Showing papers on "Base pair published in 2002"
TL;DR: A single-base-pair increase in DNA length over that used previously results in substantially improved clarity of the electron density and accuracy for the histone protein and DNA atomic coordinates, and reduced disorder has allowed for the first time extensive modeling of water molecules and ions.
1,375 citations
TL;DR: This paper presents the 4 x 4 'isostericity matrices' summarizing the geometric relationships between the 16 pairwise combinations of the four standard bases, A, C, G and U, and helps identify isosteric pairs that co-vary or interchange in sequences of homologous molecules while maintaining conserved three-dimensional motifs.
Abstract: RNA molecules exhibit complex structures in which a large fraction of the bases engage in non-Watson-Crick base pairing, forming motifs that mediate long-range RNA-RNA interactions and create binding sites for proteins and small molecule ligands. The rapidly growing number of three-dimensional RNA structures at atomic resolution requires that databases contain the annotation of such base pairs. An unambiguous and descriptive nomenclature was proposed recently in which RNA base pairs were classified by the base edges participating in the interaction (Watson-Crick, Hoogsteen/CH or sugar edge) and the orientation of the glycosidic bonds relative to the hydrogen bonds (cis or trans). Twelve basic geometric families were identified and all 12 have been observed in crystal structures. For each base pairing family, we present here the 4 x 4 'isostericity matrices' summarizing the geometric relationships between the 16 pairwise combinations of the four standard bases, A, C, G and U. Whenever available, a representative example of each observed base pair from X-ray crystal structures (3.0 A resolution or better) is provided or, otherwise, theoretically plausible models. This format makes apparent the recurrent geometric patterns that are observed and helps identify isosteric pairs that co-vary or interchange in sequences of homologous molecules while maintaining conserved three-dimensional motifs.
753 citations
TL;DR: The x-ray crystal structure of human topoisomerase I covalently joined to double-stranded DNA and bound to the clinically approved anticancer agent Topotecan suggests that there are at least two classes of mutations that can produce a drug-resistant enzyme.
Abstract: We report the x-ray crystal structure of human topoisomerase I covalently joined to double-stranded DNA and bound to the clinically approved anticancer agent Topotecan. Topotecan mimics a DNA base pair and binds at the site of DNA cleavage by intercalating between the upstream (−1) and downstream (+1) base pairs. Intercalation displaces the downstream DNA, thus preventing religation of the cleaved strand. By specifically binding to the enzyme–substrate complex, Topotecan acts as an uncompetitive inhibitor. The structure can explain several of the known structure–activity relationships of the camptothecin family of anticancer drugs and suggests that there are at least two classes of mutations that can produce a drug-resistant enzyme. The first class includes changes to residues that contribute to direct interactions with the drug, whereas a second class would alter interactions with the DNA and thereby destabilize the drug-binding site.
731 citations
TL;DR: It is shown that DNA strands control and fuel the device cycle by inducing the interconversion between two robust topological motifs, paranemic crossover (PX) DNA and its topoisomer JX2 DNA, in which one strand end is rotated relative to the other by 180°.
Abstract: Controlled mechanical movement in molecular-scale devices has been realized in a variety of systems-catenanes and rotaxanes, chiroptical molecular switches, molecular ratchets and DNA-by exploiting conformational changes triggered by changes in redox potential or temperature, reversible binding of small molecules or ions, or irradiation. The incorporation of such devices into arrays could in principle lead to complex structural states suitable for nanorobotic applications, provided that individual devices can be addressed separately. But because the triggers commonly used tend to act equally on all the devices that are present, they will need to be localized very tightly. This could be readily achieved with devices that are controlled individually by separate and device-specific reagents. A trigger mechanism that allows such specific control is the reversible binding of DNA strands, thereby 'fuelling' conformational changes in a DNA machine. Here we improve upon the initial prototype system that uses this mechanism but generates by-products, by demonstrating a robust sequence-dependent rotary DNA device operating in a four-step cycle. We show that DNA strands control and fuel our device cycle by inducing the interconversion between two robust topological motifs, paranemic crossover (PX) DNA and its topoisomer JX2 DNA, in which one strand end is rotated relative to the other by 180 degrees. We expect that a wide range of analogous yet distinct rotary devices can be created by changing the control strands and the device sequences to which they bind.
697 citations
TL;DR: The crystal structure of Thermus aquaticus RNA polymerase holoenzyme (α2ββ′ωσA) complexed with a fork-junction promoter DNA fragment has been determined by fitting high-resolution x-ray structures of individual components into a 6.5-angstrom resolution map.
