Biomedical subjects

S H Chou

Publications and source records attributed to S H Chou.

At least 19 recordsLinked to original sources

PubMed2004

Fiber-optic bronchoscopic classification of inhalation injury: prediction of acute lung injury.

BACKGROUND: Fiber-optic bronchoscopy is widely used for the early diagnosis of inhalation injury. However, there is no current bronchoscopic classification of inhalation injury for the prediction of acute lung injury (ALI). Our goal was to devise such a classification. METHODS: Between February 1993 and January 2002, 167 patients with highly suspicious inhalation injuries were collected. All patients received fiber-optic bronchoscopy within 24 h after their accident. In total, 108 patients were diagnosed as positive under direct inspection. The patients were divided into three groups (G(1), G(2), and G(3)) according to the depth of mucosal damage. Six patients were found to be positive by biopsy and were assigned to group Gb. Of these 114 positive cases, 27 developed ALI. Meanwhile, 53 patients were diagnosed as negative; these patients were assigned to group G(0). RESULTS: After analysis, the following results were noted: G(0) (n = 53), two ALI (3.8%); G(1) (n = 49), two ALI (4%); G(2) (n = 46), 15 ALI (33%); G(3)(n = 13),10 ALI (77%); Gb (n = 6), no ALI. We discovered that the deeper the mucosal injuries, the higher the rate of ALI. There were no deaths related to the procedure. CONCLUSIONS: Fiber-optic bronchoscopy is a safe and effective method for the early diagnosis of inhalation injuries. Also, it is a good predictor of ALL. We hope that in the near future, this classification will serve as a treatment guideline for the early prevention of ALI. The more severe the damage, the more alert clinicians need to be to improve the patient's chances for survival.

Adolescent↗

PubMed2001

Increased engraftment and GVHD after in utero transplantation of MHC-mismatched bone marrow cells and CD80low, CD86(-) dendritic cells in a fetal mouse model.

BACKGROUND: Bone marrow transplantation (BMT) is the only known cure for a variety of inherited diseases and requires the administration of high doses of immunosuppressive and myeloablative therapy. Because the fetus is immunoincompetent early in gestation, in utero stem cell transplantation (IUT) could avoid the need for this toxic conditioning. A major limitation to date of IUT is the low level of engraftment and failure to induce tolerance. Dendritic cells (DC) are considered very potent antigen-presenting cells, but DC progenitors (pDC) are strongly tolerogenic. METHODS: We examined the effect of donor pDC on the degree of engraftment and tolerance induction after IUT. Bone marrow-derived pDC (CD80low, CD86-) from male C57BL/6 mice (H2b) were injected with and without donor bone marrow (BM) intraperitoneally into 13 to 15-day BALB/c (H2d) fetuses. Engraftment was determined by flow cytometry and quantitative polymerase chain reaction and tolerance by skin grafts and the mixed lymphocyte reaction. RESULTS: At 1-month posttransplant, mice that received BM+pDC showed a higher degree of engraftment (29+/-46%) than mice that received pDC-enriched cells or BM cells alone (0.11+/-0.70% and 1.71+/-1.66%, respectively, P<0.001). However, 5/19 recipients of BM+pDC died within 6 weeks; 4/5 had significant donor cell engraftment in blood and/or tissues. Also, these mice had evidence of graft-versus-host disease (GVHD). Two mice out of 15 long-term survivors in the BM+pDC group had virtually complete replacement of host with donor hematopoietic cells. Skin grafts and mixed lymphocyte reaction studies showed no durable tolerance induction other than in the two fully engrafted recipients of BM+pDC. CONCLUSIONS: These results suggest that donor pDC, along with donor BM, can have a significant impact on engraftment of MHC-mismatched donor cells associated with an increased incidence of GVHD. However, marrow-derived pDC do not result in an increase in tolerance induction in utero even when microchimerism is present.

Animals↗

PubMed2001

Quadruple intercalated G-6 stack: a possible motif in the fold-back structure of the Drosophila centromeric dodeca-satellite?

