Bulge motif

[lvelve0901]

Hi Xiangjun,

Long time no contact. How is everything going?

I am using DSSR to analyze the structure 1FUF to look for bulge motif.

The DSSR tells me there are two bulge motif in this structure. However, some of the bulge residue base have contact with other base and forms a base triple. I am not sure if these count some additional bulge or other motif?

In general, could you tell me how 3DNA detect secondary motif like bulge or internal loop? Is it just based on dot-bracket notation?

Best,
Honglue

[xiangjun]

Does the following quotation from the section "Loop identification and classification" of the 2015 DSSR NAR paper help clarify your confusion?

DSSR delineates loops using the terminal base pairs of stems and the bridging nucleotides (Figure 1F). Depending on the number of stems involved, loops are classified into three categories: a hairpin loop is delimited by one stem, an internal/bulge loop by two stems, and a junction (multi-branched) loop by three or more stems. In DSSR, a loop forms a ‘closed’ circle with any two sequential nucleotides connected either by a phosphodiester linkage or a canonical base pair, and is specified by the lengths of consecutive bridging-nucleotide segments (Figures 1F and 2C). For example, the [2,1,5,0] four-way junction loop in tRNA^Phe (Figure 2C) contains two bridging nucleotides between stems S1 and S2, one between S2 and S3,  five between S3 and S4, and zero between S4 and S1.

For your own understanding and the benefit of other viewers of this thread, could you provide the secondary structure diagram of 1FUF? You could start from the "dssr-2ndstrs.ct" auxiliary output file, using VARNA (as I did in the original DSSR paper).

Best regards,

Xiang-Jun

[lvelve0901]

Here is the secondary structure. However, in the real pdb structure, the U6, U11, A18 forms a base triple. I am not sure if these base triple will impact the secondary structure landscape?

[xiangjun]

From the secondary structure diagram, DSSR is working as expected. Base triple interactions (or other tertiary interactions for that matter) are not considered in the classification of different loops.

Xiang-Jun

[lvelve0901]

I understand.

Thanks.

Best,
Honglue