Abstract: The crystal structure of Thermus aquaticus RNA polymerase holoenzyme (α2ββ′ωσA) complexed with a fork-junction promoter DNA fragment has been determined by fitting high-resolution x-ray structures of individual components into a 6.5-angstrom resolution map. The DNA lies across one face of the holoenzyme, completely outside the RNA polymerase active site channel. All sequence-specific contacts with core promoter elements are mediated by the σ subunit. A universally conserved tryptophan is ideally positioned to stack on the exposed face of the base pair at the upstream edge of the transcription bubble. Universally conserved basic residues of the σ subunit provide critical contacts with the DNA phosphate backbone and play a role in directing the melted DNA template strand into the RNA polymerase active site. The structure explains how holoenzyme recognizes promoters containing variably spaced –10 and –35 elements and provides the basis for models of the closed and open promoter complexes.
651 citations
TL;DR: In this article, crystal structures of the 30S ribosomal subunit with codon and near-cognate tRNA anticodon stem loops bound at decoding center and compare affinities of equivalent complexes in solution were reported.
634 citations
TL;DR: This review describes the biological functions of DNA methylation in bacteria, fungi, plants, and mammals and the structures and mechanisms of the DNA methyltransferases, which enable them to specifically recognize their DNA targets and to induce such large conformational changes of theDNA.
Abstract: DNA methyltransferases catalyze the transfer of a methyl group from S-adenosyl-L-methionine to cytosine or adenine bases in DNA. These enzymes challenge the Watson/Crick dogma in two instances: 1) They attach inheritable information to the DNA that is not encoded in the nucleotide sequence. This so-called epigenetic information has many important biological functions. In prokaryotes, DNA methylation is used to coordinate DNA replication and the cell cycle, to direct postreplicative mismatch repair, and to distinguish self and nonself DNA. In eukaryotes, DNA methylation contributes to the control of gene expression, the protection of the genome against selfish DNA, maintenance of genome integrity, parental imprinting, X-chromosome inactivation in mammals, and regulation of development. 2) The enzymatic mechanism of DNA methyltransferases is unusual, because these enzymes flip their target base out of the DNA helix and, thereby, locally disrupt the B-DNA helix. This review describes the biological functions of DNA methylation in bacteria, fungi, plants, and mammals. In addition, the structures and mechanisms of the DNA methyltransferases, which enable them to specifically recognize their DNA targets and to induce such large conformational changes of the DNA, are discussed.
582 citations
TL;DR: The bacterial Hfq protein this article belongs to the large family of Sm and Sm-like proteins: it contains a conserved sequence motif known as the Sm1 motif, forms a doughnut-shaped structure, and has RNA binding specificity very similar to the Sm proteins.
530 citations
TL;DR: The initial stages of L1 element transposition in vitro is reconstituted and evidence for specific positioning of the L1 RNA with the ORF2 protein is found, probably mediated in part by the polyadenosine portion of L 1 RNA.
Abstract: L1 elements are ubiquitous human transposons that replicate via an RNA intermediate. We have reconstituted the initial stages of L1 element transposition in vitro. The reaction requires only the L1 ORF2 protein, L1 3' RNA, a target DNA and appropriate buffer components. We detect branched molecules consisting of junctions between transposon 3' end cDNA and the target DNA, resulting from priming at a nick in the target DNA. 5' junctions of transposon cDNA and target DNA are also observed. The nicking and reverse transcription steps in the reaction can be uncoupled, as priming at pre-existing nicks and even double-strand breaks can occur. We find evidence for specific positioning of the L1 RNA with the ORF2 protein, probably mediated in part by the polyadenosine portion of L1 RNA. Polyguanosine, similar to a conserved region of the L1 3' UTR, potently inhibits L1 endonuclease (L1 EN) activity. L1 EN activity is also repressed in the context of the full-length ORF2 protein, but it and a second cryptic nuclease activity are released by ORF2p proteolysis. Additionally, heterologous RNA species such as Alu element RNA and L1 transcripts with 3' extensions are substrates for the reaction.
479 citations
TL;DR: Under near-physiological conditions of pH, temperature and salt concentration, telomeric DNA was predominantly in a double-helix form, however, at lower pH values or higher temperatures, the G-quadruplex and/or the i-motif efficiently competed with the duplex.