The purine-rich strand d(GTACGGGACCGA)(n) of the Drosophila centromeric dodeca-satellite sequence is highly conserved and was found to form stable fold-back structures in which the homopurine 5'-GGGA-3' sequence was determined to play a crucial role. Here, we report the stable formation of the d(GGGA)(2) motif in the stem of a DNA hairpin closed by a single-residue d(ACC) loop. Similar to the zipper-like d(GGA)(2) motif observed in the human centromeric (TGGAA)(n) sequence, the central four guanosine bases in the d(GGGA)(2) motif do not pair, but interdigitate to form an elongated zipper-like quadruple-intercalated G-6 stack bracketed by sheared G.A base-pairs. Comparison between the current d(GGGA)(2) structure and the published crystal d(GAAA)(2) structure implies that the alignment of the unpaired purine bases plays an important role in determining the minor groove width of the purine-rich d(GPuPuA)(2) motif. Similarity between the zipper-like motifs possibly present in the Drosophila centromeric dodeca-satellite sequence and in the human centromeric (TGGAA)(n) sequence led us to propose that these special zipper-like motifs may constitute common cores in organizing eukaryotic centromeres.

Animals↗

PubMed2001

Zipper-like Watson-Crick base-pairs.

A series of DNA heptadecamers containing the DNA analogues of RNA E-like 5'-d(GXA)/(AYG)-5' motifs (X/Y is complementary T/A, A/T, C/G, or G/C pair) were studied using nuclear magnetic resonance (NMR) methodology and distance geometry (DG)/molecular dynamics (MD) approaches. Such oligomers reveal excellent resolution in NMR spectra and exhibit many unusual nuclear Overhauser effects (NOEs) that allow for good characterization of an unusual zipper-like conformation with zipper-like Watson-Crick base-pairs; the potential canonical X.Y H-bonding is not present, and the central X/Y pairs are transformed instead into inter-strand stacks that are bracketed by sheared G.A base-pairs. Such phenomenal structural change is brought about mainly through two backbone torsional angle adjustments, i.e. delta from C2'-endo to C3'-endo for the sugar puckers of unpaired residues and gamma from gauche(+) to trans for the following 3'-adenosine residues. Such motifs are analogous to the previously studied (GGA)(2) motif presumably present in the human centromeric (TGGAA)(n) tandem repeat sequence. The novel zipper-like motifs are only 4-7 deg. C less stable than the (GGA)(2) motif, suggesting that inter-strand base stacking plays an important role in stabilizing unusual nucleic acid structures. The discovery that canonical Watson-Crick G.C or A.T hydrogen-bonded pairs can be transformed into stacking pairs greatly increases the repertoire for unusual nucleic acid structural motifs.

Base Pairing↗

PubMed2001

Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs.

A series of DNA 21-mers containing a variety of the 4 x 4 internal loop sequence 5'-CAAG-3'/3'-ACGT-5' were studied using nuclear magnetic resonance (NMR) methodology and distance geometry (DG)/molecular dynamics (MD) approaches. Such oligomers exhibit excellent resolution in the NMR spectra and reveal many unusual NOEs (nuclear Overhauser effect) that allow for the detailed characterization of a DNA hairpin incorporating a track of four different non-Watson-Crick base-pairs in the stem. These include a wobble C.A base-pair, a sheared A.C base-pair, a sheared A.G base-pair, and a wobble G.T base-pair. Significantly different twisting angles were observed between the base-pairs in internal loop that results with excellent intra-strand and inter-strand base stacking within the four consecutive mismatches and the surrounding canonical base-pairs. This explains why it melts at 52 degrees C even though five out of ten base-pairs in the stem adopt non-Watson-Crick pairs. However, the 4 x 4 internal loop still fits into a B-DNA double helix very well without significant change in the backbone torsion angles; only zeta torsion angles between the tandem sheared base-pairs are changed to a great extent from the gauche(-) domain to the trans domain to accommodate the cross-strand base stacking in the internal loop. The observation that several consecutive non-canonical base-pairs can stably co-exist with Watson-Crick base-pairs greatly increases the limited repertoire of irregular DNA folds and reveals the possibility for unusual structural formation in the functionally important genomic regions that have potential to become single-stranded.

Base Pairing↗

PubMed2001

Tolerance induction post in utero stem cell transplantation.

