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I Tinoco

Publications and source records attributed to I Tinoco.

At least 127 records · Page 7Linked to original sources
PubMed1982

Small changes in free energy assignments for unpaired bases do not affect predicted secondary structures in single stranded RNA.

We present extensive calculations of the secondary structure of mRNA which point to its insensitivity to small changes in the free energy assignments of single stranded regions. Truncating the free energies of hairpin loops, bulges, internal loops and multibranched junctions to two significant digits yields structures nearly identical to those generated using three digit values. The results show that one can safely use truncated values in RNA folding calculations. The implementation of these results enabled us to carry out secondary structure calculations on 2600 nucleotides in a single computer run.

Base Composition↗
PubMed1982

Secondary structure model for the complete simian virus 50 late precursor mRNA.

Structures for all sequences containing less than 1790 nucleotides in the 2600 nucleotide late region of the SV40 virus have been computed and saved on magnetic tape. Previously the longest sequence whose secondary structure was calculated in a single computer run contained 950 nucleotides. In the past, analysis of long molecules required numerous repeated, partially overlapping computations on much shorter segments. The structure obtained for the late half of the SV40 is Y-shaped with two unequal arms. It has 52 short hairpins. Two long range interactions between nucleotides near 650 and 1350 and between 1450 and 2450 appear to play an important role. The first is within the 16S intron; the second is in the 3' exon. The 5' and 3' ends of the molecule are close to each other and are found in the major elongated stem in the vicinity of the fork.

Base Sequence↗
PubMed1981

Comparative study of ribonucleotide, deoxyribonucleotide, and hybrid oligonucleotide helices by nuclear magnetic resonance.

The nonexchangeable base protons and the hydrogen-bonding NH--N imino protons were used to study the conformations and the helix--coil transitions in the following oligonucleotides: (I) dCT5G + dCA5G, (II) rCU5G + rCA5G, (III) dCT5 G + rCA5G, (IV) rCU5G + dCA5G. The first three mixtures all form stable double-helical structures at 5 degrees C, whereas IV forms a triple strand with an rCU5G:dCA5G 2:1 ratio. The chemical shifts of the imino protons in the double strands indicate that I, II, and III have different conformations in solution. For example, the hydrogen-bonded proton of one of the C.G base pairs is more deshielded (a 0.4-ppm downfield shift) in helix I than in helix II or III. This implies a significant change in helical parameters, such as the winding angle, the distance between base pairs, or overlap of the bases. The coupling constants of the H1' sugar protons show that helix I has 90% 2'-endo sugar conformation, whereas helix III has greater than 85% 3'-endo conformation for the observed sugar rings. The sugar pucker data are consistent with helix I having B-family geometry; III has A-family geometry. The chemical shifts of the nonexchangeable base protons in system I were followed with increasing temperature. The midpoints for the transitions, Tm's, for all the base protons were 28--30 degrees C; this indicates an all-or-none transition.

Magnetic Resonance Spectroscopy↗
PubMed1981

Correlations between deoxyribonucleic acid structural parameters and calculated circular dichroism spectra.

Circular dichroism spectra are calculated for 68 different conformations of the bases in the double-stranded sequence of T-G-G-C-G-T-A-T-T-C-T and its complementary strand. All conformations are right-handed helices and include both published models and energy-minimized forms. Examination of the dependence of the circular dichroism band at 274 nm shows that the magnitude of the band is a linear function of both the helix winding angle and the base pair twist. Correlations of the magnitude of the circular dichroism with the distance between base pairs, the distance of the base pairs from the helix axis, or the tilt of the base pair relative to the helix axis are poorer.

Base Sequence↗
PubMed1980

DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription.

A DNA-RNA hybrid oligonucleotide duplex, dC(pA) 5pG:rC(pU)5pG, which contains a (dA:rU) 5 sequence, is at least 200 times less stable at room temperature than the corresponding duplex containing an (rA:dT) 5 sequence, rC(pA)5pG:dC(pT)5pG. This result provides an explanation for the finding that most primary RNA transcripts terminate in several consecutive rU residues, but not rA residues. It strongly supports the idea that instability of the DNA-RNA hybrid at the growing point of transcription plays a role in termination of transcription.

Base Sequence↗
PubMed1980

Conformation studies of 13 trinucleoside diphosphates by 360 MHz PMR spectroscopy. A bulged base conformation. I. Base protons and H1' protons.

The 360 MHz NMR spectra of the base protons and the H1 protons of thirteen trinucleoside diphosphates have been analyzed. The sequences chosen represent all purine-pyrimidine sequences. The chemical shifts of the base protons give evidence for strong next nearest-neighbor effects in some oligonucleotides. Although increasing chain length usually increases nearest-neighbor base-base stacking, it is not always so. Comparing ApCpG, ApUpG and GpUpG to their component dimers, one finds a decrease in stacking of the center pyrimidine with the purine on either side. The coupling constants J 1'2' also show that these three trimers show less stacking for their terminal residues than expected from their component dimers. We conclude that the sequence Pu-Py-Pu favors a conformation in which the pyrimidine is bulged out and the two purines stack on each other.

Journal Article↗
PubMed1979

Conformations of dinucleoside phosphates in aqueous solution.