Abstract: Human telomeric DNA composed of (TTAGGG/CCCTAA)n repeats may form a classical Watson-Crick double helix. Each individual strand is also prone to quadruplex formation: the G-rich strand may adopt a G-quadruplex conformation involving G-quartets whereas the C-rich strand may fold into an i-motif based on intercalated C*C+ base pairs. Using an equimolar mixture of the telomeric oligonucleotides d[AGGG(TTAGGG)3] and d[(CCCTAA)3CCCT], we defined which structures existed and which would be the predominant species under a variety of experimental conditions. Under near-physiological conditions of pH, temperature and salt concentration, telomeric DNA was predominantly in a double-helix form. However, at lower pH values or higher temperatures, the G-quadruplex and/or the i-motif efficiently competed with the duplex. We also present kinetic and thermodynamic data for duplex association and for G-quadruplex/i-motif unfolding.
415 citations
TL;DR: The concept of active site tightness in DNA polymerases is discussed, and how it might influence steric (size and shape) effects of nucleotide selection in synthesis of a base pair is considered.
Abstract: ▪ Abstract Various physicochemical factors influence DNA replication fidelity. Since it is now known that Watson-Crick hydrogen bonds are not necessary for efficient and selective replication of a base pair by DNA polymerase enzymes, a number of alternative physical factors have been examined to explain the efficiency of these enzymes. Among these factors are minor groove hydrogen bonding, base stacking, solvation, and steric effects. We discuss the concept of active site tightness in DNA polymerases, and consider how it might influence steric (size and shape) effects of nucleotide selection in synthesis of a base pair. A high level of active site tightness is expected to lead to higher fidelity relative to proteins with looser active sites. We review the current data on what parts and dimensions of active sites are most affected by size and shape, based on data with modified nucleotides that have been examined as polymerase substrates. We also discuss recent data on nucleotide analogs displaying higher f...
TL;DR: This coupled transcription–translation system will permit the efficient synthesis of proteins with a tyrosine analog at the desired position in an Escherichia coli cell-free system.
Abstract: An unnatural base pair of 2-amino-6-(2-thienyl)purine (denoted by s) and pyridin-2-one (denoted by y) was developed to expand the genetic code. The ribonucleoside triphosphate of y was site-specifically incorporated into RNA, opposite s in a template, by T7 RNA polymerase. This transcription was coupled with translation in an Escherichia coli cell-free system. The yAG codon in the transcribed ras mRNA was recognized by the CUs anticodon of a yeast tyrosine transfer RNA (tRNA) variant, which had been enzymatically aminoacylated with an unnatural amino acid, 3-chlorotyrosine. Site-specific incorporation of 3-chlorotyrosine into the Ras protein was demonstrated by liquid chromatography-mass spectrometry (LC-MS) analysis of the products. This coupled transcription-translation system will permit the efficient synthesis of proteins with a tyrosine analog at the desired position.
TL;DR: The spectroscopic studies together with viscosity experiments and cyclic voltammetry suggest that [CuL(1)](2+) could bind to DNA by partial intercalation via pyridine ring into the base pairs of DNA.
TL;DR: The crystal structure of a T7 RNAP elongation complex with 30 base pairs of duplex DNA containing a “transcription bubble” interacting with a 17-nucleotide RNA transcript is determined at 2.1 angstrom resolution.
Abstract: To make messenger RNA transcripts, bacteriophage T7 RNA polymerase (T7 RNAP) undergoes a transition from an initiation phase, which only makes short RNA fragments, to a stable elongation phase. We have determined at 2.1 angstrom resolution the crystal structure of a T7 RNAP elongation complex with 30 base pairs of duplex DNA containing a “transcription bubble” interacting with a 17-nucleotide RNA transcript. The transition from an initiation to an elongation complex is accompanied by a major refolding of the amino-terminal 300 residues. This results in loss of the promoter binding site, facilitating promoter clearance, and creates a tunnel that surrounds the RNA transcript after it peels off a seven–base pair heteroduplex. Formation of the exit tunnel explains the enhanced processivity of the elongation complex. Downstream duplex DNA binds to the fingers domain, and its orientation relative to upstream DNA in the initiation complex implies an unwinding that could facilitate formation of the open promoter complex.
TL;DR: The structure of the PhoB effector domain in complex with its target DNA sequence, or pho box, reveals a novel tandem arrangement in which several monomers bind head to tail to successive 11-base pair direct-repeat sequences, coating one face of a smoothly bent double helix.
TL;DR: Structural analysis of the Fpg-DNA complex reveals essential features of damage recognition and the catalytic mechanism of Fpg, a bilobal protein with a wide, positively charged DNA-binding groove.