The potential advantage of in utero HSC transplantation over a postnatal BMT is that early curative therapy could be given to an affected fetus, thus eliminating standard intensive immunosuppressive, marrow-ablative conditioning. It is apparent from studies in animals and humans that MHC-mismatched donor HSC of either fetal or adult origin can engraft in fetal recipients if the transplants are done sufficiently early in gestation. However, except for SCID, the percentage of donor pluripotent HSC that engraft is unacceptably low. We had hoped that for diseases such as thalassemia there would be a selective survival advantage for committed donor progenitor cells resulting in a high percentage of donor cell engraftment. At least based upon the experience in human fetuses with alpha- or beta-thalassemia, this has not been the case. Furthermore, for the majority of potential recipients of in utero HSC transplants, the marrow is non-defective, and the small percentage of pluripotent donor HSC that engraft would not be expected to selectively expand post-transplant. Our own results suggest that the non-defective fetal mouse and rhesus monkey are excellent models in which to study both stem cell engraftment, rejection, and tolerance induction. In our studies in non-defective mice with normal hematopoiesis, while the percentage of donor cells that are present is quite low, in only a small number of these animals were we able to induce permanent skin graft tolerance. Thus, while we found microchimerism in approximately 75% of recipients, less than 10% became tolerant. Even when we co-injected a large number of DC precursors, similar to what has been shown to induce tolerance to allogeneic liver, most of the animals failed to become tolerant to donor skin grafts. Interestingly, donor c-kit+ cells can be recruited with cytokines into the peripheral blood in engrafted mice, although these cells do not seem to be sufficient to induce tolerance to donor skin grafts, suggesting that the type (and location) of the engrafted donor cell plays a key role in tolerance induction. Our results in the fetal monkey model parallel those in the mouse, i.e., only a small number of donor cells engraft with limited tolerance induction. Interestingly, we found in our study of DC that GVHD was induced in those murine recipients of both allogeneic marrow and DC. It is likely that there were a sufficient number of mature DC in the preparation to facilitate a donor cytotoxic response towards the host. As a consequence there was also a significant increase in the percentage of donor cells that engrafted in the survivors. Future studies will focus on ways of blocking the graft vs host reaction while still maintaining the graft-promoting role of the donor T cell.

Animals↗

PubMed2001

The solution structure of [d(CGC)r(amamam)d(TTTGCG)]2.

The solution structure and hydration of a DNA.RNA hybrid chimeric duplex [d(CGC)r(amamam)d(TTTGCG)]2 in which the RNA adenines were substituted by 2'-O-methylated riboadenines was determined using two-dimensional NMR, simulated annealing, and restrained molecular dynamics. Only DNA residue 7T in the 2'-OMe-RNA.DNA junction adopted an O4'-endo sugar conformation, while the other DNA residues including 3C in the DNA.2'-OMe-RNA junction, adopted C1'-exo or C2'-endo conformations. The observed NOE intensity of 2'-O-methyl group to H1' proton of 4am at the DNA.2'-OMe-RNA junction is much weaker than those of 5am and 6am. The 2'-O-methyl group of 4am was found to orient towards the minor groove in the trans domain while the 2'-O-methyl groups of 5am and 6am were found to be in the gauche (+) domain. In contrast to the long-lived water molecules found close to the RNA adenine H2 and H1' protons and the methyl group of 7T in the RNA-DNA junction of [d(CGC)r(aaa)d(TTTGCG)]2, there were no long-lived water molecules found in [d(CGC)r(amamam)d(TTTGCG)]2. This is probably due to the hydrophobic enviroment created by the 2'-O-methylated riboadenines in the minor groove or due to the wider minor groove width in the middle of the structure. In addition, the 2'-O-methylation of riboadenines in pure chimeric duplex increses its melting temperature from 48.5 degrees C to 51.9 degrees C. The characteristic structural features and hydration patterns of this chimeric duplex provide a molecular basis for further therapeutic applications of DNA.RNA hybrid and chimeric duplexes with 2'-modified RNA residues.

Base Sequence↗

PubMed2001

Novel cross-strand three-purine stack of the highly conserved 5'-GA/AAG-5' internal loop at the 3'-end termini of Parvovirus genomes.

We have used two-dimensional nuclear magnetic resonance (2D-NMR), distance geometry (DG) and molecular dynamics / energy minimization (MD/EM) methods to study a 2 x 3 asymmetric internal loop structure of the highly conserved 5'-(GA)/(AAG)-5' bubble' present at the 3'-end hairpin of the single-stranded DNA genome of parvoviruses. This motif contains an unpaired adenosine stacked between two bracketed sheared G.A pairs. However, the phenomenal cross-strand G-G and A-A stacking in the tandem sheared G.A pairs has undergone considerable change. A novel three-purine stacking pattern is observed instead; the inserted A18 base is completely un-stacked from its neighboring G 17 and A 19 bases, but well stacked with the cross-strand A4 and G3 bases to form a novel A4/A18/G3 stack that is different from the double G/G, A/A or quadruple G/G/G/G stack present in the 5'-(GA)/(AG)-5' or 5'-(GGA)/(AGG)-5' motifs. Unlike the bulged purine residue that usually causes about 20 degree kink in the helical axis of the parent helix when bracketed by canonical G.C or A.T base pairs, no significant kink is observed in the present helix containing a bulged-adenine that is bracketed by sheared G.A pairs. The phosphodiesters connecting G3-A4 and G17-A18 residues adopt unusual zeta torsional angles close to the trans domain, yet that connecting A18-A19 residues resumes the normal zeta(g-) value. The well structured '5'-(GAA)/(AG)-5" internal loop in the parvovirus genomes explains its resistance to single-strand specific endonuclease susceptibility.

