Large helical conformational deviations from ideal B-DNA and prokaryotic regulatory sites

Prediction of function in DNA sequence analysis

Recognition of function of newly sequenced DNA fragments is an important area of computational molecular biology. Here we present an extensive review of methods for prediction of functional sites, tRNA, and protein-coding genes and discuss possible further directions of research in this area.

Long range and symmetry considerations in the DNA

The common description of DNA is that of a polymer composed of overlapping dinucleotide base pairs. Conformational, thermodynamic and flexibility calculations of the DNA are frequently based on that description. As demonstrated by the good fit with experimental data, such as the free energy of opening the double stranded DNA and the correspondence between the DNA crystal and computed structures, this approach is to a large extent a faithful reproduction of the DNA. Here I show that longer range effects should be considered as well. Statistically strong longer-range sequence patterns are described. Such sequence preferences are clearly translated in the DNA into long range structural propagation. Long range effects have also been observed in some experimental studies, like gel mobility and patterns of DNA cleavage. Long range structural effects are the likely explanation of the effect of mutations at a distance from a protein binding site. They might also aid in understanding DNA looping.

Sequence signals in eukaryotic upstream regions

Two DNA sequence elements are known to recur frequently upstream of eukaryotic polymerase II-transcribed genes. The TATAAA, at position -40, specifies the transcription initiation site. The GGCCAATCT is less frequent around -80. Sequence analysis of upstream regions reveals that the underlined yeast UAS2 consensus sequence, TGATTGGT, is also very frequent at -80 in higher polymerase II-transcribed animal sequences. The underlined CCAAT box and yeast UAS sequences are complementary. Structural analysis suggests some symmetry in their DNA structures. Upstream of the TATAAT-rich region there is an abundance of GC sequences. Analysis of nucleotide tracts indicates that these are preferentially flanked by their complementary nucleotides with a pyrimidine-purine junction, i.e., TTAN, CCGn, CnGG, TnAA. Here, I discuss DNA structural consideration in upstream regions along with protein readout of the major and minor groove information content. These sequence-structure aspects are put in the general context of protein (factors)-DNA (elements) recognition and regulation.

Analysis of sequences of twist angles in DNA double helix

By assuming that the realistic DNA chains are random sequence of bases and using the Tung-Harvey formula for the prediction of twist angles, it is shown that the mean value of the sequence of twist angles is almost sequence-independent. In general the variance for the A, T-rich sequence is larger than that of G, C-rich sequence. There exists an upper bound for the variance of all possible sequences, i.e., the variance is not greater than 27 deg2. It is pointed out that the large conformational deviation from ideal DNA is an important factor for the recognition of DNA with protein/enzyme.

N.m.r. assignments and temperature-dependent conformational transitions of a mutant trp operator-promoter in solution

A total of 145 protons in the mutant trp operator-promoter sequence CGTACTGATTAATCAGTACG were assigned by one-dimensional and two-dimensional n.m.r. methods. Except at the sites of mutation (underlined), the chemical shifts and other n.m.r. parameters are very similar to those observed in the symmetrized wild-type sequence [Lefèvre, Lane & Jardetzky (1987) Biochemistry 26, 5076-5090]. Spin-spin-relaxation rate constants of the resolved base protons and intra- and inter-nucleotide nuclear-Overhauser-enhancement intensities argue for a sequence-dependent structure similar to that of the wild-type, except at and close to the sites of the mutation. The overall tumbling time as a function of temperature was determined from cross-relaxation rate constants for the H-6-H-5 vectors of the four cytosine residues. The values are consistent with the oligonucleotide maintaining a double-helical conformation over the entire temperature range 5-45 degrees C, and that internal motions of the bases are of small amplitude on the subnanosecond time scale. The temperature-dependence of chemical shifts, spin-spin-relaxation rate constants and cross-relaxation rate constants show the occurrence of two conformational transitions localized to the TTAA sequence in the centre of the molecule. The thermodynamics of the transition at the lower temperature (tm = 16 degrees C) were analysed according to a two-state process. The mid-point temperature is about 6 degrees C higher than in the wild-type sequence. The conformational transition does not lead to rupture of the Watson-Crick hydrogen bonds, but probably involves changes in the propellor twists of T.A-9 and T.A-10. The second transition occurs at about 40 degrees C, but cannot be fully characterized. This conformational variability seems to be a property of the sequence TTAA, and may have functional significance in bacterial promoters.