TL;DR: Overall, the structure of the damaged DNA differs from undamaged DNA to an extent that DNA repair proteins may recognize this conformation, and the various components of the replicational and transcriptional machinery may be interfered with due to the perturbed local and global structure.
Abstract: It is well known that exposure to UV induces DNA damage, which is the first step in mutagenesis and a major cause of skin cancer. Among a variety of photoproducts, cyclobutane-type pyrimidine photodimers (CPD) are the most abundant primary lesion. Despite its biological importance, the precise relationship between the structure and properties of DNA containing CPD has remained to be elucidated. Here, we report the free (unbound) crystal structure of duplex DNA containing a CPD lesion at a resolution of 2.0 A. Our crystal structure shows that the overall helical axis bends approximately 30 degrees toward the major groove and unwinds approximately 9 degrees, in remarkable agreement with some previous theoretical and experimental studies. There are also significant differences in local structure compared with standard B-DNA, including pinching of the minor groove at the 3' side of the CPD lesion, a severe change of the base pair parameter in the 5' side, and serious widening of both minor and major groves both 3' and 5' of the CPD. Overall, the structure of the damaged DNA differs from undamaged DNA to an extent that DNA repair proteins may recognize this conformation, and the various components of the replicational and transcriptional machinery may be interfered with due to the perturbed local and global structure.
TL;DR: Electrochemical sensors have been developed, based upon the sensitivity of DNA charge transport to base pair stacking, and these sensors provide a completely new approach to diagnosing single base mismatches in DNA and monitoring protein-DNA interactions electrically.
TL;DR: The crystal structure of BmrR-TPP-DNA reveals a novel mechanism of transcription activation, whereby the drug-bound protein activates the bmr promoter by local DNA unwinding and base pair disruption.
TL;DR: A statistical analysis of 9000 flanking sequence tags characterizing transferred DNA (T‐DNA) transformants in Arabidopsis sheds new light on T‐DNA insertion by illegitimate recombination.
Abstract: A statistical analysis of 9000 flanking sequence tags characterizing transferred DNA (T-DNA) transformants in Arabidopsis sheds new light on T-DNA insertion by illegitimate recombination. T-DNA integration is favoured in plant DNA regions with an A-T-rich content. The formation of a short DNA duplex between the host DNA and the left end of the T-DNA sets the frame for the recombination. The sequence immediately downstream of the plant A-T-rich region is the master element for setting up the DNA duplex, and deletions into the left end of the integrated T-DNA depend on the location of a complementary sequence on the T-DNA. Recombination at the right end of the T-DNA with the host DNA involves another DNA duplex, 2–3 base pairs long, that preferentially includes a G close to the right end of the T-DNA.
TL;DR: The experiments define the minimal number of components and the conditions required to achieve in vitro RNA guide-directed 2′-O-methylation of ribose in a target RNA.
Abstract: The genomes of hyperthermophilic Archaea encode dozens of methylation guide, C/D box small RNAs that guide 2′-O-methylation of ribose to specific sites in rRNA and various tRNAs. The genes encoding the Sulfolobus homologues of eukaryotic proteins that are known to be present in C/D box small nucleolar ribonucleoprotein (snoRNP) complexes were cloned, and the proteins (aFIB, aNOP56, and aL7a) were expressed and purified. The purified proteins along with an in vitro transcript of the Sulfolobus sR1 small RNA were reconstituted in vitro, into an RNP complex. The order of assembly of the three proteins onto the RNA was aL7a, aNOP56, and aFIB. The complex was active in targeting S-adenosyl methionine (SAM)-dependent, site-specific 2′-O-methylation of ribose to a short fragment of ribosomal RNA (rRNA) that was complementary to the D box guide region of the sR1 small RNA. The presence of aFIB was essential for methylation; mutant proteins having amino acid replacements in the SAM-binding motif of aFIB were able to assemble into an RNP complex, but the resulting complexes were defective in methylation activity. These experiments define the minimal number of components and the conditions required to achieve in vitro RNA guide-directed 2′-O-methylation of ribose in a target RNA.
TL;DR: A Ag(I)-mediated base pair or a base triplet in a double- or triple-stranded DNA is accomplished by introducing a pair of pyridine nucleobases in the middle of the sequence by significantly stabilized the DNA duplex and triplex.