Adenine↗

PubMed2000

Hydration of [d(CGC)r(aaa)d(TTTGCG)](2).

We have studied the hydration and dynamics of RNA C2'-OH in a DNA. RNA hybrid chimeric duplex [d(CGC)r(aaa)d(TTTGCG)](2). Long-lived water molecules with correlation time tau(c) larger than 0.3 ns were found close to the RNA adenine H2 and H1' protons in the hybrid segment. A possible long-lived water molecule was also detected close to the methyl group of 7T in the RNA-DNA junction but not to the other two thymine bases (8T and 9T). This result correlates with the structural studies that only DNA residue 7T in the RNA-DNA junction adopts an O4'-endo sugar conformation (intermediate between B-form and A-form), while the other DNA residues including 3C in the DNA-RNA junction, adopt C1'-exo or C2'-endo conformations (in the B-form domain). Based on the NOE cross-peak patterns, we have found that RNA C2'-OH tends to orient toward the O3' direction, forming a possible hydrogen bond with the 3'-phosphate group. The exchange rates for RNA C2'-OH were found to be around 5-20 s(-1), compared to 26.7(+/-13.8) s(-1) reported previously for the other DNA.RNA hybrid duplex. This slow exchange rate may be due to the narrow minor groove width of [d(CGC)r(aaa)d(TTTGCG)](2), which may trap the water molecules and restrict the dynamic motion of hydroxyl protons. The distinct hydration patterns of the RNA adenine H2 and H1' protons and the DNA 7T methyl group in the hybrid segment, as well as the orientation and dynamics of the RNA C2'-OH protons, may provide a molecular basis for further understanding the structure and recognition of DNA.RNA hybrid and chimeric duplexes.

Adenine↗

PubMed2000

Natural abundance heteronuclear NMR studies of the T3 mini-loop hairpin in the terminal repeat of the adenoassociated virus 2.

A DNA hairpin containing a T3 loop, as occurs in the terminal repeat of a popular gene therapy vector (Adenoassociated Virus 2, AAV2), has been extensively studied using homo- and heteronuclear NMR experiments. Almost complete assignment of the proton and carbon resonances, including H5'(Pro-S) and H5'(Pro-R) protons, has been accomplished at natural abundance. NOESY spectra in H2O and D2O have revealed many unusual NOEs, which, when combined with the epsilon, beta, gamma, and chi torsion angles determined from heteronuclear 1H-13C, 1H-31P, and 13C-31P coupling constants, have allowed for a more detailed picture of the T3 mini-loop hairpin. The three loop thymidines are all unpaired, yet are highly structured when bracketed by a 5'-GC...GC-3' stem sequence. The structure determined in this manuscript is considerably different from several other structures reported so far. Contrary to an RNA oligomer with a central U3 sequence that has the tendency to form a duplex with three U*U mismatches, the d(GAAGC-TTT-GCTTC) sequence exists mostly as a hairpin under millimolar NMR conditions. Since T3 triloop was found to be an essential element for the site-specific non-homologous integration of the AAV2 virus, and modification of the T3 loop residue abolishes such capability, the structure we report here may be of biological significance.

DNA, Viral↗

PubMed2000

Elucidation of the solution structure of cardiotoxin analogue V from the Taiwan cobra (Naja naja atra)--identification of structural features important for the lethal action of snake venom cardiotoxins.

