Abstract : Nucleotide analog interference mapping (NAIM) is a combinatorial approach that probes individual atoms and functional groups in an RNA molecule and identifies those that are important for a specific biochemical function. Here, we show how NAIM can be adapted to reveal functionally important atoms and groups on RNA substrates of helicases. We explain how NAIM can be used to investigate translocation and unwinding mechanisms of helicases and discuss the advantages and limitations of this powerful chemogenetic approach.. ...
Although interferon (IFN) signaling induces genes that limit viral infection, many pathogenic viruses overcome this host response. As an example, 2-O methylation of the 5′ cap of viral RNA subverts mammalian antiviral responses by evading restriction of Ifit1, an IFN-stimulated gene that regulates protein synthesis. However, alphaviruses replicate efficiently in cells expressing Ifit1 even though their genomic RNA has a 5′ cap lacking 2-O methylation. We show that pathogenic alphaviruses use secondary structural motifs within the 5′ untranslated region (UTR) of their RNA to alter Ifit1 binding and function. Mutations within the 5′-UTR affecting RNA structural elements enabled restriction by or antagonism of Ifit1 in vitro and in vivo. These results identify an evasion mechanism by which viruses use RNA structural motifs to avoid immune restriction.. ...
Disclosed is a method for detecting a nucleic acid target sequence by formation of triple helix nucleic acid structures. The method may, but need not, involve amplifying the nucleic acid in vitro using cycles of denaturation and amplification to yield product duplexes, and detecting the product duplexes by hybridizing a third strand of nucleic acid to the product duplexes without denaturation. The triple helix-forming duplex sequences may be endogenous to the target sequence being detected, or they may be introduced in the probes used during amplification.
A miRNA-inhibiting RNA complex has a double-stranded structure, in which at least one RNA strand that includes a miRNA-binding sequence is linked to the two strands at at least one end of the double-stranded structure. The complex can efficiently inhibit miRNAs. In particular, RNAs in which two RNAs containing a miRNA binding sequence are positioned between two double-stranded structures were able to strongly inhibit miRNA. These RNAs can be expressed from, for example, a PolIII promoter, and by integration into a vector, miRNAs can be stably inhibited for a long period of time.
The RNA shapes studio comprises four RNA secondary structure prediction tools, which make heavy use of shape abstraction. An abstract shape is a mathematically well defined coarse grained view of an RNA structure, supporting the user to focus only on "interesting" structural features. RNAshapes and pKiss operate on single sequence inputs. Their counterparts RNAalishapes and pAliKiss take an multiple sequence alignment as input. RNAshapes and RNAalishapes predict purely nested secondary structures. pKiss and pAliKiss additionally consider H-type pseudoknots and kissing hairpins. KnotInFrame - KnotInFrame is a pipeline to predict ribosomal -1 frameshift sites with a simple pseudoknot as secondary structure in DNA and RNA sequences.. pAliKiss - pAliKiss is a tool for secondary structure prediction including kissing hairpin motifs.. pKiss - pKiss is a tool for secondary structure prediction including kissing hairpin motifs.. pknotsRG - RNA folding and thermodynamic matching RapidShapes - Computes a ...
A common problem for researchers working with RNA is to determine the three-dimensional structure of the molecule. However, in the case of RNA much of the final structure is determined by the secondary structure or intra-molecular base-pairing interactions of the molecule. This is shown by the high conservation of base-pair across diverse species. One of the first attempts to predict RNA secondary structure was made by Ruth Nussinov and co-workers who used dynamic programming method for maximising the number of base-pairs [1]. However, there are several issues with this approach, most importantly the solution is not unique. Nussinov et al published an adaptation of their approach to use a simple nearest-neighbour energy model in 1980 [2]. Michael Zuker and Patrick Stiegler in 1981 proposed using a slightly refined dynamic programming approach that models nearest neighbour energy interactions that directly incorporates stacking into the prediction [3]. The energies that are minimized by the ...
Since the famous discovery of the structure of the DNA double helix, referred to as the canonical, right-handed B-form DNA by Watson and Crick, experimental evidence has revealed the existence of more than a dozen alternative (or non-B) DNA secondary structures. These include, among others, stem-loops (also known as cruciforms or hairpins), triplexes or H-DNA, quadruplexes or G4 DNA, A-DNA, and Z-DNA The important role of DNA secondary structures in various genomic processes is documented experimentally in genomes of many organisms from bacteria to humans. It was shown that stem-loop structures can function as terminators, attenuators, promoter and recognition elements, while cruciform structures play roles in DNA replication, and genetic instability. Triplexes (H-DNA) have been shown to play roles in transcriptional repression, recombination, and genetic instability. Quadruplexes can regulate DNA replication, gene expression, and telomere maintenance. A-DNA can play an essential role in
One focus of our research is to further our understanding of the physico-chemical properties of non-canonical nucleic acid structures. In this work, DNA hairpins are used to mimic a common motif present in RNA, i.e., a stem-loop motif with a bulge or inte
The initial interaction between the ColE1 plasmid specific transcripts RNA I and RNA II, which function as antisense regulators of plasmid replication, comprises a transient complex between complementary loops found within the RNA secondary structures. Multidimensional heteronuclear magnetic resonance spectroscopy was used to characterize complexes formed between model RNA hairpins having seven nucleotide complementary loops. Seven base pairs are formed in the loop-loop helix, with continuous helical stacking of the loop residues on the 3 side of their helical stems. A sharp bend in the loop-loop helix, documented by gel electrophoresis, narrows the major groove and allows bridging of the phosphodiester backbones across the major groove in order to close the hairpin loops at their 5-ends. The bend is further enhanced by the binding of Rom, a ColE1 encoded protein that regulates replication. ...