Abstract: We have recently reported the first artificial nucleoside for alternative DNA base pairing through metal complexation (J. Org. Chem. 1999, 64, 5002-5003). In this context, we have accomplished a Ag(I)-mediated base pair or a base triplet in a double- or triple-stranded DNA, respectively, by introducing a pair of pyridine nucleobases in the middle of the sequence. As a result, the incorporated Ag(I) complex significantly stabilized the DNA duplex and triplex. This strategy would be expanded to the regulation of thermodynamic stability of DNA duplex or triplex by adding transition metal ions from outside, or to labeling applications in biotechnology.
TL;DR: The synthesis of a hydroxypyridone-bearing nucleoside and the incorporation of a neutral Cu(2+)-mediated base pair of hydroxylated nucleobases (H-Cu-H) in a DNA duplex are reported, which could be developed for controlled and periodic spacing of neutral metallobase pairs along the helix axis of DNA.
Abstract: Recently, we reported the first artificial nucleoside for alternative DNA base pairing through metal complexation (J. Org. Chem. 1999, 64, 5002−5003). In this regard, we report here the synthesis of a hydroxypyridone-bearing nucleoside and the incorporation of a neutral Cu2+-mediated base pair of hydroxypyridone nucleobases (H−Cu−H) in a DNA duplex. When the hydroxypyridone bases are incorporated into the middle of a 15 nucleotide duplex, the duplex displays high thermal stabilization in the presence of equimolar Cu2+ ions in comparison with a duplex containing an A−T pair in place of the H−H pair. Monitoring temperature dependence of UV-absorption changes verified that a Cu2+-mediated base pair is stoichiometrically formed inside the duplex and dissociates upon thermal denaturation at elevated temperature. In addition, EPR and CD studies suggested that the radical site of a Cu2+ center is formed within the right-handed double-strand structure of the oligonucleotide. The present strategy could be develope...
TL;DR: The random amplified polymorphic DNA (RAPD) assay and related techniques like the arbitrarily primed polymerase chain reaction (AP-PCR) have been shown to detect genotoxin-induced DNA damage and mutations but further research is required to better understand the potential and limitations of the RAPD assay.
Abstract: The random amplified polymorphic DNA (RAPD) assay and related techniques like the arbitrarily primed polymerase chain reaction (AP-PCR) have been shown to detect genotoxin-induced DNA damage and mutations. The changes occurring in RAPD profiles following genotoxic treatments include variation in band intensity as well as gain or loss of bands. However, the interpretation of the molecular events responsible for differences in the RAPD patterns is not an easy task since different DNA alterations can induce similar type of changes. In this study, we evaluated the effects of a number of DNA alterations on the RAPD profiles. Genomic DNA from different species was digested with restriction enzymes, ultrasonicated, treated with benzo[a]pyrene (B[a]P) diol epoxide (BPDE) and the resulting RAPD profiles were evaluated. In comparison to the enzymatic DNA digestions, sonication caused greater changes in the RAPD patterns and induced a dose-related disappearance of the high molecular weight amplicons. A DNA sample substantially modified with BPDE caused very similar changes but amplicons of low molecular weight were also affected. Appearance of new bands and increase in band intensity were also evident in the RAPD profiles generated by the BPDE-modified DNA. Random mutations occurring in mismatch repair-deficient strains did not cause any changes in the banding patterns whereas a single base change in 10-mer primers produced substantial differences. Finally, further research is required to better understand the potential and limitations of the RAPD assay for the detection of DNA damage and mutations.
TL;DR: An extended analysis of the DNA binding specificity of XPC-HR23B using various defined DNA substrates indicates that the presence of bases, which cannot form normal Watson-Crick base pairs in double-stranded DNA, is a critical factor in determining the specificity ofXPC- HR23B binding.
TL;DR: This work has identified a 'pocket' in the N-terminal domains of archaeal DNA polymerases that is positioned to interact with the template strand and provides interacting groups that discriminate uracil from the four normal DNA bases (including thymine).
Abstract: Deamination of cytosine to uracil in a G-C base pair is a major promutagenic event, generating G-C-->A-T mutations if not repaired before DNA replication. Archaeal family B DNA polymerases are uniquely able to recognize unrepaired uracil in a template strand and stall polymerization upstream of the lesion, thereby preventing the irreversible fixation of an A-T mutation. We have now identified a 'pocket' in the N-terminal domains of archaeal DNA polymerases that is positioned to interact with the template strand and provide this ability. The structure of this pocket provides interacting groups that discriminate uracil from the four normal DNA bases (including thymine). These groups are conserved in archaeal polymerases but absent from homologous viral polymerases that are unable to recognize uracil. Using site-directed mutagenesis, we have confirmed the biological role of this pocket and have engineered specific mutations in the Pfu polymerase that confer the ability to read through template-strand uracils and carry out PCR with dUTP in place of dTTP.
