This paper now shows that naked dna itself can transiently adopt a hoogsteen basepairing arrangement. Here, we use structural features unique to hg bps syn purine base, hg hydrogen bonds and constricted c1c1 distance across the bp to search for hg bps in xray structures of dna duplexes in the. 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. To understand the anomalous collisioninduced dissociation cid behavior of the protonbound hoogsteen base pair of cytosine c and guanine g, c. This excited state base pairing provides a means to expand the chemistry and structure of dna. Jan 26, 2011 this paper now shows that naked dna itself can transiently adopt a hoogsteen base pairing arrangement. Aug 06, 2015 free energy landscape and transition pathways from watsoncrick to hoogsteen base pairing in free duplex dna article pdf available in nucleic acids research 4316 august 2015 with 182 reads. The au or at hoogsteen pair is a wellknown type of base pair bp, named after the scientist who discovered it. An important aspect of the oligonucleotides of the present invention is that they are capable of watsoncrick base pairing and hoogsteen base pairing and reverse hoogsteen base pairing. Hoogsteen base pairs have been known for more than 40 years. In all of these cases, the base stacking energy barrier to forming the hoogsteen base pair rather than the more typical watsoncrick base pair is presumably lowered by the intercalation of drugs, bending and unwinding of the dna, or the presence of free, unpaired bases, all of which have the flexibility to allow the flipping of a purine base.
Dot bracket notation for rna and dna nanostructures. Base pairing the rules of base pairing or nucleotide pairing are. This page was last edited on 24 november 2018, at 07. Introduction pictures of the double helix of deoxyribonucleic acid. Kimsey and bharathwaj sathyamoorthy and shan yang and jane s. Here we describe an nmr strategy for characterizing hoogsteen base pairs in protein. C n 1methylated purines disrupt wc bps via steric clashes red dashes and loss of hydrogen bonding interactions. 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. Thus, incorporation of the flexible base stacking monomer of the present invention into an oligonucleotide allows the oligonucleotide to form a triplex. Geometrically, hg bp in duplex dnas can be formed by a 180 rotation of a purine target base adenine a or guanine g in a wc bp about its glycosidic bond c1n9 from an anti wc to a syn hg conformation. At the end of your monthly term, you will be automatically renewed at the promotional monthly subscription rate until the end of the promo period, unless you elect to. A schematic diagram illustrating the transition from watsoncrick wc to hoogsteen hg base pairing. B base sequence of the a 6dna studied in this work.
Hoogsteen versus watsoncrick at basepairing in dna. European synchrotron radiation facility, bp 220, f38043 grenoble. Another form of base pairing is known as hoogsteen base pairs, but in this conformation the g. However, the contribution of each hoogsteen basepair at different positions to whole stability of the gquadruplex has not been known. Rates and populations were obtained using nmr relaxation dispersion methods as described previously. Pdf free energy landscape and transition pathways from. Hoogsteen hg base pairs bps provide an alternative pairing geometry to watsoncrick wc bps and can play unique functional roles in duplex dna. Figure 1 from new insights into hoogsteen base pairs in. Xray crystallography and nmr relaxation experiments revealed the presence of hg base pair in naked dna duplex and proteindna complex but no hg base pair was observed in rna. This hyperreactive segment may be an altered form of righthanded dna that is entirely hoogsteen basepaired. In stabilization of the gquadruplex, formation of a hoogsteen base pair between the guanine g bases is essential. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses.
Sep, 2018 to understand the anomalous collisioninduced dissociation cid behavior of the protonbound hoogsteen base pair of cytosine c and guanine g, c. Moreover, a 12 base pair 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. The base pairs use the n7 nitrogen atom as the accepter rather than the n1 as observed in watsoncrick base. Hoogsteen base pairs proximal and distal to echinomycin. A hoogsteen base pair is a variation of base pairing in nucleic acids such as the at pair. The usual formation of dna at neutral ph is the bform duplex and this is destabilized by the addition of a hoogsteen base pair. The formation of a tribase pairing from free nucleobases is rare. Xray crystallography and nmr relaxation experiments revealed the presence of hg base pair in naked dna duplex and protein. A vital question is whether this mode of base pairing also occurs opposite. C n 1methylated purines disrupt wc bps via steric clashes red dashes and loss of. Pdf transient hoogsteen base pairs in canonical duplex dna. C sequences isnt stable at neutral ph, instead being more stable with more acidic ph values. Resolving a role in normal biological processes and human diseases ghosal, gargi.