Dodecamer d-AGATCTAGATCT and a Homologous Hairpin form Triplex in the Presence of Peptide REWER. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Functional RNAs (fRNAs) are being recognized as an important regulatory component in biological processes. Interestingly, recent computational studies suggest that the number and biological significance of functional RNAs within coding regions (coding fRNAs) may have been underestimated. We hypothesized that such coding fRNAs will impose additional constraint on sequence evolution because the DNA primary sequence has to simultaneously code for functional RNA secondary structures on the messenger RNA in addition to the amino acid codons for the protein sequence. To test this prediction, we first utilized computational methods to predict conserved fRNA secondary structures within multiple species alignments of Saccharomyces sensu strico genomes. We predict that as much as 5% of the genes in the yeast genome contain at least one functional RNA secondary structure within their protein-coding region. We then analyzed the impact of coding fRNAs on the evolutionary rate of protein-coding genes because a
A complex secondary structure in U1A pre-mRNA that binds two molecules of U1A protein is required for regulation of polyadenylation.: The human U1A protein-U1A
Does very low or very high free energy ensure a successful design?. No. In nature, RNA does not always adopt its minimum free energy structure. Furthermore, the tools used to predict the minimum free energy structure are imperfect.. What is the optimal free energy?. No specific value of free energy is ideal. Most successful lab designs do not attempt achieve the maximum or minimum value of free energy possible for a given secondary structure.. Why shouldnt I use all GC pairs in a lab design?. GC-rich sequences are difficult to synthesize and prone to being caught in folding traps. Furthermore, the use of only one type of base pair increases the likelihood of undesired pairing.. Why shouldnt I use all AU or GU pairs in a lab design?. AU and GU pairs are weaker than GC pairs. Alone, they are unlikely to hold an RNA molecule in a specific structure. Furthermore, the use of only one type of base pair increases the likelihood of undesired pairing.. What is the optimal balance of AU, GU, and ...
The secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids. Secondary structure was predicted by using the programs PSIPRED and ALB. The residues predicted as helical are marked by H by PSIPRED and by H and & by ALB, and those predicted as -structural are marked by E by PSIPRED and by S and B by ALB ...
The RNA hairpin loops represent important RNA motifs with nominally unpaired single strand segment folded on itself to terminate an A-RNA double helix. The most frequently observed hairpin loops with indispensable biological functions are tetraloops (TLs)
Note that the one of the principle extrinsic curvatures at any point on the two-dimensional infinite standard cylinder of some radius r would be by definition 1/r, while the intrinsic curvature would be zero (There is no distortion in the parallel transport of a vector on a closed curve embedded in the cylinder). The intrinsic curvature is non-zero on a sphere, where parallel-transport of a vector on a closed curve does result in a disagreement. The motivation is that one does not need to reference an external space or embedding in order to measure the intrinsic curvature of a manifold (ie., measuring the 4-dimensional curvature of spacetime ...
Unusual DNA Structures Associated With Germline Genetic Activity in Caenorhabditis elegans: We describe a surprising long-range periodicity that underlies a sub
In living cells, two major classes of ribonucleic acid (RNA) molecules can be found. The first class called the messenger RNA (mRNA) contains the genetic information that allows the ribosome to read and translate it into proteins. The second class called non-coding RNA (ncRNA), do not code for proteins and are involved with key cellular processes, such as gene expression regulation, splicing, differentiation and development. NcRNAs fold into an ensemble of thermodynamically stable secondary structures, which will eventually lead the molecule to fold into a specific 3D structure. It is widely known that ncRNAs carry their functions via their 3D structure as well as their molecular composition. The secondary structure of ncRNAs is composed of different types of structural elements (motifs) such as stacking base pairs, internal loops, hairpin loops and pseudoknots. Pseudoknots are specifically difficult to model, are abundant in nature and known to stabilize the functional form of the molecule. Due ...
The Alternative Structure Browser creates an interactive graphical representation of the Bill of Materials (BOM) with advanced visualization.
Local variations in B-DNA helix structure are compared among three decamers and eight dodecamers, which contain examples of all ten base-pair step types. All pairwise combinations of helix parameters are compared by linear regression analysis, in a search for internal relationships as well as correlations with base sequence. The primary conclusions are: (1) Three-center hydrogen bonds between base-pairs occur frequently in the major groove at C-C, C-A, A-A and A-C steps, but are less convincing at C-C and C-T steps in the minor groove. The requirements for large base-pair propeller are (1) that the base-pair should be A.T rather than G.C, and (2) that it be involved in a major groove three-center hydrogen bond with the following base-pair. Either condition alone is insufficient. Hence, a large propeller is expected at the leading base-pair of A-A and A-C steps, but not at A-T, T-A, C-A or C-C steps. (2) A systematic and quantitative linkage exists between helix variables twist, rise, cup and roll, of
Three-way helical junctions (3WJs) arise in genetic processing, and they have architectural and functional roles in structured nucleic acids. An internal bulge at the junction core allows the helical domains to become oriented into two possible, coaxially stacked conformers. Here, the helical stacking arrangements for a series of bulged, DNA 3WJs were examined using ensemble…
The initial version was coded after several unfruitful attempts at finding a RNA secondary structure drawing software to be used inside of a webserver. Indeed, it seemed at the time that most of the webservers dedicated to the secondary structure of RNA offered rather clumsy renderings (Mostly static, cgi-bin generated, PS or PNG files). In 2008, I (Yann Ponty) was unable to find a tool that would be at the same time available, easy to install and still running (SStructView was no longer tolerated by latest Java plugins security policies; RNAMLViews goal was rather to display a projection of the 3D structure, and RNAMovies was more tailored towards animations...). Therefore, I coded a basic software from scratch, initially using a radial layout strategy adopted by the software RNAViz, later to be extended to other classic algorithms such that NAView, a classic Feynman-diagram representation and a linear one, hoping it would be useful to some... VARNA development team was subsequently joined by ...
... software free downloads. Dna Double Helix shareware, freeware, demos: OnScreen DNA By-the-Day by OnScreen Science Inc, OnScreen DNA Model by OnScreen Science Inc, RC-AirSim by Fabricated Reality etc...
Decomposition of pseudoknotted secondary structures into components has generally not been explained explicitly, although a number of authors have already used it implicitly. In particular, the word pseudoknot is used both for the entire non-orthodox secondary structure, and for the subset of bonds that actually form the knot, though it is generally quite clear from the context which is meant.. One common and natural definition is that the pseudoknot contains the minimal sets of knotted ladders. In the semi-circle representation of ladders, this means that semi-circles that cross are grouped together. This causes the ladders to be partitioned in a unique way into what I call the knot-components. In an orthodox structure, all knot-components are just a single ladder; otherwise, there is at least one knot-component with knotted ladders, and these are the ones I call pseudoknots.. The orthodox secondary structure has a natural tree-representation as two ladders are either nested (one semi-circle ...