The conformations of dinucleoside phosphates have been reexamined by semiempirical potential energy calculations. Conformations I, II, and III, proposed by Lee & Tinoco [Lee, C. H., & Tinoco, I., Jr. (1977) Biochemistry 16, 5403], are possible species after refinement of their structures by potential energy minimization. These three conformers can represent three types of dinucleoside phosphate species in solution. Dhingra et al. [Dhingra, M. M., Sarma, R. H., Giessner-Prettre, C., & Pullman, B. (1978) Biochemistry 17, 5815] had concluded that conformations of type II and III were unlikely or impossible. They favored conformations g-g- (equivalent to I), g+g+,g+t, and tg+; the last three conformations have little stacking and are calculated to be energetically less favorable by more than 5 kcal/mol. Common structures of the types I, II, and III are found for dinucleoside phosphates with different purine-pyrimidine sequences. The sequence dependence of the potential energy of these three conformers has been calculated. The experimental nuclear magnetic resonance data of dinucleoside phosphates are consistent with these three conformations.

Calorimetry↗
PubMed1979

Interactions of 4-nitroquinoline 1-oxide with deoxyribodinucleotides.

The interactions of 4-nitroquinoline 1-oxide (NQO), a potent mutagen and carcinogen, with several self- and non-self-complementary deoxydinucleotides were probed by using absorption spectra of the charge transfer bands and 1H and 13C NMR spectra. Absorption spectra were analyzed by using Benesi-Hildebrand-type equations to yield stoichiometries and equilibrium constants of complex formation. Non-self complementary dimers form weak l:1 complexes [dpTpG:NQO, K(25 degrees C) = 22 M-1] while self-complementary dimers form strong 2:1 complexes [dpCpG)2:NQO, K(25 degrees C) = 2.2 X 10(4) M-2]. A mixture of dpTpG and dpCpA with NQO gives a 2:1 complexes [dpCpG)2:NQO, K(25 degrees C) = 2.2 X 10(4) M-2]. A mixture of dpTpG and dpCpA, K(25 degrees C) = 8.6 X 10(3) M-2]. Analyses of the changes in 13C and 1H NMR chemical shifts with complex formation gave approximate orientations for the intercalation of NQO with self-complementary dimer minihelixes. In the (dpCpG)2:NQO and (dpGpC)2:NQO complexes, the NO2 group of NQO probably lies in the major grove and the NO2, NO containing NQO ring is stacked near the purine imidazole ring. In the (dpTpA)2:NQO and (dpApT)2NQO complexes, the NO2 seems to project into the minor grove and the NQO benzenoid ring is over the purine imidazole ring.

4-Nitroquinoline-1-oxide↗
PubMed1978

Interactions of 4-nitroquinoline 1-oxide with four deoxyribonucleotides.

The interactions of 4-nitroquinoline 1-oxide (NQO) with the four 5'-deoxyribonucleotides were probed using absorption spectra of the charge transfer bands and 1H and 13C nuclear magnetic resonance (NMR) spectra of nucleotide-NQO mixtures. Spectral data yielded equilibrium constants (K(dpG:NQO) = 16 M-1, K(dpA:NQO) = 12 M-1, K(dpT:NQO) = K(dpC:NQO) = 4 M-1) which suggest the preference of NQO for the guanine residue in a DNA. This is in agreement with the data of Okano, T., et al. [(1969) Gann 60, 295]. From 13C and 1H NMR data on nucleosides, a structure for the dpG:NQO complex is proposed.

4-Nitroquinoline-1-oxide↗
PubMed1977

Studies of the conformation of modified dinucleoside phosphates containing 1,N6-ethenoadenosine and 2'-O-methylcytidine by 360-MHz 1H nuclear magnetic resonance spectroscopy. Investigation of the solution conformations of dinucleoside phosphates.

Seven dinucleoside monophosphates containing epsilonA (1,N6-ethenoadenosine) and 2'-O-methylcytidine were studied by 360-MHz proton magnetic resonance and compared with unmodified dimers and component monomers at 4, 20, 45, and 75 degrees C. These studies show that the dimers exhibit preference for the gg and g'g' conformations for the C-4'-C-5' and C-5'-O-5' bonds, respectively, and that dimerization induces an increase of the population and inflexibility of the 3'-endo conformations for the ribose ring. Three stacked (or stable) conformations for dimers, I, II, and III, in equilibrium with an unstacked (or open) form in solution, are suggested by dimerization shifts of ribose protons. Conformation I exhibits anti, gg, 3'-endo, phi' = 203 to approximately 211 degrees, omega' = 300 degrees, omega = 290 degrees, g'g', gg, 3'-endo, and anti conformation from the 5' end to the 3' end of the dimer. Conformation II shows anti, gg, 3'-endo, phi' = 203-211 degrees, omega = 30 degrees, omega = 100 degrees, g'g', gg, 3'-endo, and anti conformation. Conformation III is anti, gg, 2'-endo, phi' = 260 degrees, omega' = 50 degrees, omega = 220 degrees g'g', gg, 3'-endo, and anti (x approximately 100 degrees) conformation. The dimers, PupPu and PupPy, prefer conformations I and II, while PypPu and PypPy prefer conformation II. Introduction of epsilonA for the base of -pN induces an increase of conformations II and III, while the epsilonA substitution for the Np- residue induces an increase of conformation I. 2'-O-methylation of the Cp- residue of CpC decreases conformation I and increases conformation II. Based on the stable solution conformations of these dimers, a possible conformation of the anticodon loop is proposed, which is an alternative to the one observed in the crystal of tRNAPhe.

Adenosine↗