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Introduction

The classification of DNA local conformations

A basic structural unit in our classification system of local DNA conformations is a dinucleotide. Dinucleotides are classified into conformational classes NtC based on the analysis of their backbone torsions δ, ε, ζ, α1, β1, γ1 and δ1, and glycosidic torsions χ and χ1 (Fig.).

Figure:    Dinucleotide unit of DNA structure with the set of selected torsions.

NtC classes are defined by torsion angle ranges and each class is annotated by a short description describing its main structural features (Tab. 1).

NtC class Annotation δ ε ζ α1 β1 γ1 δ1 χ χ1
AA00 the most frequent, "canonical" A-DNA (identical to A-RNA) 83 206 287 293 174 55 83 199 202
AA01 A-DNA with α1/γ1 crank (150/180) 82 194 291 149 193 182 87 205 188
AA02 A-DNA with BI-like χ/χ1 88 203 275 294 161 54 88 244 245
AA03 A-DNA similar to AA01, high α1 83 214 273 330 165 26 86 202 215
AA04 A-DNA similar to AA01, low α1 80 198 301 255 175 91 83 202 192
AB01 A-to-B: δ C3'-endo, δ1 C2'-endo, χ/χ1 have A/B pattern 86 193 283 299 180 55 142 221 255
AB02 A-to-B: δ~O4'-endo, extremely low ε, χ/χ1 are B-like 92 61 59 208 185 64 133 237 253
AB03 A-to-B: similar to AB01 with high α1 and low ζ, β1, γ1 96 195 253 344 151 33 131 220 250
BA01 BI-to-A complex conformer with δ1 from C4'-exo, χ/χ1 are B-like 133 190 259 292 169 51 89 247 230
BA05 BI-to-A complex conformer with δ1 from O4'-endo, χ/χ1 are B-like 130 184 266 295 171 53 101 249 235
BA08 B-to-A: β1~120, χ1 A-like 141 212 188 302 129 55 85 271 211
BA09 BI-to-A: β1~60, α1/γ1 crank (250/170), χ1 A-like 135 199 287 254 71 168 86 265 187
BA10 B-to-A complex cluster: α1~100, γ1~180, χ1 A-like 135 201 217 103 229 195 88 258 195
BA13 BII-to-A complex cluster: α1~60, γ1~180, χ1 A-like 142 231 197 74 232 197 89 266 199
BA16 BII-to-A: χ1 A-like 145 255 187 63 226 196 87 260 201
BA17 BII-to-A: δ1~O4'-endo, β1~120 148 255 177 294 130 44 96 272 234
BB00 the most frequent DNA conformer, "canonical" B form, also called BI 138 183 259 303 180 44 138 252 258
BB01 less populated variant of BI form 132 181 265 301 177 49 121 248 244
BB02 BI with α1/γ1 crank (30/300) 140 194 246 32 194 297 150 252 253
BB03 BI with α1/γ1 crank (170/170) 145 176 276 166 164 173 146 239 232
BB04 BI-to-BII conformer 140 201 214 315 153 46 140 263 253
BB05 BI-to-BII with α1/γ1 crank (70/230), χ1 A-like 143 220 202 67 231 221 124 268 209
BB07 BII form, typical by ε/ζ switch compared to BI 144 245 171 297 141 46 141 270 259
BB08 BII form, variant, α1/γ1 crank (60/210) 142 248 195 64 230 210 142 262 230
BB10 B form with extremely low values of α1, β1, γ1 139 195 191 23 106 19 129 257 258
BB11 B form with α1/γ1 crank (120/180) 144 200 199 121 226 189 143 258 222
BB12 BI with α1/γ1 crank (250/170), low β1 70, χ1 A-like 140 196 287 248 73 172 144 263 212
BB13 BI with α1/γ1 crank (210/160), low β1 100, χ1 A-like 143 186 291 216 104 161 147 252 219
BB14 B-form with extremely low ε 121 104 303 229 260 73 132 264 263
BB15 BI with high α1 and γ1 near 0 149 187 261 341 192 354 148 250 261
BB16 complex cluster of B-like conformers: A-like χ, bases may be unstacked to incorporate intercalated drug, occurs where backbone accommodates deformation (metal ion near, strand crossing in Holliday junctions, ends of duplexes) 145 227 281 288 173 51 142 197 267
AB1S A-to-B-like but χ1 syn, mostly in duplexes 91 214 280 295 176 56 139 238 67
BBS1 BI-like but χ syn, may be in duplex but many G-G in quadruplexes 146 189 275 294 174 52 135 62 261
BB1S G-G in quadruplexes, unusual β1, γ1, χ1 syn 140 202 282 307 258 304 151 236 65
BB2S BI-like but χ1 syn, mostly G-G in quadruplexes, α1 g+, γ1 g- 137 196 225 33 187 295 145 257 70
NS1S partially unstacked T-G/G-T in quadruplexes, χ1 syn, unusual ζ, α1, γ1 143 206 61 82 204 192 146 242 68
NS02 start of loop in quadruplex or hairpin, G-X, untypical ζ, α1, γ1 145 225 67 74 189 191 137 264 258
NS03 partially unstacked T-T in quadruplexes, unusual combination of ε, ζ, α1, γ1, χ1 143 294 111 153 197 53 151 262 185
NS04 unstacked, in 4-way junction, ε, ζ high values 140 275 279 304 191 56 150 266 210
NS05 5'-end of dsDNA, base open (unstacked), ζ, α1 ~60 154 242 77 63 177 64 137 237 249
ZZ1S Z form, Y-R step 148 264 76 66 186 179 95 205 60
ZZ2S Z form, Y-R step, δ1 C2'-endo 141 263 71 78 179 185 148 208 77
ZZS1 ZI form, R-Y step 97 242 294 209 230 55 144 63 205
ZZS2 ZII form, R-Y step 95 186 63 169 162 44 144 58 213