UNAFold is a comprehensive software package for nucleic acid folding and hybridization prediction. The name is derived from "Unified Nucleic Acid Folding". Folding of single-stranded RNA or DNA, or hybridization between two single-strands, is accomplished in a variety of ways. Partition functions can be computed to derive base pair probabilities and stochastic samples of foldings or hybridizations. Energy minimization methods compute minimum free energy foldings or hybridizations, and can also compute suboptimal foldings that mimic the performance of the famous mfold software. ...
The non-coding RNA (ncRNA) elements in the 3 untranslated regions (3-UTRs) are known to participate in the genes post-transcriptional regulation, such as their stability, translation efficiency, and subcellular localization. Inferring co-expression patterns of the genes by clustering their 3-UTR ncRNA elements will provide invaluable knowledge for further studies of their functionalities and interactions under specific physiological processes. In this work, we propose an improved RNA structural clustering pipeline that takes into account the length-dependent distribution of the structural similarity measure. Benchmark of the proposed pipeline on Rfam data clearly demonstrates over 10% performance gain, when compared to a traditional hierarchical clustering pipeline. By applying the proposed clustering pipeline to Drosophila melanogaster s 3-UTRs, we have successfully identified 184 ncRNA clusters, of which 91.3% appear to be true RNA structural elements, based on RNAzs prediction. Among ...
Secondary structure formation of FRA16B DNA following denaturation and re-annealing (reduplexing) reaction. (A) Gel electrophoresis analysis of re-annealed FRA1
Interacting selectively and non-covalently with DNA containing secondary structure elements such as four-way junctions, bubbles, loops, Y-form DNA, or double-strand/single-strand junctions.
Restriction enzymes (restriction endonuclease) cut through the DNA at certain points. Their restriction sites where they cut through a specific sequence are about 10 bases long. They catalyse a hydrolysis reaction that breaks the sugar-phosphate backbone of the DNA double helix which gives a staggered cut or sticky end (short run of unpaired, exposed bases that can anneal to other complementary sticky ends). When separate fragments of DNA need to be stuck together, DNA ligase catalyses the condensation reaction that joins the sugar-phosphate backbone.. In order to join fragments they mustve been cut by the same restriction enzyme as this makes them complementary and allows the bases to pair up and anneal. DNA ligase seals the backbone.. DNA formed this way is called recombinant DNA (combining DNA from different sources in a single organism).. ...
Many processes in genetics require that proteins be able to recognize and bind to specific sequences of basepairs in double-stranded DNA. Since the bases are only accessible via the grooves, this is generally accomplished by H-bond and apolar contacts between the protein and certain features on the major and minor groove edges of the basepairs. In this view, the H-bond acceptors in the grooves have been colored yellow, while the H-bond donors have been colored green. The thymine methyl groups (the main surfaces in the grooves available for apolar contact with proteins) have been colored magenta. All a protein can sense when it is searching for a particular sequence is the spatial arrangement of these various H-bonding and apolar groups. Carefully examine the major and minor grooves at various points along the length of the molecule to get a feel for what it is that a protein sees when it is attempting to recognize a specific DNA sequence ...
The Masters will cover the following topics: fundamental aspects of RNA functions in cellular metabolism; RNA molecules as targets and therapeutic tools; strategies for recombinant DNA cloning and RNA and recombinant protein production; transcriptome analysis by high-throughput technologies and bioinformatics; RNA structure analysis and studies of RNA modification and RNA-protein interactions; methods for studying and engineering enzymes; biotechnology and the impact of enzyme on the health sciences. Teaching modules. COMMON COURSES and optional teaching depending on the specialty chosen by the student (e.g. RNA Sciences or ENZYMES Sciences) Options RNA and ENZYMES are almost exclusive due to rather tight schedule during the autumn semester. Please contact us if you envisage to take cources from BOTH options. Please take into account that a total of EXACTLY 60 ECTS for the year is required to get a Diploma.. ...
Genetic information is written by a variation in sequence on the one hand, and the physical stability of the double-stranded structure is determined by the base composition on the other hand. … DNA...
This thesis is based on ten publications (Papers I-X). The phosphodiester backbone makes DNA or RNA to behave as polyelectrolyte, the pentose sugar gives the flexibility, and the aglycones promote the self-assembly or the ligand-binding process. The hydrogen bonding, stacking, stereoelectronics and hydration are few of the important non-covalent forces dictating the self-assembly of DNA/RNA. The pH-dependent thermodynamics clearly show (Papers I and II) that a change of the electronic character of aglycone modulates the conformation of the sugar moiety by the tunable interplay of stereoelectronic anomeric and gauche effects, which are further transmitted to steer the sugar-phosphate backbone conformation in a cooperative manner. 3-anthraniloyl adenosine (a mimic of 3-teminal CCAOH of the aminoacyl-tRNAPhe) binds to EF-Tu*GTP in preference over 2-anthraniloyl adenosine, thereby showing (Paper III) that the 2-endo sugar conformation is a more suitable mimic of the transition state geometry ...
This thesis is based on ten publications (Papers I-X). The phosphodiester backbone makes DNA or RNA to behave as polyelectrolyte, the pentose sugar gives the flexibility, and the aglycones promote the self-assembly or the ligand-binding process. The hydrogen bonding, stacking, stereoelectronics and hydration are few of the important non-covalent forces dictating the self-assembly of DNA/RNA. The pH-dependent thermodynamics clearly show (Papers I and II) that a change of the electronic character of aglycone modulates the conformation of the sugar moiety by the tunable interplay of stereoelectronic anomeric and gauche effects, which are further transmitted to steer the sugar-phosphate backbone conformation in a cooperative manner. 3-anthraniloyl adenosine (a mimic of 3-teminal CCAOH of the aminoacyl-tRNAPhe) binds to EF-Tu*GTP in preference over 2-anthraniloyl adenosine, thereby showing (Paper III) that the 2-endo sugar conformation is a more suitable mimic of the transition state geometry ...
Basepairs involving Hoogsteen(H) edge of Adenine and WatsonCrick(W) edge of Guanine is shown. Highlighted examples are found from RNA crystal structures obtained from PDB. Base pairs stabilized by N-H...N/O type hydrogen bonds ...
NUPARM-Plus :: DESCRIPTION NUPARM-Plus is a program for analysis of sequence dependent variations in nucleic apdb_id (DNA & RNA) double helices ::DEVELOPER Prof. Manju Bansal Lab, MBU, IISc, Bangalore, Ind
Buy The Double Helix Mini DNA Models, Let Students Build A Human DNA Strand With Free UK Delivery On Orders Over 50. A Wide Range Of Biology Aids Available.