Files are available under licenses specified on their description page. Dot bracket notation for rna and dna nanostructures slides by reem mokhtar. The a16t9 base pair highlighted in a blue rectangular box is the location where the transition from the wc to hg base pair takes place. An important aspect of the oligonucleotides of the present invention is that they are capable of watsoncrick base pairing and hoogsteen base pairing and. Deviations from classical watsoncrick base pairing nikolova et al. Geometric nomenclature and classification of rna base pairs. The hoogsteen base pair, formed by a syn adenine base and an anti thymine base, occurs within a 2.
Free energy landscape and transition pathways from watsoncrick to hoogsteen base pairing in free duplex dna changwon yang1, eunae kim2 and youngshang pak1, 1department of chemistry and institute of functional materials, pusan national university, busan 609735, south korea and 2college of pharmacy, chosun university, gwangju 501759, south. In contrast to previously reported p53dna complexes that show standard watsoncrick base pairs, the newly reported structures show noncanonical hoogsteen base pairing geometry at the central at doublet of each halfsite. Free energy landscape and conformational kinetics of hoogsteen basepairing in dna vs rna d. Transient hoogsteen base pairs in canonical duplex dna. Table 1 from new insights into hoogsteen base pairs in dna. New insights into hoogsteen base pairs in dna duplexes. The oligonucleotide may be any oligonucleotide capable of watsoncrick base pairing and hoogsteen base pairing and reverse hoogsteen base pairing. Genetic information is encoded in the dna double helix which, in its physiological milieu, is characterized by the iconical watsoncrick nucleobase pairing. 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. This file is licensed under the creative commons attributionshare alike 4. By dragging your pages in the editor area you can rearrange them or delete single pages.
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. Free energy landscape and transition pathways from watsoncrick to hoogsteen base pairing in free duplex dna article pdf available in nucleic acids research 4316 august 2015 with 182 reads. Identifying hoogsteen base pairs in dna duplexes remains challenging due to difficulties in resolving syn versus antipurine bases with x. Crystal structure of an antiparallel dna fragment with hoogsteen base pairing nicola g. Some deviations from this canonical pairing have been observed when dna is bound to a ligand. A structural comparison of bform dna and aform rna. Shown are wc and hg at and gc bps with highlighted key geometrical differences.
Here we describe an nmr strategy for characterizing. Kimsey and bharathwaj sathyamoorthy and shan yang and jane. Characterizing the protonation state of cytosine in. B wc bps in bdna exist in dynamic equilibrium with hg bps. This paper now shows that naked dna itself can transiently adopt a hoogsteen base pairing arrangement. Just draganddrop your pdf file in the box above, wait for the compression to complete and download your file. Recent nmr relaxation experiments revealed the transient presence of an alternative, hoogsteen base pairing pattern in naked dna duplexes and estimated its relative stability and lifetime. The helical structure of dna is variable and depends on the sequence as well as the environment. To merge pdfs or just to add a page to a pdf you usually have to buy expensive software. Synthesis and base pairing of oligonucleotides containing 1.
Free energy landscape and conformational kinetics of. T hoogsteen base pairs can form in duplex dna and play roles in recognition, damage repair, and replication. What is the difference between watsoncrick and hoogsteen. Hoogsteen base pairs form through concurrent rotation of the purine base about the glycosidic bond from an anti to a syn conformation and constriction of the c1c1 distance across the base pair. A, b and zdna helix families david w ussery,danish technical university, lyngby, denmark there are three major families of dna helices. Noah4, hin hark gan2,4,5, tamar schlick2,4,5 and cynthia wolberger1,2, 1department of biophysics and biophysical chemistry and 2howard hughes medical institute, johns hopkins university school of medicine, baltimore, md 212052185, usa, 3department of chemistry and. Characterizing the protonation state of cytosine in transient. Feb 24, 2011 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 base pairing. 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. Your files will be permanently deleted from our server after one hour.
No one has access to your files and privacy is 100% guaranteed. Hoogsteen gg base pairing is dispensable for telomere healing in yeast. The synthesis of the corresponding phosphoramidite building block 7 was analogous to that for the natural riboseries 27, and started from the bicyclic sugar analog 1 and the nitrobase 2 fig. Hoogsteen base pairing in the upper gquartet viewed from top.
In this manner, two nucleobases, one on each strand, can be held together by hydrogen bonds in the major groove. Biochemical evidence for the requirement of hoogsteen base. Soon after the model of dna was proposed 14 several attempts were made to demonstrate that watsoncrick pairing was favored by isolated bases. Figure 1 from new insights into hoogsteen base pairs in dna. Free energy landscape and transition pathways from watson. The cid experiments were performed in an energyresolved way ercid under both. Also, you can add more pdfs to combine them and merge them into one single document. Significance formation of unconventional hoogsteen hg base pairing is an important problem in dna biophysics owing to its key role in facilitating the binding of dna repairing enzymes, proteins and drugs to damaged dna.
