Talk:BE.109:Bio-material engineering/Sequence analysis

From OpenWetWare

Jump to: navigation, search

Tuesday/Thursday Lab Sequence Data

team color candidate number sequence relative strength comments/notes
Green A XXWAPAXXXXXX 1/18 of pCT-CON This sequence did not show significant binding ability, although because of the poor sequencing data, we can not make any definite conclusions on the cause of the poor gold binding ability.
Green B XXXXVGXXXXXX 3.5 of pCT-CON This sequence has some gold binding ability, however unlike D, the sequence data obtained for this colony is quite poor. As a result, we can not make any definite conclusions on what lead to it's binding.
Green C XXXXXXXXSLFL .83 of pCT-CON This sequence did not show significant binding ability, although because of the poor sequencing data, we can not make any definite conclusions on the cause of the poor gold binding ability.
Green D LRXXTXGLSLCR 7.83 of pCT-CON Colony D was the only one from which we got some sort of meaningful sequence data from. Luckily, it was also our strongest binder. The sequence data shows a prevalence of Yellow Aliphatic Groups (Leucine) and Green Hydroxyl Groups (Serine), which may be important for gold binding.
Purple B WRxxxACRCVxx 0.3 x pCT-CON 2 cysteines may be signficant
Purple C MYYVAASxSVLM 2 x pCT-CON 2 methionines and 2 serines may be significant
Purple D *LARPVA*xxIx 10 x pCT-CON best binder. stop codons are TAG and TGA
Yellow A EXXXPIXXXXXX 1.89 of pCT-CON We do not know very much about sequence A, but we hypothesize that it contains aromatic amino acids. Here is a color coded chart of our sequences: Image:SequenceChart.jpg
Yellow B RXRLRVXXXXVR 0.413 of pCT-CON This sequence is the weakest gold binder and also exhibits the most amount of basic amino acids, which indicates that basic amino acids may prevent gold binding. Sequence A shows no basic amino acids, and sequence D contains two basic amino acids which may be the reason that sequence A bonds gold more strongly than sequence D, despite its lack of aromatic amino acids.
Yellow C EGXXPXXXXXXX 0.55 of pCT-CON We do not know very much about sequence C. One observation that we had about sequences B and C is that they contained no aromatic residues, but they did contain acidic amino acids. But there is still even a chance that C and A are identical.
Yellow D FWCQSRWXEILV 1.72 of pCT-CON This sequence contains three aromatic residues, which is rare in the library, which is a significant feature. Also, the weakly binding sequences (B and C) do not show any aromatic residues, which indicates that aromatic residues may be responsible for gold binding.
Blue! A LCVIQAXXKSIV relatively good Binding: more colonies than pCT-CON, but much less than on pAu1. Sequence: This sequence contains lots of aliphatic residues, and one cysteine.
Blue! B XXXXXPXXXRXX not good Binding: As many colonies formed as pCT-CON. Sequence: We do not have enough sequence data to comment on this sequence.
Blue! C XXXXXXXXXXAX good binder Binding: More colonies than pCT-CON, but much less than on pAu1. Sequence: We do not have enough sequence data to comment on this sequence.
Blue! D LXXXXXXXGMGX good binder Binding: More colonies than pCT-CON, but much less than on pAu1. Sequence: We do not have enough sequence data to comment on this sequence (has at least two Glycines though!).
Pink A VAASRLVCCXXXL 6 x pCT-CON 2 cysteines right next to each other might mean that disulfide bonds cannot occur so sulfur available to bind to gold.
Pink D XXADKLLXHAPQ* 6 x pCT-CON Histidine present which if we enrinched the species, histidine would probably be present in greater amounts :)
Red A PDGT*LXVXXXX 3.125 x pCT-CON Very similar to Sequence D. Similar relative strength to D. Has a proline next to a aspartic acid (acidic AA).
Red B DXXHPEYGPHCK 14.375 x pCT-CON Very similar to sequence C. Similar relative strength to C. Has proline next to glutamic acid (acidic AA). Also has a proline further down sequence.
Red C XXXHPEYGPPXK 9.5 x pCT-CON Very similar to sequence B. Similar relative strength to B. Has proline next to glutamic acid, and 2 prolines further down sequence next to each other.
Red D PDGT*LYXXXLX .5 x pCT-CON Very similar to sequence A. Similar relative strength to A. Has Proline next to aspartic acid (AA). --- Commonality between all four library sequences is presence of proline next to acidic AA, as well as extra prolines further into sequence.

It's the last day of lab!!! Summer is coming. YAIY.

Wednesday/Friday Lab Sequence Data

team color candidate number sequence relative strength comments/notes
Green A FXXXXXXXXXNX ~same as pCT-CON This sequence did not display significant gold binding ability, and due to the poor sequencing data we can not make any definite conclusions on the cause of the poor gold binding ability.
Green B CGXXGAXPPLXL ~same as pCT-CON 2 prolines and 1 cysteine may be significant
Green C APEGKLXTRARX ~same as pCT-CON 1 proline and 3 basic amino acids may be significant
Green D EXXXXXXXXFSX ~same as pCT-CON This sequence did not display significant gold binding ability, and due to the poor sequencing data we can not make any definite conclusions on the cause of the poor gold binding ability.
Pink A CGXXGAXXPXCL a little bit less strong than pAu1 We see aliphatic and sulfur-containing AA's, as well as a Glycine and a Proline - which are important in determining the shape and rotation of the peptide.
Pink B pAu1 We must have accidentaly contaminated our samples with pAu1.
Pink C XXXFFXXXXX* a little less strong than pAu1 We see no pattern between our two samples besides X's - : (
Pink D pAu1 See B - contamination - eek!
purple A unknown .3xpCT-CON Our peptide sequence data could not be determined because of the large number of ambiguities in the sequence of the DNA. This may be due to difficuly sequencing the DNA because it was not cleaned. This was actually the worst gold-binder.
purple B unknown .4xpCT-CON This peptide sequence data also could not be determined because of the ambiguities. This was the second-worst binder.
purple C unknown 1.7xpCT-CON This was the best gold-binder, but the peptide sequence could not be determined.
purple D unknown .78xpCT-CON This was the second-best gold binder and had the same problems with the sequence data.
Red A Image:redseq.jpg .27xpCT-CON Much of our peptide data (50%) could not be determined because of the large number of ambiguities. This was the weakest gold-binder.
Red B see above 2.67xpCT-CON This peptide was our second strongest binder. It contained many types of amino acids, all except amide and sulfur-containing.
Red C see above 2xpCT-CON This was the third strongest binder, perhaps because its sequence was truncated by four amino acids.
Red D see above 3.53xpCT-CON This was the strongest gold binder. There was only one ambiguity in the sequence. Two prolines were adjacent to each other, a consistent trend with other groups as well.
Blue A-D Image:blueseq.jpg Library samples A-C were stronger than pCT-CON. Library D bound with about the same strength as pCT-CON 2 Cysteins in sample B and 2 Glutaminein sample D could effect binding
Gold A LXXXX XXXXX PX triple lots of Xs
Gold B LXLGX XXXXX PP same some Xs
Gold C GSQXV AXXRX YX triple
Gold D GXTXX MAXXX DX Five times

|}

HAVE A GREAT SUMMER!!

Personal tools