Decoding and Targeting RNA Machines in Living Cells RNA molecules fold into structures and intermolecular interactions to execute a second layer of genetic instructions beyond encoding proteins. Functions of RNA structures are pervasive and diverse, including many levels of gene regulation, guiding, scaffolding and catalysis. RNA molecules are directly involved in a variety of human…
DNA molecule. Computer artwork of a molecule of DNA (deoxyribonucleic acid). DNA is composed of two strands (outside) twisted into a double helix. Each strand consists of a sugar-phosphate backbone attached to nucleotide bases (spheres). There are four bases: adenine, cytosine, guanine and thymine. The bases are joined together by hydrogen bonds (rods between spheres). DNA contains sections called genes that encode the bodys genetic information. - Stock Image G110/1050
HB plot is the hydrogen-bonding network of a protein (see the reference on the HBplot tab; Bikadi et al., 2007). The axis represent the amino acid residues of the protein, a dot indicates if a hydrogen bond is present connecting two residues. From the HB plot secondary structure can be easily visualized. Moreover, bonds that contribute to 3D stability can be simply spotted as well. Amino acid residues that interact with the docked ligand are indicated on the right panel and on the plot as well ...
HB plot is the hydrogen-bonding network of a protein (see the reference on the HBplot tab; Bikadi et al., 2007). The axis represent the amino acid residues of the protein, a dot indicates if a hydrogen bond is present connecting two residues. From the HB plot secondary structure can be easily visualized. Moreover, bonds that contribute to 3D stability can be simply spotted as well. Amino acid residues that interact with the docked ligand are indicated on the right panel and on the plot as well ...
DNA molecule. Computer artwork of the structure of deoxyribonucleic acid (DNA). DNA is composed of two strands twisted into a double helix. Each strand consists of a sugar-phosphate backbone (on outside of helix) attached to nucleotide bases (between strands). There are four different bases: guanine, cytosine, thymine and adenine. DNA contains sections called genes, which encode the bodys genetic information. - Stock Image G110/1024
One of the ways to improve formability of Advanced High Strength Steel grades is by modifying the surface during downstream production process. In this study, Galvannealed DP980 grade was selected to understand the impact of a change in the annealing furnace atmosphere before hot-dip coating on product attributes such as diffusible hydrogen content in the steel, bendability, etc. Results showed that an increase in the dew point in the furnace resulted in an increase in surface decarburization which correlates with an improvement in bendability. Along with a decarburized layer, changes in diffusible hydrogen amounts were also observed with furnace atmosphere changes. This paper will also discuss the relationship between hydrogen diffusivity and delayed fracture (DF) susceptibility associated with the presence or absence of a decarburized layer.. ...
Professor Horst Klump, Department of Molecular and Cell Biology, will lecture on the thermodynamics and kinetics of protein folding and ligand binding and will discuss the structures of nucleic acid structures including, DNA, RNA and ribozymes. Professor Klump is internationally renowned for his work on DNA triple helices.. ...
That morning, Watson and Crick knew, although still in mind only, the entire structure: it had emerged from the shadow of billions of years, absolute and simple, and was seen and understood for the first time. Twenty angstrom units in diameter, seventy-none billionths of an inch. Two chains twinning coaxially, clockwise, one up the other down, a complete turn the screw in 34 angstroms. The bases flat in their pairs in the middle, 3.4 angstroms and a tenth of a revolution separating a pair from the one above or below. The chains held by the pairing closer to each other around the circumference one way than the other, by an eighth of a turn, one groove up the outside narrow, the other wide. A melody for the eye of the intellect, not a note wasted. In itself, physically, structure carried the means of replication-positive to negative, complementary. As the strands unwound, at double template was there in the base pairing, so that only complementary nucleotides could form bonds and drop into place ...
Ive read some of the responses dealing with 5 RACE, but didnt see anything about possible secondary structure. Ive been having problems getting anything on my gels for 5 RACE (even using touchdown pcr). I think that it may be due to 2* structure. Does anyone have any protocols for relaxing the 2 ...
During DNA replication, nucleotides are specifically matched to their complementary base pair. According to PBS, DNA resembles a long spiraling ladder consisting of a sugar-phosphate backbone and...
Two polynucleotide strands join together to form a double-helix. - The nucleotides join up between the phosphate group of one nucleotide and the sugar of another, creating a sugar-phospahte backbone.. - Two DNA polynucleotide starnds join together by hydrogen bonds between the bases.. - Each base can only join with one particular partner- this is called specific base pairing.. - Adenine always pairs with Thymine and Guanine always pairs with Cytosine. - The two strands wind up to form the DNA double helix.. ...
A simple physical energy function, which uses electrostatics, solvation, hydrogen bonds and atom-packing terms to model direct readout and sequence-specific DNA conformational energy to model indirect readout of DNA sequence …
1. Both have three components - sugar, phosphate and a nitrogenous base - which form nucleotide units that are connected by covalent bonds to form a linear molecule with 3 and 5 ends, with the nitrogenous bases perpendicular to the sugar-phosphate backbone ...
1JTN: Crystal Structures of a T4-lysozyme Duplication-extension Mutant Demonstrate that the Highly Conserved beta-Sheet Region has Low Intrinsic Folding Propensity
Eternabot 2.0 is a set of rules developed by the Eterna project (eternagame.org) to predict sequences for a target RNA secondary structure
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I am fascinated by a fundamental question in biology; How is regulation of gene expression as a response to external stimulus achieved? My laboratory
In this activity, students build a paper model of DNA and use their model to explore key structural features of the DNA double helix. This activity can be used to complement the short film The Double Helix.. ...
In this activity, students build a paper model of DNA and use their model to explore key structural features of the DNA double helix. This activity can be used to complement the short film The Double Helix.. ...
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What is the structure of DNA? Five amazing facts about the molecular structure of DNA. Find out more about the DNA molecule and the structure of DNA.
