions. Triplex formation involves the approach and binding of a negatively charged third strand to a double-negatively charged duplex. Furthermore, triplex formation involves conformational changes on the part of the third strand, and some distortion of the underlying duplex genetic cancer definition 4049 - 52 ].
This is necessary for the second Hoogsteen hydrogen bond, although the resultant positive charge apparently makes the more important contribution to triplex stability [ 53 ].
Pyrimidine motif triplexes containing adjacent cytosines are often less stable than those with isolated cytosines. Traditionally this has been ascribed to charge-charge repulsion effects [ 54 ], although a recent study suggests incomplete protonation of adjacent cytosines may be the critical factor [ 55 ].
All these factors impose kinetic barriers on triplex formation and reduce the stability of triplexes once formed most triplexes, even under optimal conditions in vitro, are less stable than the underlying duplex [ 57 ].
Strategies to counteract the limitations The first and foremost problem encountered in triple helical antigene strategy is the instability of the triplex formed by the TFOs under physiological conditions which consequently limits the utilization of this very fascinating strategy meant for gene correction to variable extent. Hence various approaches and strategies have been proposed to confer stability to the triple helical structure formed. Oligonucleotide directed triple helices could be stabilized by using nucleic acid ligands that genetic cancer definition stabilize triple helices.
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For example, ethidium bromide has been shown to bind and stabilize a triple helix made of poly dT ·poly dA × poly dTwhich contains only T·A×T triplets [ 58 ].
Benzopyridoindole derivatives were the first molecules reported to strongly stabilize this latter type of triple helices even though they have a preference for T·A×T stretches [ 60 ]. Several other intercalators [ 61 ] as well as various DNA minor groove ligands [ 62 - 64 ] have also been shown to bind to DNA triple helices.
For example triple helices can be stabilized by chemical modification of oligonucleotides such as, psoralene attached to oligonucleotides has been shown to enhance their biological activity following UV irradiation [ 6566 ].
Intercalators usually stabilize to a greater extent triple helices containing T·A×T triplets, whereas minor groove binders usually destabilize triplexes, except in a particular case where the triple helix involved an RNA strand [ 67 ]. Because no structural data are available on triple helix-ligand complexes, not much is known about the interactions that direct specific intercalation into triple helices.
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BPI derivatives have been shown to intercalate between T·A×T base triplets by excitation fluorescence energy transfer from base triplets to ligands [ 6068 ] and by linear and circular dichroism [ 69 ]. Pyrimidine-parallel morpholino oligonucleotides were found to be able to form a triplex with duplex target. As expected, this motif required a low pH for triplex formation, as required by the pyrimidine-parallel motif phosphodiester TFO.
It may be possible to overcome this pH dependence with such substitutions as 5-methylcytosine for the cytosines in the TFO [ 70 ].
An alternative approach by which triple helices can be stabilized is via chemical modifications of oligonucleotides, such as covalent attachment of an acridine molecule [ 71 ]. It has been shown that acridine substitution strongly increases the inhibition of restrictin enzyme cleavage and also it does not genetic cancer definition sequence specificity for triplex genetic cancer definition [ 71 ].
Applications of Triple Helix DNA The formation of intermolecular DNA triple helices offers the possibility of designing compounds with extensive sequence recognition properties, which may be useful as antigene agents or tools in molecular biology [ 72 ]. During the past decade, a new approach using DNA analogues, as therapeutic agents, is emerging in medicinal chemistry.
It is affected through sequence-specific binding of complementary oligonucleotides to either DNA duplex sensul paraziților în telugu triplex formation to inhibit production of mRNA or interfere in the translation of the latter to proteins.
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Since oligonucleotides do not enter cells easily and are amenable to destruction by cellular nucleases, a variety of chemically modified analogues of oligonucleotides are being designed, synthesized and evaluated for development as therapeutic agents.
Figure 4: Principles of antigene and antisense therapeutics The specific recognition of homopurine-homo pyrimidine regions in duplex DNA by triplex-forming oligonucleotides TFOs provides an attractive strategy for genetic manipulation, with the ultimate goal of repairing genetic defects in human cells.
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Efficient tools based on triple helices were developed for various biochemical applications such as the development of highly specific artificial nucleases. The antigene strategy remains one of the most fascinating fields of triplex application to selectively control gene expression Table 1. Targeting of genomic sequences is now proved to be a valuable concept on a still limited number of studies; local mutagenesis is in this respect an interesting application of triplex-forming oligonucleotides, on cell cultures [ 74 ].