Andricioaei duplexdnabeyondwhatcanbeachievedbywatsoncrickbasepairingalone. These base pairing intercede in the watsoncrick base pairing, forging a base pair triplex. When the base pairing probability matrix is calculated by symbols, are used for bases that are essentially unpaired, weakly. A hoogsteen base pair is a variation of basepairing in nucleic acids such as the at pair. Jul 26, 2005 because of the near geometric identity of watsoncrick wc gc and at base pairs, a given dna polymerase forms the four possible correct base pairs with nearly identical catalytic efficiencies. Characterizing watsoncrick versus hoogsteen base pairing. Gc hoogsteen base pairs are thought to be stabilized by protonation of cytosine n3, which affords a second key hydrogen bond, but experimental evidence for this is sparse because the proton cannot be directly visualized by xray crystallography and.
Gc hoogsteen base pairs are thought to be stabilized by protonation of cytosine n3, which affords a second key hydrogen bond, but experimental evidence for this is sparse because the proton cannot be directly visualized by xray crystallography and nuclear. A comparable result is expected for the gquadruplex in which the g 8 is replaced because it does not participate in the hoogsteen basepairing. Transient hoogsteen base pairs in canonical duplex dna nature. In this manner, two nucleobases on each strand can be held together by hydrogen bonds in the major groove. Dec 01, 2002 in all of these cases, the base stacking energy barrier to forming the hoogsteen base pair rather than the more typical watsoncrick base pair is presumably lowered by the intercalation of drugs, bending and unwinding of the dna, or the presence of free, unpaired bases, all of which have the flexibility to allow the flipping of a purine base. By contrast to a wc base pair where the complementary purine and pyrimidine bases are both in the anti configuration fig. The effects of the replacement on the binding mode of tmpyp were also investigated. In stabilization of the gquadruplex, formation of a hoogsteen basepair between the guanine g bases is essential. Jp5284084b2 stable and selective formation of hoogsteen. Hoogsteen hg base pairing is an alternative basepairing scheme for dna double helices figure 1a. Offer starts on jan 8, 2020 and expires on sept 30, 2020.
In contrast to previously reported p53dna complexes that show standard watsoncrick base pairs, the newly reported structures show noncanonical hoogsteen basepairing geometry at the central at doublet of each halfsite. A nature paper on spontaneous flipping of normal watsoncrick wc base pairs into hoogsteen hg base pairs in naked dna under most normal conditions1 produced the bombshell effect throughout the world community of nucleic acids biophysicists. Effects of deficient of the hoogsteen basepairs on the g. All structured data from the file and property namespaces is available under the creative commons cc0 license. Gc hoogsteen base pairs can form transiently in duplex dna and play important roles in dna recognition, replication, and repair. A comparable result is expected for the gquadruplex in which the g 8 is replaced because it does not participate in the hoogsteen base pairing. Characterizing watsoncrick versus hoogsteen base pairing in. Crystal structure of an antiparallel dna fragment with.
The base pairs use the n7 nitrogen atom as the accepter rather than the n1 as. A hoogsteen base pair embedded in undistorted bdna jun aishima1, rossitza k. Resolving a role in normal biological processes and human diseases hoogsteen basepairing revisited. Hoogsteen base pairing cationic porphyrin circular dichroism abstract background. Why are hoogsteen base pairs energetically disfavored in a.
However, the contribution of each hoogsteen base pair at different positions to whole stability of the gquadruplex has not been known. Jan 26, 2011 some deviations from this canonical pairing have been observed when dna is bound to a ligand. Heavy atoms involved in hg hydrogen bonds in red, syn angle in orange and constricted c1. Hoogsteen base pairing in crystal structures and in the presence of antibiotics recently, the quinoxaline antibiotics echinomycin fig. A cocrystal structure obtained from an equimolar mixture of 6isopropyluracil and adenine shows the formation of a tribase pairing, where one molecule of free adenine is adhered to two molecules of the free pyrimidine nucleobase, involving.
The observation of hoogsteen basepairs 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 basepairs as a means of expanding its structural complexity beyond that which can be achieved based on watsoncrick basepairing. The synthesis of the corresponding phosphoramidite building block 7 was analogous to that for the natural riboseries 27, and started from the bicyclic sugar analog 1 and the nitrobase 2. Pronunciation of hoogsteen with 3 audio pronunciations and more for hoogsteen. Proton transfer accounting for anomalous collisioninduced.
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