Table 1:    NtC classes.

While NtC classes are useful for DNA structure fine analysis, a coarser classification is needed to facilitate the human understanding of DNA structure and to better characterize the type of DNA on a local level. Thus, we assembled dinucleotide classes NtC into twelve groups forming a structural alphabet CANA (Tab. 2).

CANA class Annotation NtC classes merged into the CANA
AAA A-form conformers AA00 + AA01 + AA02 + AA03 + AA04
A-B conformers bridging A- to B-form AB01 + AB02 + AB03
B1A conformers bridging BI- to A-form BA01 - BA10
B2A conformers bridging BII- to A-form BA13 - BA17
BBB the most frequent "canonical" B-form BB00
2B1 less populated BI conformer BB01
3B1 less populated BI conformers with switched a/g values BB02 + BB03
B12 conformer bridging BI- to BII-form BB04 + BB05
BB2 BII conformers BB07 + BB08
miB various minor B conformers BB10 - BB16
SQZ conformers with bases in syn orientation, may occure in quadruplexes & other non-duplexes AB1S + BBS1 + BB1S + BB2S + NS1S + NS02 + NS03 + NS04 + NS05
ZZZ Z-forms ZZ1S + ZZ2S + ZZS1 + ZZS2

Table 2:    CANA alphabet.

Terminology

To build queries effectively and to understand search results, the terminology of DNA structure and its entities must be mastered first. A terminology used in the Dolbico database consists of the following terms: a structural unit, child, parent, neighbour and opposite.

A structural unit. A structural unit is the fragment of DNA structure. The Dolbico database recognizes and operates with six types of a structural unit: a structure, chain, residue, dinucleotide, base pair and base step.

structure

chain

residue

dinucleotide

base pair

base step

Figure:    Structural unit.

A child structural unit. For each structural unit, with the exception of a residue, one or more child units are defined. Child units are smaller structural units a given structural unit is composed from. The type of a child structural unit is different from the type of a given structural unit.

structural unit has child structural unit
structure chain, dinucleotide, base step, base pair, residue
chain dinucleotide, residue
residue
dinucleotide residue
base pair residue
base step base pair, dinucleotide, residue

Table:    Child structural unit.

A parent structural unit. For each structural unit, with the exception of a structure, one or more parent units are defined. Parent units are larger structural units that consist of a given structural unit. The type of a parent structural unit is different from the type of a given structural unit.

structural unit has parent structural unit
structure
chain structure
residue chain, structure
dinucleotide chain, structure
base pair structure
base step structure

Table:    Parent structural unit.

A neighbour structural unit. A neighbour structural unit is a sequentially subsequent structural unit of the same type. A neighbour structural unit is defined only for a residue, dinucleotide, base pair and base step. The neighbour base step consists of two base pairs being immediately adjacent to a given base step.

neighbour dinucleotide

neighbour residue

neighbour base pair

neighbour base step

Figure:    Neighbour structural unit.

