Four different base-specific chemical reactions generate a means of directly sequencing RNA terminally labeled with 32P. After a partial, specific modification of each kind of RNA base, an amine-catalyzed strand scission generates labeled fragments whose lengths determine the position of each nucleotide in the sequence. Dimethyl sulfate modifies guanosine. Diethyl pyrocarbonate attacks primarily adenosine. Hydrazine attacks uridine and cytidine, but salt suppresses the reaction with uridine. In all cases, aniline induces a subsequent strand scission. The electrophoretic fractionation of the labeled fragments on a polyacrylamide gel, followed by autoradiography, determines the RNA sequence. RNA labeled at the 3' end yields clean cleavage patterns for each purine and pyrimidine and allows a determination of the entire RNA sequence out to is attacked yet random with regard to the position of the base along the polynucleotide strand. In addition, it is a limited reaction. Thus, strand scission at the site of a chemical attack generates a nested set of radioactive fragments which can be resolved according to length by electrophoresis through a polyacrylamide gel. An autoradiograph of the polyacrylamide gel displays a series of bands in four lanes that corresponds to the set of radioactive fragments. Each band corresponds to a nucleotide fragment of discrete length generated by cleavage at a specific base, and the four lanes correspond to cleavages at the bases as follows: guanosine (G), adenosine (A > G), cytidine (C > U), and uridine (U). Thus, the sequence can be read directly from the autoradiograph (see Fig. 1 Adenosine > Guanosine Reaction. In aqueous solutions, diethyl pyrocarbonate reacts with nucleic acids by carbethoxylation of base nitrogens. The imidazole rings of both adenosine and guanosine open in the course of this reaction due to carbethoxylation at the N-7 of adenosine and at the N-7 of guanosine (14), thereby allowing aniline-catalyzed strand scission at these sites. Diethyl pyrocarbonate reacts with adenosine faster than with guanosine (15), and under my conditions, the reaction is about 7 times faster.Uridine Reaction. Unprotonated molecules of hydrazine react with the pyrimidine bases (16-21) in the order U >> C > T (22), and the reaction occurs via nucleophilic addition to the pyrimidine 5,6 double bond (23). The base is effectively removed, and the sites of hydrazinolysis along the RNA strand are vulnerable to aniline attack. Treatment with either anhydrous or aqueous hydrazine, followed by aniline, induces strand scission at uridines.Cytidine > Uridine Reaction. Aqueous hydrazine reacts with thymidine and cytidine in DNA, but the addition of 2 M sodium chloride suppresses hydrazinolysis of the thymidines (1). Although aqueous or anhydrous hydrazine preferentially attacks uridines in RNA, the presence of 3 M sodium chloride in anhydrous hydrazine markedly decreases the attack on uridine and hydrazinolysis of cytidine becomes the dominant reaction. A subsequent aniline treatment produ...

An analysis of the small subunit ribosomal RNA (16S-like rRNA) from the protozoan Giardia lamblia provided a new perspective on the evolution of nucleated cells. Evolutionary distances estimated from sequence comparisons between the 16S-like rRNAs of Giardia lamblia and other eukaryotes exceed similar estimates of evolutionary diversity between archaebacteria and eubacteria and challenge the phylogenetic significance of multiple eukaryotic kingdoms. The Giardia lamblia 16S-like rRNA has retained many of the features that may have been present in the common ancestor of eukaryotes and prokaryotes.

Three chemical reactions can probe the secondary and tertiary interactions of RNA molecules in solution. Dimethyl sulfate monitors the N-7 of guanosines and senses tertiary interactions there, diethyl pyrocarbonate detects stacking of adenosines, and an alternate dimethyl sulfate reaction examines the N-3 of cytidines and thus probes base pairing. The reactions work between 0C and 90'C and at pH 4.5-8.5 in a variety of buffers. As an example we follow the progressive denaturation of yeast tRNA"h terminally labeled with 32P as the tertiary and secondary structures sequentially melt out. A single autoradiograph of a terminally labeled molecule locates regions of higher-order structure and identifies the bases involved.The three-dimensional configuration of an RNA molecule determines many of its biological properties. Chemical reagents provide sensitive probes of the conformation of nucleic acids in solution, detecting such properties as base pairing, base stacking, or the shielding of reactive groups by tertiary structure or complex formation with a protein or ion. With a base-specific reagent and a terminally labeled polynucleotide, a single experiment can probe such properties of that base wherever it occurs in the molecule. Our base-specific reagents weaken the glycosyl bond between the base and the ribosyl moiety of the polynucleotide. Thus, an initial, limited, base-specific modification appears ultimately as a chemically induced strand scission. The distance of the strand scission from the terminal label locates the position of the attacked base'along the molecule. The resultant nucleotide fragments are electrophoretically separated by size on polyacrylamide gels and their lengths are determined by autoradiography. This approach underlies the chemical determination of the sequence of DNA (1) and RNA (2) molecules. It has also been used to study .Dimethyl sulfate alkylates the N-7 position of guanosines (6) and the N-3 position of cytidines (7); diethyl pyrocarbonate carbethoxylates the N-7 of adenosines (8). However, these reactions occur only if the sites are not involved in structural interactions and, hence, are available for chemical modification. Furthermore, the diethyl pyrocarbonate reaction appears to be sensitive to the stacking of adenosines. Thus, these reagents effectively probe conformation by providing structure-specific data as well as base-specific information. If an RNA molecule is modified under totally denaturing conditions, a full sequence spectrum is generated on the autoradiograph that displays the electrophoretically separated labeled fragments (2). However, if the molecule is probed under native or semidenaturing conditions, only a partial sequence spectrum.appears (see Fig. 1 for example). Thus, when the probing reactions are run in parallel with the chemical sequencing reactions, a single autoradiograph locates regions of higher-order structure and simultaneously identifies the bases involved. The RNA can be labeled before or after the initial reactions.By using yeast tRNA...