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Introduction] Cooperative binding by proteins to DNA results in higher sequence specificity as well as greater sensitivity to concentration changes. We recently reported cooperative binding of two oligonucleotides at abutting sites by triple helix formation on double helical DNA. However, the enhanced binding observed was modest (a factor of 3.5) and likely due to favorable basestacking interactions between adjacent oligonucleotides and/or induced conformational changes propagated to adjacent binding sites. Thus, the issue arises whether cooperativity in oligonucleotide-directed triple helix formation can be enhanced by the addition of discrete dimerization domains. We report here the binding properties of oligonucleotides that dimerize by Watson-Crick hydrogen bonds and bind neighboring sites on double helical DNA by triple helix formation. ...
A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982. Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots. The structural configuration of pseudoknots does not lend itself well to bio-computational detection due to its context-sensitivity or "overlapping" nature. The base pairing in pseudoknots is not well nested; that is, base pairs occur that "overlap" one another in sequence position. This makes the presence of pseudoknots in RNA sequences more difficult to predict by the standard method of dynamic programming, which use a recursive scoring system to identify paired stems and consequently, most cannot detect non-nested base pairs. The newer method of stochastic context-free grammars suffers from the same problem. Thus, popular secondary ...
Circular dichroism (CD) spectroscopy is an optical technique that measures the difference in the absorption of left and right circularly polarized light. This technique has been widely employed in the studies of nucleic acids structures and the use of it to monitor conformational polymorphism of DNA has grown tremendously in the past few decades. DNA may undergo conformational changes to B-form, A-form, Z-form, quadruplexes, triplexes and other structures as a result of the binding process to different compounds. Here we review the recent CD spectroscopic studies of the induction of DNA conformational changes by different ligands, which includes metal derivative complex of aureolic family drugs, actinomycin D, neomycin, cisplatin, and polyamine. It is clear that CD spectroscopy is extremely sensitive and relatively inexpensive, as compared with other techniques. These studies show that CD spectroscopy is a powerful technique to monitor DNA conformational changes resulting from drug binding and also
Filip CHIRALEU, Maria MAGANU and Călin DELEANU. Pyridines with long alkyl substituents as ligands in oligomerization of isopropene. Download Art 19 (PDF). Key words: pyridines; ligands; homogeneous catalysts; terpenes. 20. Camelia HULUBEI and Maria BRUMĂ. Maleimide type polymers based on N-(3-acetoxy-4-carboxy-phenyl)maleimide. Download Art 20 (PDF). Key words: maleimide copolymers; azobenzene; metal complexes; crosslinked networks. 21. Ion SAVA. Influence of conformational parameters on physical properties of some poly(amide-ester)s. Download Art 21 (PDF). Key words: poly(amide-ester)s; isopropylidene; benzonitrile; Monte Carlo; conformational parameters. 22. Ion SAVA and Corneliu HAMCIUC. Polyisophthalamides with pendent acetoxybenzamide or imide groups. Download Art 22 (PDF). Key words: polyisophthalamides; pendent; tetrachlorophthalimide; acetoxybenzamide; conformational parameters. 23. Elena HAMCIUC, Maria BRUMĂ, Corneliu HAMCIUC and Ramona LUNGU. Aromatic polyimides containing polar ...
Filip CHIRALEU, Maria MAGANU and Călin DELEANU. Pyridines with long alkyl substituents as ligands in oligomerization of isopropene. Download Art 19 (PDF). Key words: pyridines; ligands; homogeneous catalysts; terpenes. 20. Camelia HULUBEI and Maria BRUMĂ. Maleimide type polymers based on N-(3-acetoxy-4-carboxy-phenyl)maleimide. Download Art 20 (PDF). Key words: maleimide copolymers; azobenzene; metal complexes; crosslinked networks. 21. Ion SAVA. Influence of conformational parameters on physical properties of some poly(amide-ester)s. Download Art 21 (PDF). Key words: poly(amide-ester)s; isopropylidene; benzonitrile; Monte Carlo; conformational parameters. 22. Ion SAVA and Corneliu HAMCIUC. Polyisophthalamides with pendent acetoxybenzamide or imide groups. Download Art 22 (PDF). Key words: polyisophthalamides; pendent; tetrachlorophthalimide; acetoxybenzamide; conformational parameters. 23. Elena HAMCIUC, Maria BRUMĂ, Corneliu HAMCIUC and Ramona LUNGU. Aromatic polyimides containing polar ...
Our results establish that the extent of stable DNA wrapping in RPo depends on the sequence of the promoter and, in particular, on sequence determinants in the upstream region of the promoter (UP elements). The presence of αCTD and an intact α‐linker is required to maintain extensive stable DNA wrapping. Our results further indicate that the sequence of the upstream region of the promoter can affect DNA wrapping even in the absence of αCTD and thus even in the absence of αCTD-DNA interactions. For example, RPo prepared using ΔαCTDI/ΔαCTDII RNAP shows an apparent DNA compaction of 13±0.6 nm at lacUV5(UPfull) but only 4±0.8 nm at lacUV5(ICAP) (Fig 3E,F). We infer that the sequence of the upstream region of the promoter can affect compaction not only through effects on αCTD-DNA interaction but also through other effects. We suggest that these other effects involve intrinsic DNA curvature, noting that UP‐element subsites and UP elements are A/T‐rich sequences (Fig 1A; Ross et al, ...
The dimerization initiation site (DIS) stem-loop within the HIV-1 RNA genome is vital for the production of infectious virions in T-cell lines but not in primary cells. In comparison to peripheral blood mononuclear cells (PBMCs), which can support the replication of both wild type and HIV-1 DIS RNA mutants, we have found that DIS RNA mutants are up to 100 000-fold less infectious than wild-type HIV-1 in T-cell lines. We have also found that the cell-type-dependent replication of HIV-1 DIS RNA mutants is largely producer cell-dependent, with mutants displaying a greater defect in viral cDNA synthesis when viruses were not derived from PBMCs. While many examples exist of host pathogen interplays that are mediated via proteins, analogous examples which rely on nucleic acid triggers are limited. Our data provide evidence to illustrate that primary T-lymphocytes rescue, in part, the replication of HIV-1 DIS RNA mutants through mediating the reverse transcription process in a cell-type-dependent ...
A hammerhead ribozyme was demonstrated to be a metalloenzyme. By controlling the metal-binding ability of the hammerhead ribozyme in the presence or absence of a specific sequence of interest, we engineered an allosterically controllable ribozyme, designated the maxizyme. Hybrid ribozymes were then constructed by coupling the site-specific cleavage activity of a hammerhead ribozyme with the unwinding activity of an endogenous RNA helicase. This leads to extremely efficient cleavage of target mRNA, not only in vitro, but also in vivo, and eliminates one of the major problems arising in the application of ribozymes for cleavage of mRNA in vivo: that many target sites on the RNA were previously inaccessible to cleavage owing to secondary and/or tertiary structure formation. Since hybrid ribozymes can efficiently attack target sites within mRNA, libraries were made of hybrid ribozymes with randomized binding arms, which were then introduced into cells. This procedure made it possible to readily ...