The aim of the present study is to understand the structural features responsible for the lethal activity of snake venom cardiotoxins. Comparison of the lethal potency of the five cardiotoxin isoforms isolated from the venom of Taiwan cobra (Naja naja atra) reveals that the lethal potency of CTX I and CTX V are about twice of that exhibited by CTX II, CTX III, and CTX IV. In the present study, the solution structure of CTX V has been determined at high resolution using multidimensional proton NMR spectroscopy and dynamical simulated annealing techniques. Comparison of the high resolution solution structures of CTX V with that of CTX IV reveals that the secondary structural elements in both the toxin isoforms consist of a triple and double-stranded antiparallel beta-sheet domains. Critical examination of the three-dimensional structure of CTX V shows that the residues at the tip of Loop III form a distinct "finger-shaped" projection comprising of nonpolar residues. The occurrence of the nonpolar "finger-shaped" projection leads to the formation of a prominent cleft between the residues located at the tip of Loops II and III. Interestingly, the occurrence of a backbone hydrogen bonding (Val27CO to Leu48NH) in CTX IV is found to distort the "finger-shaped" projection and consequently diminish the cleft formation at the tip of Loops II and III. Comparison of the solution structures and lethal potencies of other cardiotoxin isoforms isolated from the Taiwan cobra (Naja naja atra) venom shows that a strong correlation exists between the lethal potency and occurrence of the nonpolar "finger-shaped" projection at the tip of Loop III. Critical analysis of the structures of the various CTX isoforms from the Taiwan cobra suggest that the degree of exposure of the cationic charge (to the solvent) contributed by the invariant lysine residue at position 44 on the convex side of the CTX molecules could be another crucial factor governing their lethal potency.

Amino Acid Sequence↗

PubMed1999

Stable formation of a pyrimidine-rich loop hairpin in a cruciform promoter.

We have determined the solution structure of a TCC-loop hairpin in the cruciform promoter for the bacteriophage N4 virion RNA polymerase (N4 vRNAP). This hairpin and its complementary GGA-loop hairpin are extruded at physiological superhelical density and are required for vRNAP recognition. Contrary to its complementary GGA-loop, the three pyrimidines in the TCC-loop are all unpaired. However, with the help of two juxtaposed stem Watson-Crick G.C base-pairs, each nucleotide in the loop employs a special method to stabilize the hairpin structure. The resulting structures display extensive loop base-stacking rearrangement yet minor backbone distortion, which is largely accomplished through some loop zeta and alpha torsional angle changes. Consistent with the structural studies, UV melting of the GAAGCTCCGCTTC hairpin revealed a higher melting temperature (66 degrees C) than that of the GAACGTCCCGTTC hairpin (58 degrees C) with reversed stem G.C base-pairs, indicating significant contribution from the extra three loop-stem H-bonds. Thermodynamic parameters DeltaG degrees 25of the GAAGCTCCGCTTC hairpin and its complementary GAAGCGGAGCTTC hairpin are -4.1 and -4. 3 kcal/mol respectively, indicating approximately equal contribution of each hairpin to the cruciform formation of the N4 virion RNA polymerase promoter. No significant loop dynamics in the microsecond to millisecond NMR time-scale was observed, and the abundant well-defined exchangeable and non-exchangeable proton NOEs allowed us to efficiently determine a well-converged family for the final structures of the TCC-loop hairpin.

Base Pairing↗

PubMed1999

Stable sheared A.C pair in DNA hairpins.

Single-residue d(Pu1NPu2) (Pu1.Pu2=G.A, G.G or A.A) hairpin loops can be stably closed by sheared purine.purine pairs. These special motifs have been found in several important biological systems. We now extend these loop-closing base-pairs to a sheared purine. pyrimidine (A.C) pair at a neutral pH condition. High-resolution NMR spectroscopy, distance geometry, and molecular dynamics methods were used to study d(GTACANCGTAC) oligomers. Numerous idiosyncratic nuclear Overhauser enhancements, especially those across the A.C base-pair between C4NH2left and right arrow AH1', C4NH2left and right arrow AH2, and CH5left and right arrow AH2 proton pairs, clearly define the novel sheared nature of the closing A.C base-pair. This novel base-pair is possibly present in several biological systems and in two single-stranded DNA aptamers selected from oligonucleotide libraries.

Base Pairing↗

PubMed1999

Cross-strand purine-pyrimidine stack and sheared purine.pyrimidine pairing in the human HIV-1 reverse transcriptase inhibitors.

Cross-strand homo purine-purine (G-G or A-A) stacks and sheared purine.purine pairing have been found to be important motifs in nucleic acid duplex structures. We now report novel cross-strand purine-pyrimidine (A-C) and hetero purine-purine (G-A) stacks that are established from a sheared purine.pyrimidine (A.C) pair adjacent to a sheared G.A pair in the 5'-AA/GC-3' sequence. This "internal loop" sequence is conserved in two families of single-stranded DNA inhibitors of the reverse transcriptase of type 1 human immunodeficiency virus. The distorted backbone of these inhibitors, resulting from the unique helical twists and kinks in the 5'-AA/GC-3' sequence, may be responsible for the increased affinities of these single-stranded DNA inhibitors as compared with other regular B-form duplex substrates. Two simple rules have been generalized to account for all reported cross-strand stacks.

