Rates and populations were obtained using nmr relaxation dispersion methods as described previously. Nucleic acid structure 1 nucleic acid structure 2 nucleobases 3 nucleobase aromaticity 4 base pairing 5 dna double helix structure 6 translation 7 nonwatsoncrick base pairing 8 answers nucleic acids are the biopolymers that are responsible for the storage and transmission of genetic information inall living organisms. In vitro studies have revealed at least four types of rna. Occasionally a different type of structure is found. A historical account of hoogsteen basepairs in duplex dna. The bottom left structure shows a wobble gt base pair. In a standard hoogsteen base pair the pyrimidine uses its watsoncrick surface to pair with the n1, c6, n7 side of the purine base. A hoogsteen base pair is a variation of basepairing in nucleic acids such as the at pair.
The three basepairs that we study here are asymmetric in the same manner that the normal pairings are. The nature of the intermolecular interactions existing in the 9methyladenine. C n 1methylated purines disrupt wc bps via steric clashes red dashes and loss of hydrogen bonding interactions. In this manner, two nucleobases, one on each strand, can be held. Draw a mature eukaryotic mrna, labeling the 5 cap, polya tail, exons, nuclear export signal, start codon aug, and termination codon uga 0.
A different individual was generated for each structural feature base pairing, base stacking of each model in the pdb file. In this manner, two nucleobases, one on each strand, can be held together by hydrogen bonds in the major groove. The base pairs use the n7 nitrogen atom as the accepter rather than the n1 as observed in watsoncrick base pairing. T is the average twist of the virtual base step between neighbor duplexes in a column calculated with 3dna25 from the c1c1 virtual bonds. Hoogsteen base pairing in the upper gquartet viewed from top. Most of the tertiary interactions shaping the complex folding and functions of 3d. Conserved geometrical basepairing patterns in rna volume 31 issue 4 neocles b. The raman spectra evidence that the structure contains hoogsteen base pairing.
The labeling does not require a covalent bond and is based on watson. The effects of the replacement on the binding mode of tmpyp were also investigated. Crick base pairs and are thought to play important biochemical roles. Proceedings of the national academy of sciences of the. As shown in the figure below left, in the hoogsteen bp scheme, adenine uses its n7 acceptor and n6 donor atoms at the major groove edge to form two hbonds with the n3 donor and o4 acceptor atoms from uracil, respectively. This page was last edited on 24 november 2018, at 07. We have fabricated a dnabased nanofiber created by selfassembly of guanine quadruplex hoogsteen base pairing and doublestranded dna watsoncrick base pairing. These base pairing intercede in the watsoncrick base pairing, forging a base pair triplex. In the two crystal structures obtained of the trna. Hoogsteen hydrogen bonds may also occur in cg base pairs, but they are less.
A hoogsteen base pair applies the n7 position of the purine base as a hydrogen bond acceptor and c6 amino group as a donor, which bind the watsoncrick. Here, we refer to reverse basepairs as the pairing of the nucleotide bases in which the glycosidic bonds are oriented essentially antiparallel to each other. Hoogsteen base pairing interferes with g reaction reaction at n7. The dna double helix is usually stabilized by watsoncrick wc hydrogen bonds between the bases. Pdf new insights into hoogsteen base pairs in dna duplexes. This file contains additional information such as exif metadata which may have been added by the digital camera, scanner, or software program used to create or digitize it. Another form of base pairing is known as hoogsteen base pairs, but in this conformation the g. Structure of the dna duplex dattaat2 with hoogsteen. Reverse watsoncrick purinepurine base pairs biorxiv. W cis base pairs in the context of the wobble hypothesis, or the hoogsteen base pairing in the context of triple helices and g quartet formation were initial indicators. Sequence specificity of transient hoogsteen basepairs in. Free fulltext pdf articles from hundreds of disciplines, all in one place watsoncrick basepairing properties of bicyclodna pdf paperity toggle navigation. Convergence in line1 nucleotide variations can benefit. This results in a triple helix structure instead of the normal double helix.
This excited state base pairing provides a means to. Dna transiently morph into hoogsteen hg basepairs in the context of canonical duplex dna. Hoogsteen base pairs proximal and distal to echinomycin. Subsequent xray analyses of guanine and cytosine derivatives yielded the expected watsoncrick basepairing but those of adenine and thymine or uridine.
For mouse and human lines, the parameters were subject to the conditions suitable for hoogsteen baseparing with xistxist rnas, which predominantly contain ruc motifs, whereas, for opossum lines, the parameters were subject to the conditions suitable for reverse hoogsteen baseparing with rsx rna, where rag motifs are predominant. Files are available under licenses specified on their description page. Crystal structure of an antiparallel dna fragment with hoogsteen. The observation of hoogsteen base pairs in dna duplexes specifically bound to transcription factors and in damaged dna sites implies that the dna double helix intrinsically codes for excited state hoogsteen base pairs as a means of expanding its structural complexity beyond that which can be achieved based on watsoncrick basepairing. Even with these pairs, however, it has been demonstrated that the tight coupling between the two loops may have some flexibility. This type of pairing can lead to a triplex dna oligonucleotide structure, with the hoogsteen base pairs in the major groove of the watsoncrick duplex structure. Evidence for hoogsteen gc base pairs in the protoninduced.