The invention is directed to an expandable self-expanding stent for implantation in a body lumen, such as an artery. The stent is made with a plurality of cylindrical elements which are interconnected by a plurality of interconnecting members which connect adjacent cylindrical elements, some of the interconnecting members have one or more bending points formed therein for promoting the bendability of the interconnecting member. The bending point can be formed by reducing the strut wall thickness of the interconnecting member to promote the bending of the strut or it can be formed by reducing the strut width of the interconnecting member, or a combination of both. The bending points on the interconnecting member enhances the bendability and flexibility of the composite stent device by creating mechanical hinges which help to bend the stent as it is delivered through the tortuous anatomy of the patient or conforms to a curved portion of a body vessel, where the stent may be implanted.
TY - JOUR. T1 - She2p is a novel RNA binding protein with a basic helical hairpin motif. AU - Niessing, Dierk. AU - Hüttelmaier, Stefan. AU - Zenklusen, Daniel. AU - Singer, Robert H.. AU - Burley, Stephen K.. PY - 2004/11/12. Y1 - 2004/11/12. N2 - Selective transport of mRNAs in ribonucleoprotein particles (mRNP) ensures asymmetric distribution of information within and among eukaryotic cells. Actin-dependent transport of ASH1 mRNA in yeast represents one of the best-characterized examples of mRNP translocation. Formation of the ASH1 mRNP requires recognition of zip code elements by the RNA binding protein She2p. We determined the X-ray structure of She2p at 1.95 Å resolution. She2p is a member of a previously unknown class of nucleic acid binding proteins, composed of a single globular domain with a five α helix bundle that forms a symmetric homodimer. After demonstrating potent, dimer-dependent RNA binding in vitro, we mapped the RNA binding surface of She2p to a basic helical hairpin in ...
This chapter relates the intricate architecture of the L11-RNA complex to previous studies that delineated crucial features of the RNA tertiary structure and protein-RNA interface. In describing the structure, it is interesting to note how conservation and variation of different nucleotides and amino acids serve as a guide to critical features of the complex, and the authors use the extreme conservation of some bases to speculate about functional surfaces of the rRNA domain. Lastly, the chapter discusses the possibility that the functional role of L11-C76 is to promote a correct RNA tertiary fold. Relatively few RNA structures that have noncanonical interactions have been determined at atomic resolution, and of these only tRNA and the P4-P6 domain of group I intron have extensive tertiary structure. From nuclear magnetic resonance (NMR) studies of the free L11 RNA binding domain (L11-C76), it was known that the protein folds into three α-helices that are superimposable on the α-helices of the
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Despite often being referred to as the inactive storage medium of genetic information DNA is of very dynamic and polymorphic nature adopting a variety of alternative secondary structures. In particular evidence for G-quadruplexes (GQPs), four-stranded helical complexes that are assembled from multiple stacked guanine tetrads, as important components in cellular processes has been increasing in recent years. These transiently formed alternative DNA structures have been shown to perform regulative roles in close to all integral biological processes such as recombination, replication, transcription and translation. In addition their polymorphic structure and high stability makes them attractive building blocks to be used in DNA nanoarchitectures and nanodevices.,br /,,br /,In the first part of this thesis the GQP folding properties of the DNA sequence (G,sub,4,/sub,CT),sub,3,/sub,G,sub,4,/sub, were characterized. The G-rich sequence was recently identified as a potential quadruplex-forming sequence ...
We have used laser tweezers to unfold single RNA molecules at room temperature and in physiological-type solvents. The forces necessary to unfold the RNAs are over the range 10-20 pN, forces that can be generated by cellular enzymes. The Gibbs free energy for the unfolding of TAR (transactivation-responsive) RNA from HIV was found to be increased after the addition of argininamide; the TAR hairpin was stabilized. The rate of unfolding was decreased and the rate of folding was increased by argininamide.. ...
The function of a noncoding RNA sequence is mainly determined by its secondary structure and therefore a family of noncoding RNA sequences is much more conserved on the structural level than on the sequence level. Understanding the function of noncoding RNA sequence families requires two things: a hand-crafted or hand-improved alignment and detailed analyses of the secondary structures. There are several tools available that help performing these tasks, but all of them are specialized and focus on only one aspect, editing the alignment or plotting the secondary structure. The problem is both these tasks need to be performed simultaneously. 4SALE is designed to handle sequence and secondary structure information of RNAs synchronously. By including a complete new method of simultaneous visualization and editing RNA sequences and secondary structure information, 4SALE enables to improve and understand RNA sequence and secondary structure evolution much more easily. 4SALE is a step further for
A method apparatus for a radially expandable stent for implantation within a body vessel, comprising a first wire formed winding and a second wire formed winding. The first wire formed winding has a hollow cylindrical shape including a preformed pattern such as a sinusoidal wave form and being wound into a continuous helix the length of the stent. The second wire formed winding has a hollow cylindrical shape including a preformed pattern such as a sinusoidal wave form and being wound into a continuous helix the length of the stent. The second winding helix is opposite that of the first winding helix. The second winding has a greater inner diameter than the outer diameter of the first winding. The second winding is coaxial with the first winding, the pattern of the first winding symmetrically intersects with the pattern of the second winding to form a uniform series of crossings thereby permitting even expansion of the first and second windings. The proximal end of the first winding may be attached to
12/10-Helical beta-Peptide with Dynamic Folding Propensity: Coexistence of Right- and Left-Handed Helices in an Enantiomeric ...