An opposite structural unit. An opposite structural unit is an unit of the same type which is right opposite to a given structural unit. An opposite structural unit is defined only for a residue and dinucleotide.

opposite dinucleotide

opposite residue

Figure:    Opposite structural unit.

Home page

Fulltext search

The search field (Fig. A) on the top of the Home page enables a fulltext search in the whole database. Database records can be searched by a PDB ID, author name or keyword. Keyword searches are performed within a structure title, authors and structure publication abstract. The search field is case insensitive. By hitting the Search button, relevant records with a searched term highlighted in red are returned.

Figure:    Fulltext search.

Browse

From the Home page, the database can be browsed by its dinucleotide content. Dinucleotide browse can be further restricted by a sequence, NtC or CANA class. Browsing the database by other characteristics (i.e., by structures, chains, residues, base pairs or base steps) is available from a separate Browse section.

Updates

DNA structural data are retrieved from the PDB database (http://www.pdb.org) every Wednesday at 10:00 UTC. The date of the last update and a number of structures in the database are given in the bottom of the Home page. The details of the key measures of the database coverage are available from the separate Statistics section.

Statistics

A Statistics section describes the database coverage in terms of individual structural units: structures, chains, dinucleotides, residues, base pairs and base steps. Data about each structural unit are arranged into a three-boxed layout. A first box contains the depiction of a structural unit (Fig. A), a second box lists the available type of statistics (Fig. B) that is, upon a mouse click, graphed in a third box (Fig. C). The graph of a selected statistic can be printed or saved as an image (Fig. D) in PNG, JPG, PDF or SVG format.

Figure:    Statistics for structures in Dolbico database.

Advanced search

Advanced search enables to build flexible and powerful queries over the Dolbico database. Each query begins by the definition of a searched structural unit (Fig. A). Structural unit search can be made more specific by defining limiting terms (Fig. B). Limiting terms are added using the plus sign (Fig. C) and removed by using the minus sign (Fig. D). A whole search branch can be removed by selecting a "choose ..." option from the first leftmost drop box. If a parent structural unit is defined for a searched structural unit, parent structural unit selector appears (Fig. E) and a search can further be limited by properties of a parent structural unit. This enables, for example, to search all A-form dinucleotides (a searched structural unit) in DNA structures resolved by X-ray with the resolution between 1 Å and 2 Å (Fig.).

Figure:    Advanced search.

Results

The search output is divided into several sections. A header (Fig. A) shows the count of records matching a query followed by three icons enabling the export of results and by an icon turning on and off the display of the statistics of found records. In Dolbico, two following types of results can be exported: (i) details about structures (e.g., PDB ID, structure title, experimental metadata) containing structural units complying with a given query and (ii) details about found structural units. Results are exported as comma-separated values (CSV) files which enables their further analysis in specialized statistical software.

Below a header, a pagination enabling a quick movement between result pages is displayed (Fig. B). Each result page consists of query result panel (Fig. C) and visualization panel (Fig. D). The content of query result panel differs depending on the type of a searched structural unit. For example, if a searched structural unit is a base pair, the following details are shown (Fig. C) in query result panel: structure PDB ID, identification (residue names and IDs) of a base pair complying a query, an indication, if a base pair is classified as Watson-Crick or not and base pair parameters. If a line with one qery result is clicked, a corresponding structural unit is highlighted in red in visualization panel employing the interactive JSmol (http://sourceforge.net/projects/jsmol) applet (Fig. D).

Figure:    Output of search.

Browse

The Browse section enables the content of the Dolbico database to be browsed by any type of a structural unit with respect to defined properties (Fig. A). If the "any" value is specified (Fig. B), a given property is ignored.

Figure:    Browse for structures by defined properties.

Analyse database

The Analyse database section enables the quick overview of dinucleotide content in the Dolbico database. The distribution (Fig. E) of individual torsions (Fig. D) can be displayed either for each CANA (Fig. A), or for each NtC (Fig. B) class. If CANA class is selected, its underlying NtC classes are framed in blue (Fig. B). In addition to distribution graph, basic statistics of a selected torsion angle are displayed (Fig. C).

Figure:    Analysis of dinucleotide content of the database.

Analyse structure

The Analyse structure section enables a user to upload its own DNA structure (Fig. A) and to analyse its NtC and CANA content. Uploaded file must be in the PDB file format and must contain DNA data, otherwise the error message is issued. Results of the dinucleotide class assignment are displayed at the results page from where can be downloaded as comma-separated value (CSV) file.

Figure:    Form to upload DNA structure.