Upper limit for the variances of some helical parameters in DNA double helix

Assuming that the realistic DNA chains are random sequences of purines and pyrimidines and, by using the Dickerson sum functions, it is shown that there exists an upper limit for the variance of helical twist angles, the base-plane roll angles and the other helical parameters respectively in the DNA sequences. The estimates of the variances of all the above helical parameters for the DNA sequences in the Los Alamos data base have been performed and found to be in good agreement with the theoretical results obtained in this paper.

The distributions of nucleotides near bacterial transcription initiation and termination sites show distinct signals that may affect DNA geometry

Compilation and analysis of all bacterial sequences which are aligned by their transcription initiation sites show a dramatic behavior of the four nucleotides. Large peaks of T and A are observed. This highly nonrandom distribution is likely to affect the DNA geometry in addition to affecting the strength of binding between the two DNA strands. Following this site, the G and C rise above their overall bacterial mean. Alignment by transcription termination sites indicates that this behavior continues till the mRNA 3' termini. At this site the concentrations of A and T rise again above the mean. Analysis of the distributions of the 256 quartets in the 1000 nucleotide regions surrounding both transcription initiation and termination sites has been carried out. Some A/T combination sequences may serve as signals to the bacterial transcription machinery, in addition to the well-established TTGACA and TATAAT at positions -35 and -10, respectively, and a run of Ts at the transcription termination site. The frequent occurrences of (dA)/(dT) runs in the vicinity of these sites may result in curved DNA structures, affecting recognition and the nature of the interaction between the RNA polymerase and the DNA.

Computer modelling of DNA structures involved in chromosome maintenance

Sequence-dependent DNA bending of synthetic and natural molecules was studied by computer analysis. Modelling of synthetic oligonucleotides and of 107 kb of natural sequences gave results which closely resembled published electrophoretic data, demonstrating the powerful predictive capacity of the procedure. The analysis was extended to the study of DNA structures involved in chromosome maintenance. Centromeric DNAs from yeast were found to have sequences in their functional elements which cause them to be unusually straight. Autonomous replicating sequences were found to have two structural domains, one consisting of unusually straight sequences surrounding the consensus and the other of bending elements in flanking DNA. In addition to a structural homology, centromeric and autonomous replicating sequences share common sequence elements. These observations show that computer modelling of natural sequences is a viable approach to the study of the biological implications of alternative DNA structures.

A common structural feature in promoter sequences of E. coli

We have searched promoter regions of E. coli, structural genes of the same organism, and computer-generated random sequence DNA for the occurrence of common structural features. This is done by converting the base sequence to a series of numbers representing the sequence of helix twist angles and examining these numerical sequences statistically. Common structural features are shared by the promoter regions with a much higher frequency than are found in structural genes or in random sequences. These structures appear to be scattered randomly throughout the promoters, both in terms of the number of such structures per promoter and in terms of location within each promoter. One particular structure consisting of five successive helix twist angles is reported, along with a list of 60 different hexanucleotide sequences that share this structure. The locations of these structural elements in 61 E. coli promoters are also tabulated.

The interaction of the trp repressor from Escherichia coli with the trp operator

We have examined the interaction of the trp repressor from Escherichia coli with a 20 base-pair synthetic operator. Nonspecific binding was relatively strong (Kd = 2 microM), but only weakly sensitive to the concentration of added salt [d log Kd)/(d log [Na]) = -1). 1H-NMR studies indicate that the structure of the repressor is not greatly altered on forming the complex, and that few if any of the lysine and arginine residues make direct contact with the DNA. However, the mobility of one of the two tyrosine residues is significantly decreased in the complex. The repressor makes close contact with the major grooves of the operator such that the base protons are broadened much more than expected on the basis of increased correlation time. There are large, differential changes in chemical shifts of the imino protons on forming the complex, as well as changes in the rate constants for exchange. The fraying of the ends is greatly diminished, consistent with a target size of about 20 base-pairs. The effects of the repressor on the NMR spectra and relaxation rate constants can be interpreted as a change in the conformation of the operator, possibly a kinking in the centre of the molecule.

Theoretical molecular biology: prospectives and perspectives

I briefly discuss some aspects of theoretical molecular biology. Specifically, I include the issues of searches for homologies via string matchings, for patterns of specific nucleotide groupings and of sequence-structure relationship. The various approaches developed in order to achieve this end are described, attempting to convey some of the excitement in this quickly growing field.