We investigate the empirical complexity of the RNA secondary structure design problem, that is, the scaling of the typical difficulty of the design task for various classes of RNA structures as the size of the target structure is increased. The purpose of this work is to understand better the factors that make RNA structures hard to design for existing, high-performance algorithms. Such understanding provides the basis for improving the performance of one of the best algorithms for this problem, RNA-SSD, and for characterising its limitations. To gain insights into the practical complexity of the problem, we present a scaling analysis on random and biologically motivated structures using an improved version of the RNA-SSD algorithm, and also the RNAinverse algorithm from the Vienna package. Since primary structure constraints are relevant for designing RNA structures, we also investigate the correlation between the number and the location of the primary structure constraints when designing structures
RNA structure is important for RNA function and regulation, and there is growing interest in determining the RNA structure of many transcripts. Here we provide a detailed protocol for the parallel analysis of RNA structure (PARS) for probing RNA secondary structures genome-wide. In this method, enzymatic footprinting is coupled to high-throughput sequencing to provide secondary structure data for thousands of RNAs simultaneously. The entire experimental protocol takes ∼5 d to complete, and sequencing and data analysis take an additional 6-8 d. PARS was developed using the yeast genome as proof of principle, but its approach should be applicable to probing RNA structures from different transcriptomes and structural dynamics under diverse solution conditions. Nat Protoc 2013 May; 8(5):849-69.
Provides the folding functions as used in the ViennaRNA package. Here, they are in Haskell form to be used by Haskell programs.. ...
Aligning homologous non-coding RNAs (ncRNAs) correctly in terms of sequence and structure is an unresolved problem, due to both mathematical complexity and imperfect scoring functions. High quality alignments, however, are a prerequisite for most consensus structure prediction approaches, homology searches, and tools for phylogeny inference. Automatically created ncRNA alignments often need manual corrections, yet this manual refinement is tedious and error-prone. We present an extended version of CONSTRUCT, a semi-automatic, graphical tool suitable for creating RNA alignments correct in terms of both consensus sequence and consensus structure. To this purpose CONSTRUCT combines sequence alignment, thermodynamic data and various measures of covariation. One important feature is that the user is guided during the alignment correction step by a consensus dotplot, which displays all thermodynamically optimal base pairs and the corresponding covariation. Once the initial alignment is corrected, optimal and
Borodavka A, Singaram SW, Stockley PG, Gelbart WM, Ben-Shaul A, Tuma R. Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures. BIOPHYSICAL JOURNAL. 2016;111 :2077-2085.
Some sequences of DNA that possess certain guanine or cytosine-riched stretches are capable of associating into four-stranded DNA structures, namely G-quadruplex and i-motif respectively. It has been suggested that some of these quadruplex structures could exist in some biologically important regions of DNA such as at the end of chromosomes and in the regulatory regions of oncogenes. In addition, due to their distinctive structural characteristics, quadruplex structures of DNA have been widely used as building blocks in various nanotechnological applications. With the aim of exploring new properties and applications of quadruplex DNA, we have (1) constructed i-motif DNA-based molecular devices that are operable through variations of their surrounding pH values; (2) developed certain fluorescence-tagged circular G-quadruplexes to be used as molecular probes; and (3) investigated the factors that affect the G-quadruplex that could undergo self-cleavage reactions. Finally, we have designed and ...
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For sale: Principles of Nucleic Acid Structure by Wolfram Saenger. Publisher Springer-Verlag. Softcover in very good condition. For more info see: http://www.genevue.com/A_Books/DNA_2.html (First entry on page) 25$ including shipping with in the U.S. sks at monitor.net ...
An R-loop is a three-stranded nucleic acid structure, composed of a DNA:RNA hybrid and the associated non-template single-stranded DNA. R-loops may be formed in a variety of circumstances, and may be tolerated or cleared by cellular components. The term "R-loop" was given to reflect the similarity of these structures to D-loops; the "R" in this case represents the involvement of an RNA moiety. In the laboratory, R-loops may also be created by the hybridization of mature mRNA with double-stranded DNA under conditions favoring the formation of a DNA-RNA hybrid; in this case, the intron regions (which have been spliced out of the mRNA) form single-stranded loops, as they cannot hybridize with complementary sequence in the mRNA. ...
Yeast tRNA (m(7)G46) methyltransferase contains two protein subunits (Trm8 and Trm82). To address the RNA recognition mechanism of the Trm8-Trm82 complex, we investigated methyl acceptance activities of eight truncated yeast tRNA(Phe) transcripts. Both the D-stem and T-stem structures were required for efficient methyl-transfer. To clarify the role of the D-stem structure, we tested four mutant transcripts, in which tertiary base pairs were disrupted. The tertiary base pairs were important but not essential for the methyl-transfer to yeast tRNA(Phe) transcript, suggesting that these base pairs support the induced fit of the G46 base into the catalytic pocket ...
This web site contains information about the software system eXtended Dynalign (X-Dynalign for short). This program takes as input three RNA sequences and produces a three-way sequence alignment, as well as a common secondary structure. The objective function consists of a linear combination of the free-energy of each sequence, given the common secondary structure, and an empirical term for gap penalties ...
Although some polypeptides exist as linear chains, most are twisted or folded into more complex secondary structures that form when bonding occurs between amino acids with different properties at different regions of the polypeptide. The most common secondary structure is a spiral called an alpha-helix. If you were to take a length of string and simply twist it into a spiral, it would not hold the shape. Similarly, a strand of amino acids could not maintain a stable spiral shape without the help of hydrogen bonds, which create bridges between different regions of the same strand (see [link]b). Less commonly, a polypeptide chain can form a beta-pleated sheet, in which hydrogen bonds form bridges between different regions of a single polypeptide that has folded back upon itself, or between two or more adjacent polypeptide chains.. The secondary structure of proteins further folds into a compact three-dimensional shape, referred to as the proteins tertiary structure (see [link]c). In this ...
User:Catherine I. Mortensen,Catherine I. Mortensen]] 13:46, 1 March 2013 (EST): The presence of a polyuracil region is not dependent on whether or not the hairpin forms. A polymerase will transcribe through a polyuracil region but the speed at which it does this decreases because something about the chemistry of uracil (possibly due to the fact that uracil can only form 2 hydrogen bonds instead of 3 like guanine and cytosine can) slightly destabilizes the polymerase. When the hairpin forms, the polymerase becomes too unstable to hold onto the polyuracil region. Its as if the polymerase runs over a bump and loses control Id say ...
Probes and processes for their use for specific recognition and/or cleavage of double-stranded DNA or RNA at sequence specific desired loci through the intermediacy of a triple helix are disclosed. These probes may also be used as diagnostic chemotherapeutic agents through incorporation of a radiolabeled, fluorescing, or otherwise detectable molecule. Preferred assay conditions are also provided for recognition of homopurine-homopyrimidine double-helical tracts within large DNA by triple helix formation under physiological conditions. Hybridization probes for double-stranded recognition with binding site sizes that range |8 base pairs are also provided.