Base Pairing↗

PubMed1999

Structural studies of symmetric DNA undecamers containing non-symmetrical sheared (PuGAPu):(PyGAPy) motifs.

Interstrand purine-purine stacks originate from tandem sheared purine.purine pairing and represent one of the most important motifs in both DNA and RNA structures. Several RNA and DNA structures, solved recently in both solution and the solid state, contain these special motifs, which greatly increase the structural diversity of nucleic acid molecules. The direct evidence for the sheared purine-purine pairing at neutral pH in solution remains, however, elusive. In this manuscript, we have used high resolution NMR methods to study a series of symmetrical DNA duplexes containing two non-symmetrical 5'-(PuGAPu)/(PyGAPy)-3' motifs. Many strong- and medium-strength NOEs across the G.A base pair were detected in the H2O-NOESY spectra collected at a relatively low temperature (-5 degrees C). These NOEs, especially those from A-6NH2 to G-H1', G-H4', and G-2NH2, clearly define the proposed side-by-side sheared G.A pairing nature. Another interesting feature is the strong NOEs exhibited by the unpaired G-imino proton in the G.A pair to its own G-2NH2, which implies that G-2NH2 is involved in H-bonding with a base in the minor groove edge. The finding that non-symmetrical (PuGAPu):(PyGAPy) motif also form similarly stable structures loosens the requirement for a more restricted (PyGAPu)2 motif in forming the interstrand purine-purine stacks.

Base Pairing↗

PubMed1999

Finite-volume lattice Boltzmann method.

We present a finite-volume formulation for the lattice Boltzmann method (FVLBM) based on standard bilinear quadrilateral elements in two dimensions. The accuracy of this scheme is demonstrated by comparing the velocity field with the analytical solution of the Navier-Stokes equations for time dependent rotating Couette flow and Taylor vortex flow. To demonstrate the flexibility of the scheme, we have also simulated a modified rotating Couette flow, where the inner cylinder has an elliptical shape. The results agree with those obtained from the traditional marker-and-cell method. The FVLBM scheme is applicable to arbitrarily shaped two-dimensional regions, and thus the range of applicability of the lattice Boltzmann method has been significantly extended.

Journal Article↗

PubMed1999

Finite-volume lattice Boltzmann schemes in two and three dimensions.

Simple and practical finite-volume schemes for the lattice Boltzmann equation are derived in two and three dimensions through the application of modern finite-volume methods. The schemes use a finite-volume vortex-type formulation based on quadrilateral elements in two dimensions and trilinear hexahedral elements in three dimensions. It is shown that the schemes are applicable to domains with irregular boundaries of arbitrary shape in two and three dimensions.

Journal Article↗

PubMed1997

Centromeric pyrimidine strands fold into an intercalated motif by forming a double hairpin with a novel T:G:G:T tetrad: solution structure of the d(TCCCGTTTCCA) dimer.

The solution structures of the oligodeoxynucleotides d(CCCGTTTCC) and d(TCCCGTTTCCA) have been determined by two-dimensional NMR spectroscopy. These oligomers are part of a DNA box in human centromeric alpha satellite targeted by the centromere protein B (CENP-B). Both CENP-B and its recognition box in alphoid DNA are conserved in mammals, suggesting an important biological role. At acidic pH, d(CCCGTTTCC), d(TCCCGTTTCCA) and the full d(TCCCGTTTCCAACGAAG) CENP-B box strand all fold and dimerize in solution forming a stable bimolecular structure containing two GTTT hairpin loops that interact through a novel T : G : G : T tetrad. The stem region of the dimer is a four-stranded intercalated motif in which the hairpin monomers are parallel and held together by C : C+ hydrogen-bonding and intercalation. The loops are at the same end of the dimer and lie across the narrow grooves of the tetraplex. They are remarkably structured and stabilized by base-base cross-stacking, sugar-base stacking, and parallel G:G and antiparallel G:T pairing. In the d(TCCCGTTTCCA)2 structure, the intercalated motif is continued at the other end of the dimer with unpaired but stacked adenine and thymine bases. The possible biological implications of these structures are discussed.

Autoantigens↗