TL;DR: It is shown that the presence of this ψ in the pre-mRNA branch-site helix of Saccharomyces cerevisiae induces a dramatically altered architectural landscape compared with that of its unmodified counterpart, placing the nucleophile in an accessible position for the first step of splicing.
Abstract: Pairing of a consensus sequence of the precursor (pre)-mRNA intron with a short region of the U2 small nuclear (sn)RNA during assembly of the eukaryotic spliceosome results in formation of a complementary helix of seven base pairs with a single unpaired adenosine residue. The 2′ OH of this adenosine, called the branch site, brings about nucleophilic attack at the pre-mRNA 5′ splice site in the first step of splicing. Another feature of this pairing is the phylogenetic conservation of a pseudouridine (ψ) residue in U2 snRNA nearly opposite the branch site. We show that the presence of this ψ in the pre-mRNA branch-site helix of Saccharomyces cerevisiae induces a dramatically altered architectural landscape compared with that of its unmodified counterpart. The ψ-induced structure places the nucleophile in an accessible position for the first step of splicing.
TL;DR: The structure of a protein capable of mimicking approximately 20 base pairs of B-form DNA, encoded by gene 0.3 of bacteriophage T7, is solved and is demonstrated to be an efficient inhibitor in vivo of all known families of the complex type I DNA restriction enzymes.
TL;DR: Polκ is a promiscuous extender of primer-terminal mispairs opposite nondamaged DNA templates, and interestingly, it is also very efficient at extending from a G opposite the 3′T of a T–T dimer, providing biochemical evidence for a role of Polκ in the extension of mismatch base pairs during normal DNA replication.
Abstract: Both in yeast and humans, DNA polymerase (Pol) η functions in the error-free replication of UV-damaged DNA, and Polη has the unique ability to efficiently replicate through a cis-syn thymine–thymine (T–T) dimer by inserting two As opposite the two Ts of the dimer. Although human DINB1-encoded Polκ belongs to the same protein family as Polη, Polκ shows no ability to bypass this DNA lesion and its biological function has remained unclear. Here, we examine Polκ for its ability to extend from primer-terminal mispairs opposite nondamaged and damaged DNA templates. We find that Polκ is a promiscuous extender of primer-terminal mispairs opposite nondamaged DNA templates, and interestingly, it is also very efficient at extending from a G opposite the 3′T of a T–T dimer. These observations provide biochemical evidence for a role of Polκ in the extension of mismatched base pairs during normal DNA replication, and in addition, they implicate Polκ in the mutagenic bypass of T–T dimers. In its proficient mismatch extension ability, Polκ is more similar to the unrelated DNA polymerase ζ than it is to the phylogenetically related Polη or Polι. Thus, in humans, Polκ would compete with Polζ for the extension of mismatched base pairs on damaged and undamaged DNAs.
TL;DR: The problem of systematic and objective identification of canonical and non-canonical base pairs in RNA three-dimensional (3D) structures was studied, and an algorithm and its implementation in a computer program that detects and analyzes all the base pairs contained in RNA 3D structures were developed.
Abstract: The problem of systematic and objective identification of canonical and non-canonical base pairs in RNA three-dimensional (3D) structures was studied. A probabilistic approach was applied, and an algorithm and its implementation in a computer program that detects and analyzes all the base pairs contained in RNA 3D structures were developed. The algorithm objectively distinguishes among canonical and non-canonical base pairing types formed by three, two and one hydrogen bonds (H-bonds), as well as those containing bifurcated and C-H.X...H-bonds. The nodes of a bipartite graph are used to encode the donor and acceptor atoms of a 3D structure. The capacities of the edges correspond to probabilities computed from the geometry of the donor and acceptor groups to form H-bonds. The maximum flow from donors to acceptors directly identifies base pairs and their types. A complete repertoire of base pairing types was built from the detected H-bonds of all X-ray crystal structures of a resolution of 3.0 A or better, including the large and small ribosomal subunits. The base pairing types are labeled using an extension of the nomenclature recently introduced by Leontis and Westhof. The probabilistic method was implemented in MC-Annotate, an RNA structure analysis computer program used to determine the base pairing parameters of the 3D modeling system MC-Sym.