BiochemistryExpression and characterization of human FKBP52, an immunophilin that associates with the 90-kDa heat shock protein and is a component of steroid receptor complexes Communicated by Etienne-Emile Baulieu, August 17, 1992 ABSTRACT Using an FK506 affinity column to identify mammalian immunosuppressant-binding proteins, we identified an immunophilin with an apparent Mr 55,000, which we have named FKBP52. We used chemically determined peptide sequence and a computerized algorithm to search GenPept, the translated GenBank data base, and identified two cDNAs likely to encode the murine FKBP52 homolog. We amlifed a murine cDNA fragment, used it to select a human FKBP52 (hFKBP52) cDNA clone, and then used the done to deduce the hFKBP52 sequence (calculated Mr 51,810) and to express hFKBP52 in Escherichia coi. Recombinant hFKBP52 has peptidyl-prolyl cis-trans isomerase activity that is inhibited by FK506 and rapamycin and an FKBP12-like consensus sequence that probably defines the immunosuppressant-binding site. FKBP52 Is apparently common to several vertebrate species and associates with the 90-kDa heat shock protein (hsp90) in untransformed mammalian steroid receptor complexes. The putative immunosuppressant-binding site is probably distinct from the hsp90-binding site, and we predict that FKBP52 has different structural domains to accommodate these functions. hFKBP52 contains 12 protein kinase phosphorylation-site motifs MATERIALS AND METHODSPreparation of an FK506 Affinity Matrix and Isolation of FKBPs. An amino derivative of FK506 was prepared (10) and coupled to Affi-Gel 10 (Bio-Rad) in methanol overnight; unreacted groups were blocked with 50 mM ethanolamine. FKBPs from calf thymus cytosol were prepared by using the matrix as described (11), dialyzed at 40C against 10 mM Tris-HCl (pH 7.0), lyophilized, reconstituted in SDS sample buffer, and resolved in a 12.5% acrylamide gel. Proteins were stained (Fig. 1A) or electroblotted.Protein Sequence Determination of bFKBP52. The Mr 55,000 band, later called bFKBP52, was stained on and excised from Immobilon-P (Millipore) for automated aminoterminal sequencing (26). Peptides were generated with endoproteinase Lys-C (Wako Chemicals USA, Richmond, VA) and separated by microbore C18 HPLC and eluted at 200A.l/min from 5% B at 0 min to 33% B at 65 min, 60%6 B at 90 min, and 100% B at 105 min (solvent A, 0.09%o trifluoroacetic acid in water; solvent B, 0.06% trifluoroacetic acid in acetonitrile). Effluent fractions corresponding to absorption peaks at 214 nm were collected, stored immediately at -200C, and applied later to a Polybrene-precycled glass-fiber filter for sequencing.Isolation of a Human cDNA Encoding FKBP52. Using BLAST (27) to search GenPept (translated GenBank Release 64.3 with daily updates, searched on July 11, 1991) with the deduced hFKBP12 sequence (7, 8), we identified two related murine polypeptides (encoded by GenBank sequences X17068 and X17069) that shared significant sequence identity with our bFKBP52 sequence (Fig. 2). Two DNA oligomers...