The decay of eukaryotic mRNA is triggered mainly by deadenylation, which leads to decapping and degradation from the 5 end of an mRNA. Poly(A)-binding protein has been proposed to inhibit the decapping process and to stabilize mRNA by blocking the recruitment of mRNA to the P-bodies where mRNA degradation takes place after stimulation of translation initiation. In contrast, several lines of evidence show that poly(A)-binding protein (Pab1p) has distinct functions in mRNA decay and translation in yeast. To address the translation-independent function of Pab1p in inhibition of decapping, we examined the contribution of Pab1p to the stability of non-translated mRNAs, an AUG codon-less mRNA or an mRNA containing a stable stem-loop structure at the 5-UTR. Tethering of Pab1p stabilized non-translated mRNAs, and this stabilization did not require either the eIF4G-interacting domain of Pab1p or the Pab1p-interacting domain of eIF4G. In a ski2Δ mutant in which 3 to 5 mRNA degradation activity is ...
An analysis of the base pair doublet geometries in available crystal structures indicates that the often reported intrinsic curvature of DNA containing oligo-(d(A).d(T)) tracts may also depend on the nature of the flanking sequences. The presence of CA/TG doublet in particular at the 5 end of these tracts is expected to enhance their intrinsic bending property. To test this proposition, three oligonucleotides, d(GAAAAACCCCCC), d(CCCCCCAAAAAG), d(GAAAAATTTTTC), and their complementary sequences were synthesized to study the effect of various flanking sequences, at the 5 and 3 ends of the A-tracts, on the curvature of DNA in solution. An analysis of the polyacrylamide gel electrophoretic mobilities of these sequences under different conditions of salts and temperatures (below their melting points) clearly showed that the oligomer with CA/TG sequence in the center was always more retarded than the oligomer with AC/GT sequence, as well as the oligomer with AT/AT sequence. Hydroxyl radical probing ...
The kinetic theory of replication has been extended to include dual mechanisms for conversion of self-annealed single-strand RNA to double-strand molecules, which do not replicate. An analysis of experimental results established that the replicate-template annealing reaction during transcription significantly retarded replication in vitro among three RNA variants copied by Qβ replicase. Annealing between complementary RNA strands free in solution had far less significance. The finding that an RNA variant can be replicated in a multiple hairpin configuration, but not as its single, long hairpin conformer, the correlation between stability of strand secondary structure and replicative fitness, and a lack of homology in the internal sequence of RNA variants copied by Qβ replicase support the conclusion that template competence depends on strand configuration, independent of most of the underlying base sequence. Occurrence of self-annealed strands in the Qβ replicase system was attributed to its ...
Secondary structure prediction and consensus sequence of PelD and PleD. A. Secondary structure predication was made using the web-based ProteinPredict program h
Riboadenosine, or adenosine (rA) is a purine ribonucleoside, and is one of the four standard ribonucleosides that compose an RNA molecule. The presence of the OH group at the 2 -position of the ribose results in RNA being less stable to DNA (which lacks OH groups at this position), because this 2 -hydroxyl group can chemically attack the adjacent phosphodiester bond in the sugar-phosphate backbone of RNA, leading to cleavage of the backbone structure. rA forms a Watson-Crick base pair with rU (ribouridine/uridine) in RNA duplexes, and dT (deoxythymidine) in RNA-DNA duplexes.. - riboadenosine rA. ...
LOC FOR DETECTION OF HYBRIDIZATION OF NUCLEIC ACID SEQUENCES WITH PRIMER-LINKED STEM-AND-LOOP PROBES - diagram, schematic, and image 20 ...
Get your students communicating their knowledge of DNA structure and function through their analysis of a variety of DNA models! Plan your 60 minutes lesson in Science or DNA Structure and Function with helpful tips from Maria Laws
We use "Riboswitch" as our speedy switch, which can control translation. It is divided into two parts: a sensor and an actuator. Before the discovery of RNA regulatory system , the only way to induce reaction in a cell was through inducible promoters. By turning these promoters on or off, we could control the transcription of the downstream DNA into RNA thus also controlling the translation of RNA to Protein. However, with only promoters we traditionally skip the RNA system involved in the pathway of protein synthesis. By inserting a "switch" between the DNA and RNA system we can make a thorough inspection into the individual mechanism of both systems and the cross-effect between their regulatory factors. The discovery of the riboswitch was based on data which described conserved mRNA secondary structure found on 5-untranslated regions and the creation of small-molecule binding mRNA, sensors. The function of these riboswitches is similar to the function of inducible promoters in that they both ...
In early physical studies of DNA, a variety of experiments indicated that DNA molecules occur in long helixes with each helix being formed from two or more polynucleotide chains bound side by side. Chemical analyses also demonstrated that the phosphate groups were on the outside of the helix and that the number of A and T residues in DNA were always equal, as were those of G and C. With these facts in mind, Watson and Crick in 1953 proposed that the DNA molecule actually consists of two polynucleotide chains coiled around the same axis to form a double helix (Figure 3). In this model, the hydrophilic sugar-phosphate groups follow the outer edges of the molecule where they can interact with water. The hydrophobic bases face inward toward each other in the molecules center and thus avoid contact with water. The two polynucleotide strands run in opposite directions (they are anti- parallel) and are held together primarily by hydrogen and hydrophobic bonding between the bases, where A is always ...
The effects of the lesions induced by single, site-specific 1,2-GG or 1,3-GTG intrastrand adducts of cis-diamminedichloroplatinum(II) formed in oligodeoxyribonucleotide duplexes on energetics of DNA were examined by means of differential scanning calorimetry. These effects were correlated with affinity of these duplexes for damaged-DNA binding-proteins XPA and RPA; this affinity was examined by gel electrophoresis. The results confirm that rigid DNA bending is the specific determinant responsible for high-affinity interactions of XPA with damaged DNA, but that an additional important factor, which affects affinity of XPA to damaged DNA, is a change of thermodynamic stability of DNA induced by the damage. In addition, the results also confirm that RPA preferentially binds to DNA distorted so that hydrogen bonds between complementary bases are interrupted. RPA also binds to nondenaturational distortions in double-helical DNA, but affinity of RPA to these distortions is insensitive to alterations ...