Such a study may provide a model system to unravel some biologically relevant issues in rna duplex, e. A comparable result is expected for the gquadruplex in which the g 8 is replaced because it does not participate in the hoogsteen basepairing. Synapsable quadruplexmediated fibers nanoscale research. Widespread transient hoogsteen base pairs in canonical. Why are hoogsteen base pairs energetically disfavored in a. Realspace evidence of watsoncrick and hoogsteen adenine. To investigate the molecularity of the g4 formed by the hpe2 domain in potassium, we carriedout a nondenaturing page experiment fig. Moreover, a 12basepair segment of alternating at dna, which is 6 base pairs away from the nearest strong echinomycinbinding site, is also hyperreactive to diethyl pyrocarbonate in the presence of echinomycin. This study provides a detailed charge density distribution analysis supported by comprehensive energetic investigations. The interconversion pathways feature a number of intermediates, with a variable number of watsoncrick and hoogsteen base pairs. The structure is a doublehelical structure different from the bform and the zform according to circular dichroism, raman, and absorption spectroscopic studies. A hoogsteen base pair is a variation of base pairing in nucleic acids such as the at pair.
There is now little doubt that hoogsteen basepairs exist in significant abundance in genomic dna where they can expand the structural and functional versatility of duplex dna beyond that which can be achieved based only on watsoncrick basepairing. Effects of deficient of the hoogsteen basepairs on the g. Crick plus hoogsteen base pairing of the guanine base and unpaired pyrimidines of. This paper now shows that naked dna itself can transiently adopt a hoogsteen basepairing arrangement.
Skip to main content accessibility help we use cookies to distinguish you from other users and to provide you with a better experience on our websites. A 180 rotation of the pyrimidine results in formation of a reversed hoogsteen base pair. We used mcannotate over the set of pdb files that contain rna structures to identify base pairing and base stacking in terms of their adjacency and relative orientation. Sharpturn motif, noncanonical base pair, reverse watsoncrick base pair, structural. Watsoncrick basepairing properties of bicyclodna pdf. In contrast, because of the instability of hg bps in arna, these modifications disrupt base pairing all together 15. Hg bps in xray structures of dna duplexes in the protein data bank. A hoogsteen base pair applies the n7 position of the purine base as a hydrogen bond acceptor and c6 amino group as a donor, which bind the watsoncrick n3c4 face of the pyrimidine. Hoogsteen base pair an overview sciencedirect topics. Synthesis and base pairing of oligonucleotides containing 1. Hoogsteen dna base pairs bps are an alternative base pairing to canonical watson. Transient hoogsteen base pairs in canonical duplex dna. Complementary basepairing between the nucleotides b.
Charge density topological investigations lead to reliable hydrogenbond. Why are hoogsteen base pairs energetically disfavored in arna. Triple helices consisting ofonepyrimidine and two purine strands were also proposed 5, 6. The classic watsoncrick basepairing scheme is only one of several. In an effort to find evidence for hoogsteen basepairing at quinoxalinebinding sites in solution, chemical footprinting differential cleavage reactivity of echinomycin bound to. Watsoncrick, wobble, and hoogsteentype basepairs all have reverse analogues in which one base is completely inverted. Here i reexamine their xray data and find that the electron density is very weak for a hoogsteen base pair formed between a template adenine deoxyribonucleotide in the syn conformation and a deoxythymidine 5triphosphate dttp, and that the fit is better for a normal watsoncrick base pair. Pdf hoogsteen hg base pairs bps provide an alternative pairing. When duplexes containing a long stretch of contiguous guanines and singlestranded overhangs are incubated in potassiumcontaining buffer, the preformed duplexes create high molecular weight species that. If the file has been modified from its original state, some details such as the timestamp may not fully reflect those of the original file. Hoogsteen hg base pairing involves a 180 rotation of the purine base relative to watson.
In addition to the hoogsteen base pairing in synapsable dna mimicking interactions and structures found in biology,15,19,20,25, synapsable dna also has been suggested to be an attractive tool for nanofabrication 1,26 although there are no reports of specific examples utilizing synapsable dna in. A list of bps was created that satisfy one, two or all three hg criteria listed above figure. Some deviations from this canonical pairing have been observed when dna is. Pdf transient hoogsteen base pairs in canonical duplex dna.
B wc bps in bdna exist in dynamic equilibrium with hg bps. Manual inspection was used to exclude bps involved in. The standard view of the genome is that the two dna strands are linked by watsoncrick base pairing. Bases of the two antiparallel strands form hoogsteen pairs, with adenines. The au or at hoogsteen pair is a wellknown type of base pair bp, named after the scientist who discovered it.
All structured data from the file and property namespaces is available under the creative commons cc0 license. The center two ta pairs represent hoogsteen base pairs. Polypurine reversehoogsteen pprh oligonucleotides can. Wikijournal preprintsnoncanonical base pairing wikiversity. A structural comparison of bform dna and aform rna. New insights into hoogsteen base pairs in dna duplexes from a.
In contrast, because of the instability of hg bps in a rna, these modifications disrupt base pairing all together 15. The hoogsteen basepaired strandof1tiocouldonlyfit inthemajorgroove. Nucleotide bases typically take an anti conformation relative to pentose base conformation affects hydrogen bonding pattern between base pairs hoogsteen base pairing o not watsoncrick o present in regions of dna that are bound to proteins or other molecules o found in damaged or chemically modified dna allows 34 strands to be present in a helix o. Resolving a role in normal biological processes and human diseases, biochemical and biophysical research communications on deepdyve, the largest online rental service for scholarly research with thousands of academic publications available at. Karst hoogsteen october 1, 1923 august 10, 2015 was a dutchborn american biochemist famous for noting a new base pairing form in dna, now called hoogsteen base pairs. Pdf energy landscape and pathways for transitions between.
259 435 408 1026 110 1005 1283 682 1306 1110 348 759 1320 1358 590 1392 1549 679 132 1454 1365 317 1480 815 65 1227 440 91 958 1446 294 1042 821 1035 709 800 1240 1512 1238 264 152 1262 613 132 1301 1406