Department 0f 810chem15try, 5tanf0rd Un1ver51ty 5ch001 0f Med1c1ne, 5tanf0rd, Ca11f0rn1a 94305 U5AWe pre5ent a deta11ed ana1y515 0f the tran5cr1pt10na1 pr0duct5 0f the Mth0rax01d (6xd) re910n 0f the U1tra61th0rax d0ma1n 1n the 61th0rax c0mp1ex 0f Dr050ph11a me1an09a5ter. 7h15 re910n 15 tran5cr16ed tw1ce dur1n9 deve10pment: 6etween 3 and 6 hr 0f em6ry09ene515, a 5et 0f ear1y tran5cr1pt5, 1.1 t0 1.3 k6 1n 512e, 15 5ynthe512ed; fr0m the m1dth1rd 1arva1 1n5tar thr0u9h the adu1t 5ta9e5, a fate 0.8-k6 tran5cr1pt 15 5ynthe512ed. We have 5e4uenced f1ve c10ned cDNA5 repre5ent1n9 ear1y tran5cr1pt5 and three cDNA5 repre5ent1n9 the 1ate tran5cr1pt and have 10cated the1r ex0n5 w1th1n the 40 k6 0f DNA c0mpr151n9 the 6xd re910n. 51 nuc1ea5e pr0tect10n and pr1mer exten510n 0f 60th the ear1y and 1ate tran5cr1pt5 were u5ed t0 further e1uc1date the1r 5tructure. 7he ear1y RNA5 are pr0duced 6y c0mp1ex d1fferent1a1 5p11c1n9 0f a 5er1e5 0f ex0n5 der1ved fr0m a 26-k6 pr1mary tran5cr1pt. Cur10u51y, the5e RNA5 d0 n0t p055e55 519n1f1cant pr0te1n c0d1n9 p0tent1a1. 7he 1ate 6xd RNA c0mpr15e5 a 51n91e ex0n tran5cr16ed fr0m an 1ntr0n1c re910n 0f the ear1y tran5cr1pt10n un1t. 7h15 RNA, 6y c0ntra5t, p055e55e5 exce11ent c0d1n9 p0tent1a1 and, 1f tran51ated, w0u1d y1e1d a 101-am1n0-ac1d p01ypept1de.[Key W0rd5: H0me0t1c 9ene5; U1tra61th0rax (U6x); 61th0rax01d (6xd); 61th0rax c0mp1ex; Dr050ph11a Fe6ruary 6, 1987; rev15ed ver510n rece1ved and acce~ted March 4, 1987. 7he 61th0rax c0mp1ex (8X-C) 0f Dr050ph11a me1an0-9a5ter c0n515t5 0f a c1u5ter 0f h0me0t1c 9ene5 that tran5-duce p051t10na1 1nf0rmat10n 1nt0 5e9menta1 1dent1ty f0r para5e9ment5 5-13 0f the deve10p1n9 1arva and adu1t (p05ter10r 5ec0nd th0rac1c 5e9ment thr0u9h the e19hth a6d0m1na1 5e9ment; Mart1ne2-Ar1a5 and Lawrence 1985). 7he 8X-C can 6e 5u6d1v1ded 9enet1ca11y 1nt0 1nd1-v1dua1 1dent1ty funct10n5 (Lew15 1978(Lew15 , 1981 M0rata and Kerr1d9e 1981; Ca5an0va et a1. 1985; Karch et a1. 1985) that can 6e 9r0uped 1nt0 three c0mp1ementat10n 9r0up5 0r funct10na1 d0ma1n5: the U1tra61th0rax (U6x) d0ma1n, a6d0mma1-A (a6d-A) d0ma1n, and A6d0m1na1-8 (A6d-8) d0ma1n (5anche2-Herrer0 et a1. 1985; 710n9 et a1. 1985). 7he ent1re 8X-C ha5 6een c10ned and many 0f 1t5 mutat10n5 mapped m01ecu1ar1y (8ender et a1. 1983; Karch et a1. 1985). Each funct10na1 d0ma1n ha5 6een 5h0wn t0 c0nta1n a 51n91e h0me0 60x (5c0tt and We1ner 1984; Mc61nn15 et a1. 1984; 8eachy et a1. 1985; Karch et a1. 1985; Re9u15k1 et a1. 1985).7he U6x d0ma1n c0ntr015 the 1dent1ty 0f para5e9-ment5 5 and 6 (p5 5 and 6) and, t0 a 1e55er extent, that 0f p5 7-13, wh05e maj0r 1dent1ty funct10n5 der1ve fr0m the a6d-A and A6d-8 d0ma1n5. U6x mutat10n5 1nact1vate a11 1dent1ty funct10n5 0f the U6x d0ma1n, 5u65et5 0f wh1ch are 1nact1vated 6y f0ur 0ther c1a55e5 0f rece551ve ~Pre5ent addre55: D1v1510n 0f 810109y 156-29, Ca11f0rn1a 1n5t1tute 0f 7echn0109Y, Pa5adena, Ca11f0rn1a 91125 U5A. 2pre5ent addre55: Department 0f 7r0p1ca1 Pu611c Hea1th, Harvard 5ch001 0f Pu611c Hea1th, 665 Hunt1n9t0n Avenue, 805t0n, Ma55achu5ett5 02115 U5A. mutat10n5 w1th1n the d...